Starting phenix.real_space_refine on Tue Feb 20 00:48:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5opt_3844/02_2024/5opt_3844.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5opt_3844/02_2024/5opt_3844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5opt_3844/02_2024/5opt_3844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5opt_3844/02_2024/5opt_3844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5opt_3844/02_2024/5opt_3844.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5opt_3844/02_2024/5opt_3844.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2017 5.49 5 S 203 5.16 5 C 43899 2.51 5 N 15167 2.21 5 O 20933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "p ASP 37": "OD1" <-> "OD2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 159": "NH1" <-> "NH2" Residue "p ARG 187": "NH1" <-> "NH2" Residue "p TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 221": "NH1" <-> "NH2" Residue "p ARG 261": "NH1" <-> "NH2" Residue "q PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 36": "NH1" <-> "NH2" Residue "r ARG 64": "NH1" <-> "NH2" Residue "r ARG 76": "NH1" <-> "NH2" Residue "r TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 81": "NH1" <-> "NH2" Residue "t ARG 107": "NH1" <-> "NH2" Residue "u ARG 67": "NH1" <-> "NH2" Residue "u PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 116": "NH1" <-> "NH2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 150": "NH1" <-> "NH2" Residue "L ARG 153": "NH1" <-> "NH2" Residue "L ARG 197": "NH1" <-> "NH2" Residue "L ARG 206": "NH1" <-> "NH2" Residue "L PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 250": "NH1" <-> "NH2" Residue "M ASP 88": "OD1" <-> "OD2" Residue "O TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 121": "NH1" <-> "NH2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R ASP 108": "OD1" <-> "OD2" Residue "S ARG 14": "NH1" <-> "NH2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 21": "NH1" <-> "NH2" Residue "T ARG 98": "NH1" <-> "NH2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "V PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 99": "NH1" <-> "NH2" Residue "V ASP 131": "OD1" <-> "OD2" Residue "W TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 111": "NH1" <-> "NH2" Residue "W TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 175": "NH1" <-> "NH2" Residue "W ARG 196": "NH1" <-> "NH2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "W ARG 224": "NH1" <-> "NH2" Residue "X ARG 110": "NH1" <-> "NH2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 49": "NH1" <-> "NH2" Residue "Y PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b ARG 125": "NH1" <-> "NH2" Residue "f ARG 33": "NH1" <-> "NH2" Residue "f PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 171": "NH1" <-> "NH2" Residue "f ASP 209": "OD1" <-> "OD2" Residue "d ARG 84": "NH1" <-> "NH2" Residue "d PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 214": "NH1" <-> "NH2" Residue "d PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 65": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 131": "NH1" <-> "NH2" Residue "i ARG 141": "NH1" <-> "NH2" Residue "j TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 47": "NH1" <-> "NH2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 219": "NH1" <-> "NH2" Residue "P ARG 230": "NH1" <-> "NH2" Residue "P ARG 231": "NH1" <-> "NH2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k ASP 138": "OD1" <-> "OD2" Residue "l ARG 16": "NH1" <-> "NH2" Residue "l ARG 48": "NH1" <-> "NH2" Residue "l ARG 89": "NH1" <-> "NH2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 13": "NH1" <-> "NH2" Residue "o TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o ARG 145": "NH1" <-> "NH2" Residue "c TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 182": "NH1" <-> "NH2" Residue "h TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 82219 Number of models: 1 Model: "" Number of chains: 35 Chain: "p" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2405 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain: "q" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 311 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'TRANS': 37} Chain: "r" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1113 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 134} Chain: "t" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 112} Chain: "u" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 981 Classifications: {'peptide': 120} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2038 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 13, 'TRANS': 244} Chain: "M" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1116 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "O" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1493 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "Q" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1670 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 188} Chain: "R" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1143 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "S" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 829 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "U" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 64} Chain: "V" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1011 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "W" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1781 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain: "X" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1212 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "Y" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Z" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1404 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Chain: "b" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1365 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "f" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1658 Classifications: {'peptide': 207} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain: "d" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1726 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "e" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1019 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "g" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 635 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "a" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 553 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "i" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 118} Chain: "j" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "P" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1983 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain: "k" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 972 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Chain: "l" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 784 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "m" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1587 Classifications: {'peptide': 200} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 196} Chain: "n" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 780 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "o" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1116 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "c" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 53} Chain: "h" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1358 Classifications: {'peptide': 173} Link IDs: {'CIS': 10, 'PTRANS': 6, 'TRANS': 156} Chain: "E" Number of atoms: 43106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2022, 43106 Inner-chain residues flagged as termini: ['pdbres=" G E1072 "', 'pdbres=" G E1165 "', 'pdbres=" C E1523 "', 'pdbres=" C E1845 "'] Classifications: {'RNA': 2022} Modifications used: {'5*END': 5, 'rna2p_pur': 184, 'rna2p_pyr': 172, 'rna3p_pur': 886, 'rna3p_pyr': 780} Link IDs: {'rna2p': 356, 'rna3p': 1665} Time building chain proxies: 31.00, per 1000 atoms: 0.38 Number of scatterers: 82219 At special positions: 0 Unit cell: (269.88, 237.12, 215.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 203 16.00 P 2017 15.00 O 20933 8.00 N 15167 7.00 C 43899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS T 78 " - pdb=" SG CYS T 81 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.32 Conformation dependent library (CDL) restraints added in 5.8 seconds 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9150 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 57 sheets defined 32.8% alpha, 14.6% beta 468 base pairs and 895 stacking pairs defined. Time for finding SS restraints: 25.25 Creating SS restraints... Processing helix chain 'p' and resid 279 through 283 Processing helix chain 'q' and resid 34 through 38 Processing helix chain 'r' and resid 47 through 60 removed outlier: 3.759A pdb=" N ALA r 57 " --> pdb=" O LYS r 53 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL r 58 " --> pdb=" O ILE r 54 " (cutoff:3.500A) Processing helix chain 'r' and resid 79 through 102 Processing helix chain 'r' and resid 104 through 118 removed outlier: 3.541A pdb=" N LYS r 108 " --> pdb=" O ASN r 104 " (cutoff:3.500A) Processing helix chain 't' and resid 23 through 27 removed outlier: 3.776A pdb=" N GLY t 26 " --> pdb=" O THR t 23 " (cutoff:3.500A) Processing helix chain 't' and resid 28 through 35 removed outlier: 3.637A pdb=" N LEU t 32 " --> pdb=" O GLU t 28 " (cutoff:3.500A) Processing helix chain 't' and resid 36 through 44 removed outlier: 4.038A pdb=" N THR t 42 " --> pdb=" O GLU t 38 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU t 43 " --> pdb=" O GLU t 39 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 56 removed outlier: 3.577A pdb=" N ARG t 50 " --> pdb=" O ALA t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 61 through 73 removed outlier: 3.726A pdb=" N ARG t 68 " --> pdb=" O LEU t 64 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS t 71 " --> pdb=" O LEU t 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 32 removed outlier: 3.667A pdb=" N ALA u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 35 No H-bonds generated for 'chain 'u' and resid 33 through 35' Processing helix chain 'u' and resid 42 through 47 removed outlier: 3.962A pdb=" N VAL u 45 " --> pdb=" O ALA u 42 " (cutoff:3.500A) Processing helix chain 'u' and resid 64 through 74 removed outlier: 3.793A pdb=" N ILE u 68 " --> pdb=" O GLU u 64 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA u 73 " --> pdb=" O SER u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 102 through 115 removed outlier: 3.631A pdb=" N THR u 106 " --> pdb=" O ALA u 102 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG u 107 " --> pdb=" O MET u 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU u 108 " --> pdb=" O VAL u 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU u 110 " --> pdb=" O THR u 106 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP u 111 " --> pdb=" O ARG u 107 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU u 113 " --> pdb=" O ARG u 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG u 114 " --> pdb=" O GLU u 110 " (cutoff:3.500A) Processing helix chain 'u' and resid 116 through 118 No H-bonds generated for 'chain 'u' and resid 116 through 118' Processing helix chain 'u' and resid 120 through 127 removed outlier: 3.784A pdb=" N ARG u 125 " --> pdb=" O HIS u 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 48 Processing helix chain 'L' and resid 54 through 65 removed outlier: 3.600A pdb=" N ALA L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 132 No H-bonds generated for 'chain 'L' and resid 130 through 132' Processing helix chain 'L' and resid 245 through 258 Processing helix chain 'M' and resid 9 through 21 removed outlier: 3.661A pdb=" N LEU M 13 " --> pdb=" O ALA M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 32 removed outlier: 3.889A pdb=" N LYS M 28 " --> pdb=" O ASP M 24 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER M 30 " --> pdb=" O GLY M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 removed outlier: 4.200A pdb=" N GLN M 36 " --> pdb=" O THR M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'O' and resid 53 through 61 removed outlier: 3.775A pdb=" N ARG O 57 " --> pdb=" O PRO O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 91 removed outlier: 4.187A pdb=" N GLN O 74 " --> pdb=" O GLY O 70 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 105 removed outlier: 3.813A pdb=" N VAL O 97 " --> pdb=" O ASN O 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 148 removed outlier: 4.115A pdb=" N ARG O 145 " --> pdb=" O CYS O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 169 removed outlier: 3.974A pdb=" N ALA O 160 " --> pdb=" O PRO O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 187 removed outlier: 3.666A pdb=" N VAL O 185 " --> pdb=" O GLU O 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 10 removed outlier: 3.913A pdb=" N LYS Q 9 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 15 Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.719A pdb=" N SER Q 24 " --> pdb=" O GLU Q 20 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL Q 25 " --> pdb=" O ASP Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 46 Processing helix chain 'Q' and resid 69 through 71 No H-bonds generated for 'chain 'Q' and resid 69 through 71' Processing helix chain 'Q' and resid 72 through 91 removed outlier: 4.369A pdb=" N LYS Q 78 " --> pdb=" O MET Q 74 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE Q 79 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG Q 81 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR Q 82 " --> pdb=" O LYS Q 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG Q 90 " --> pdb=" O GLU Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 115 Processing helix chain 'Q' and resid 122 through 136 Processing helix chain 'Q' and resid 163 through 168 removed outlier: 3.899A pdb=" N VAL Q 167 " --> pdb=" O ASP Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 183 Processing helix chain 'R' and resid 29 through 42 removed outlier: 3.547A pdb=" N VAL R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 59 removed outlier: 3.748A pdb=" N MET R 52 " --> pdb=" O SER R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 67 Processing helix chain 'R' and resid 70 through 78 Processing helix chain 'R' and resid 85 through 105 removed outlier: 3.774A pdb=" N LEU R 91 " --> pdb=" O ASP R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 132 Processing helix chain 'S' and resid 12 through 19 removed outlier: 3.570A pdb=" N GLU S 16 " --> pdb=" O THR S 12 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET S 18 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 59 removed outlier: 4.206A pdb=" N ASP T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 85 Processing helix chain 'T' and resid 92 through 97 removed outlier: 3.736A pdb=" N LYS T 97 " --> pdb=" O THR T 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 55 Processing helix chain 'V' and resid 57 through 62 removed outlier: 3.600A pdb=" N GLU V 61 " --> pdb=" O ASP V 58 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER V 62 " --> pdb=" O ARG V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 79 removed outlier: 3.667A pdb=" N ALA V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP V 73 " --> pdb=" O MET V 69 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG V 77 " --> pdb=" O ASP V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 114 removed outlier: 4.071A pdb=" N ARG V 110 " --> pdb=" O GLN V 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 62 removed outlier: 4.031A pdb=" N TYR W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG W 62 " --> pdb=" O ALA W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 74 Processing helix chain 'W' and resid 108 through 116 removed outlier: 4.238A pdb=" N VAL W 112 " --> pdb=" O THR W 108 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR W 113 " --> pdb=" O SER W 109 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 180 removed outlier: 3.600A pdb=" N TRP W 165 " --> pdb=" O ARG W 161 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL W 166 " --> pdb=" O LEU W 162 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG W 169 " --> pdb=" O TRP W 165 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS W 180 " --> pdb=" O GLN W 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 182 through 192 removed outlier: 3.582A pdb=" N THR W 188 " --> pdb=" O ASN W 184 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU W 189 " --> pdb=" O GLU W 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 193 through 204 removed outlier: 3.858A pdb=" N ASP W 197 " --> pdb=" O ASN W 193 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG W 198 " --> pdb=" O ILE W 194 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN W 204 " --> pdb=" O ALA W 200 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 234 Processing helix chain 'X' and resid 35 through 39 removed outlier: 3.900A pdb=" N LYS X 38 " --> pdb=" O ASN X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 66 removed outlier: 4.100A pdb=" N ILE X 64 " --> pdb=" O PRO X 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 55 removed outlier: 4.036A pdb=" N ILE Y 46 " --> pdb=" O PRO Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 93 Processing helix chain 'Y' and resid 94 through 101 removed outlier: 3.584A pdb=" N LYS Y 98 " --> pdb=" O PRO Y 94 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU Y 101 " --> pdb=" O ARG Y 97 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 124 removed outlier: 3.536A pdb=" N VAL Y 114 " --> pdb=" O ALA Y 110 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS Y 122 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS Y 123 " --> pdb=" O ASN Y 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE Y 124 " --> pdb=" O ARG Y 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 93 removed outlier: 4.359A pdb=" N VAL Z 91 " --> pdb=" O SER Z 87 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 114 removed outlier: 3.596A pdb=" N LYS Z 110 " --> pdb=" O ALA Z 106 " (cutoff:3.500A) Processing helix chain 'Z' and resid 158 through 168 removed outlier: 4.193A pdb=" N LYS Z 162 " --> pdb=" O GLU Z 158 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET Z 164 " --> pdb=" O LYS Z 160 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 183 removed outlier: 3.815A pdb=" N GLN Z 179 " --> pdb=" O ALA Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 205 through 215 removed outlier: 4.069A pdb=" N PHE Z 211 " --> pdb=" O ALA Z 207 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS Z 214 " --> pdb=" O GLN Z 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 33 removed outlier: 3.575A pdb=" N ASP b 24 " --> pdb=" O LYS b 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG b 25 " --> pdb=" O GLU b 21 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU b 29 " --> pdb=" O ARG b 25 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 60 removed outlier: 4.333A pdb=" N ILE b 41 " --> pdb=" O CYS b 37 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR b 47 " --> pdb=" O ARG b 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR b 54 " --> pdb=" O LYS b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 81 removed outlier: 3.504A pdb=" N GLU b 71 " --> pdb=" O ARG b 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER b 73 " --> pdb=" O GLN b 69 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA b 74 " --> pdb=" O LEU b 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE b 75 " --> pdb=" O GLU b 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS b 79 " --> pdb=" O ILE b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 94 through 98 removed outlier: 3.562A pdb=" N LEU b 98 " --> pdb=" O VAL b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 105 removed outlier: 4.024A pdb=" N ILE b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 116 removed outlier: 3.817A pdb=" N PHE b 113 " --> pdb=" O GLN b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 130 removed outlier: 3.549A pdb=" N VAL b 126 " --> pdb=" O HIS b 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 24 Processing helix chain 'f' and resid 53 through 69 removed outlier: 3.550A pdb=" N THR f 57 " --> pdb=" O ASP f 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 75 No H-bonds generated for 'chain 'f' and resid 73 through 75' Processing helix chain 'f' and resid 83 through 97 removed outlier: 3.976A pdb=" N ARG f 88 " --> pdb=" O LEU f 84 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA f 89 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE f 91 " --> pdb=" O GLN f 87 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU f 96 " --> pdb=" O LYS f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 133 through 139 removed outlier: 3.778A pdb=" N LEU f 137 " --> pdb=" O ASP f 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 170 through 189 removed outlier: 4.171A pdb=" N ILE f 174 " --> pdb=" O GLY f 170 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET f 176 " --> pdb=" O TYR f 172 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET f 177 " --> pdb=" O SER f 173 " (cutoff:3.500A) Processing helix chain 'f' and resid 201 through 205 removed outlier: 3.655A pdb=" N LEU f 204 " --> pdb=" O LYS f 201 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 52 Processing helix chain 'd' and resid 57 through 64 removed outlier: 4.120A pdb=" N ILE d 61 " --> pdb=" O SER d 57 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE d 64 " --> pdb=" O GLU d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 78 removed outlier: 3.713A pdb=" N LEU d 77 " --> pdb=" O ILE d 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 142 removed outlier: 3.790A pdb=" N ILE d 137 " --> pdb=" O ARG d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 198 removed outlier: 3.848A pdb=" N ILE d 194 " --> pdb=" O VAL d 190 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA d 198 " --> pdb=" O ILE d 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 213 through 227 removed outlier: 3.786A pdb=" N PHE d 217 " --> pdb=" O THR d 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE d 218 " --> pdb=" O ARG d 214 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET d 219 " --> pdb=" O GLY d 215 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU d 225 " --> pdb=" O THR d 221 " (cutoff:3.500A) Processing helix chain 'd' and resid 245 through 250 Processing helix chain 'd' and resid 250 through 259 Processing helix chain 'e' and resid 5 through 20 removed outlier: 3.604A pdb=" N ASN e 9 " --> pdb=" O SER e 5 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG e 12 " --> pdb=" O ALA e 8 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N CYS e 13 " --> pdb=" O ASN e 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA e 15 " --> pdb=" O LEU e 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER e 16 " --> pdb=" O ARG e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 44 removed outlier: 3.644A pdb=" N LYS e 36 " --> pdb=" O LYS e 32 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET e 41 " --> pdb=" O PHE e 37 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 93 Processing helix chain 'e' and resid 113 through 120 Processing helix chain 'g' and resid 68 through 80 removed outlier: 3.595A pdb=" N SER g 79 " --> pdb=" O HIS g 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS g 80 " --> pdb=" O LEU g 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 60 removed outlier: 3.543A pdb=" N MET a 53 " --> pdb=" O ASP a 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER a 58 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 63 No H-bonds generated for 'chain 'a' and resid 61 through 63' Processing helix chain 'a' and resid 67 through 72 removed outlier: 3.935A pdb=" N ILE a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 67 through 72' Processing helix chain 'a' and resid 78 through 91 removed outlier: 4.419A pdb=" N LYS a 84 " --> pdb=" O ALA a 80 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU a 89 " --> pdb=" O GLY a 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 40 removed outlier: 3.657A pdb=" N GLU i 27 " --> pdb=" O PRO i 23 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL i 33 " --> pdb=" O ALA i 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 55 removed outlier: 3.685A pdb=" N ARG i 52 " --> pdb=" O SER i 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP i 55 " --> pdb=" O ALA i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 72 through 84 removed outlier: 4.167A pdb=" N THR i 78 " --> pdb=" O LYS i 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA i 79 " --> pdb=" O LYS i 75 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 102 Processing helix chain 'i' and resid 127 through 135 Processing helix chain 'P' and resid 19 through 25 removed outlier: 3.831A pdb=" N LEU P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 43 Processing helix chain 'P' and resid 140 through 148 removed outlier: 3.600A pdb=" N ILE P 144 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG P 145 " --> pdb=" O ALA P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 246 removed outlier: 4.281A pdb=" N ILE P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU P 200 " --> pdb=" O LYS P 196 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL P 202 " --> pdb=" O ALA P 198 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG P 231 " --> pdb=" O ASN P 227 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL P 236 " --> pdb=" O HIS P 232 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE P 246 " --> pdb=" O ALA P 242 " (cutoff:3.500A) Processing helix chain 'k' and resid 61 through 75 removed outlier: 3.524A pdb=" N LYS k 65 " --> pdb=" O THR k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 93 removed outlier: 3.547A pdb=" N ASN k 86 " --> pdb=" O ASP k 82 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP k 92 " --> pdb=" O ARG k 88 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL k 93 " --> pdb=" O VAL k 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 98 through 117 removed outlier: 3.690A pdb=" N LYS k 102 " --> pdb=" O SER k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 127 through 134 removed outlier: 3.728A pdb=" N ARG k 133 " --> pdb=" O GLN k 129 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 148 Processing helix chain 'k' and resid 157 through 167 removed outlier: 3.546A pdb=" N ARG k 166 " --> pdb=" O SER k 162 " (cutoff:3.500A) Processing helix chain 'l' and resid 29 through 38 removed outlier: 4.403A pdb=" N GLU l 35 " --> pdb=" O ASN l 31 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU l 38 " --> pdb=" O THR l 34 " (cutoff:3.500A) Processing helix chain 'l' and resid 39 through 41 No H-bonds generated for 'chain 'l' and resid 39 through 41' Processing helix chain 'l' and resid 94 through 101 removed outlier: 3.612A pdb=" N ILE l 98 " --> pdb=" O LEU l 94 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 28 removed outlier: 3.771A pdb=" N ILE m 11 " --> pdb=" O LYS m 7 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 59 Processing helix chain 'm' and resid 62 through 77 removed outlier: 3.969A pdb=" N ARG m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU m 72 " --> pdb=" O LEU m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 92 through 95 Processing helix chain 'm' and resid 96 through 110 Processing helix chain 'm' and resid 113 through 128 removed outlier: 3.545A pdb=" N ILE m 121 " --> pdb=" O ALA m 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER m 128 " --> pdb=" O HIS m 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 162 through 167 removed outlier: 3.731A pdb=" N PHE m 166 " --> pdb=" O ALA m 162 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 17 removed outlier: 4.343A pdb=" N ASP n 12 " --> pdb=" O ARG n 8 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL n 13 " --> pdb=" O SER n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 45 through 56 removed outlier: 3.693A pdb=" N VAL n 49 " --> pdb=" O PRO n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 76 through 88 Processing helix chain 'n' and resid 93 through 99 removed outlier: 3.910A pdb=" N HIS n 98 " --> pdb=" O VAL n 94 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS n 99 " --> pdb=" O PRO n 95 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 35 Processing helix chain 'o' and resid 65 through 77 removed outlier: 4.124A pdb=" N ARG o 73 " --> pdb=" O TRP o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 83 through 88 Processing helix chain 'o' and resid 106 through 116 removed outlier: 4.240A pdb=" N VAL o 110 " --> pdb=" O PRO o 106 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG o 111 " --> pdb=" O GLU o 107 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU o 116 " --> pdb=" O ALA o 112 " (cutoff:3.500A) Processing helix chain 'o' and resid 131 through 137 removed outlier: 3.635A pdb=" N SER o 135 " --> pdb=" O GLU o 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 137 through 143 removed outlier: 4.377A pdb=" N THR o 141 " --> pdb=" O GLY o 137 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS o 142 " --> pdb=" O HIS o 138 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 18 removed outlier: 3.986A pdb=" N GLN c 17 " --> pdb=" O LYS c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 32 through 43 removed outlier: 3.600A pdb=" N LYS c 36 " --> pdb=" O GLY c 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 88 Processing helix chain 'h' and resid 111 through 120 removed outlier: 4.008A pdb=" N LYS h 115 " --> pdb=" O ALA h 111 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE h 118 " --> pdb=" O VAL h 114 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP h 119 " --> pdb=" O LYS h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 141 through 146 Processing helix chain 'h' and resid 164 through 171 Processing helix chain 'h' and resid 193 through 202 removed outlier: 4.292A pdb=" N GLN h 197 " --> pdb=" O PRO h 193 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA h 199 " --> pdb=" O ALA h 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 224 through 240 removed outlier: 3.726A pdb=" N ALA h 237 " --> pdb=" O ARG h 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'p' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'p' and resid 16 through 20 removed outlier: 4.561A pdb=" N ALA p 18 " --> pdb=" O THR p 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER p 35 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR p 39 " --> pdb=" O SER p 35 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY p 44 " --> pdb=" O PRO p 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'p' and resid 70 through 75 removed outlier: 6.705A pdb=" N ALA p 85 " --> pdb=" O SER p 71 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL p 73 " --> pdb=" O VAL p 83 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL p 83 " --> pdb=" O VAL p 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'p' and resid 115 through 117 removed outlier: 3.801A pdb=" N THR p 116 " --> pdb=" O VAL p 125 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL p 125 " --> pdb=" O THR p 116 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU p 133 " --> pdb=" O LEU p 146 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASN p 137 " --> pdb=" O CYS p 142 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N CYS p 142 " --> pdb=" O ASN p 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'p' and resid 158 through 160 Processing sheet with id=AA6, first strand: chain 'p' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'p' and resid 240 through 242 removed outlier: 3.630A pdb=" N GLN p 242 " --> pdb=" O ALA p 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'r' and resid 11 through 18 removed outlier: 3.707A pdb=" N VAL r 12 " --> pdb=" O VAL r 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'r' and resid 36 through 37 removed outlier: 3.793A pdb=" N VAL r 37 " --> pdb=" O VAL r 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'u' and resid 14 through 15 Processing sheet with id=AB2, first strand: chain 'L' and resid 6 through 7 removed outlier: 4.236A pdb=" N LEU L 6 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AB4, first strand: chain 'L' and resid 72 through 73 Processing sheet with id=AB5, first strand: chain 'L' and resid 143 through 145 removed outlier: 6.893A pdb=" N VAL L 135 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL L 126 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET L 137 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL L 158 " --> pdb=" O ASP L 168 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP L 168 " --> pdb=" O VAL L 158 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN L 160 " --> pdb=" O VAL L 166 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL L 166 " --> pdb=" O ASN L 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 214 through 218 removed outlier: 7.261A pdb=" N ILE L 204 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE L 195 " --> pdb=" O ILE L 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARG L 206 " --> pdb=" O MET L 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 47 through 57 removed outlier: 5.367A pdb=" N VAL M 51 " --> pdb=" O GLN M 73 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN M 73 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE M 120 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA M 47 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 124 through 125 Processing sheet with id=AB9, first strand: chain 'O' and resid 109 through 111 removed outlier: 9.839A pdb=" N ALA O 124 " --> pdb=" O VAL U 86 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN U 88 " --> pdb=" O ALA O 124 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N VAL U 65 " --> pdb=" O GLY U 57 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLY U 57 " --> pdb=" O VAL U 65 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLN U 67 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL U 55 " --> pdb=" O GLN U 67 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG U 69 " --> pdb=" O ILE U 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE U 53 " --> pdb=" O ARG U 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN U 48 " --> pdb=" O LEU U 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 51 through 55 Processing sheet with id=AC2, first strand: chain 'Q' and resid 188 through 191 removed outlier: 8.117A pdb=" N GLY Q 189 " --> pdb=" O MET Q 155 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL Q 157 " --> pdb=" O GLY Q 189 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N MET Q 191 " --> pdb=" O VAL Q 157 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU Q 159 " --> pdb=" O MET Q 191 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY Q 142 " --> pdb=" O PHE Q 158 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP Q 160 " --> pdb=" O VAL Q 140 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N VAL Q 140 " --> pdb=" O ASP Q 160 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE e 50 " --> pdb=" O CYS Q 147 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU e 49 " --> pdb=" O ASN e 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 43 through 48 removed outlier: 3.979A pdb=" N ALA S 43 " --> pdb=" O CYS S 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 22 through 23 Processing sheet with id=AC5, first strand: chain 'T' and resid 38 through 41 Processing sheet with id=AC6, first strand: chain 'V' and resid 48 through 50 removed outlier: 3.527A pdb=" N TYR V 27 " --> pdb=" O PHE V 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS V 25 " --> pdb=" O HIS V 36 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY V 22 " --> pdb=" O HIS V 87 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS V 89 " --> pdb=" O GLY V 22 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL V 24 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG V 91 " --> pdb=" O VAL V 24 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE V 26 " --> pdb=" O ARG V 91 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU V 86 " --> pdb=" O ILE V 119 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG V 121 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL V 88 " --> pdb=" O ARG V 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 27 through 33 removed outlier: 3.803A pdb=" N CYS W 48 " --> pdb=" O GLU W 28 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY W 44 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 66 through 69 removed outlier: 3.674A pdb=" N TYR W 66 " --> pdb=" O PHE W 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL W 86 " --> pdb=" O SER W 68 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER W 104 " --> pdb=" O LYS W 87 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL W 89 " --> pdb=" O PHE W 102 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE W 102 " --> pdb=" O VAL W 89 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLN W 91 " --> pdb=" O THR W 100 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR W 100 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL W 93 " --> pdb=" O LEU W 98 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU W 98 " --> pdb=" O VAL W 93 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N HIS W 103 " --> pdb=" O VAL W 219 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL W 219 " --> pdb=" O HIS W 103 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG W 215 " --> pdb=" O MET W 107 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU W 212 " --> pdb=" O PHE W 144 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE W 144 " --> pdb=" O LEU W 212 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE W 214 " --> pdb=" O ILE W 142 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE W 142 " --> pdb=" O ILE W 214 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS W 216 " --> pdb=" O PHE W 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 85 through 88 removed outlier: 3.534A pdb=" N GLY X 88 " --> pdb=" O VAL X 138 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU X 137 " --> pdb=" O VAL X 158 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU X 156 " --> pdb=" O ILE X 139 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY X 141 " --> pdb=" O VAL X 154 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL X 154 " --> pdb=" O GLY X 141 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 99 through 109 Processing sheet with id=AD2, first strand: chain 'Y' and resid 12 through 17 removed outlier: 6.642A pdb=" N ILE Y 29 " --> pdb=" O SER Y 15 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE Y 17 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN Y 27 " --> pdb=" O PHE Y 17 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE Y 82 " --> pdb=" O LYS Y 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE Y 28 " --> pdb=" O GLY Y 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY Y 78 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR Y 77 " --> pdb=" O PHE Y 67 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE Y 67 " --> pdb=" O THR Y 77 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE Y 79 " --> pdb=" O PHE Y 65 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 42 through 47 removed outlier: 3.582A pdb=" N SER Z 44 " --> pdb=" O ARG Z 56 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 62 through 67 removed outlier: 3.585A pdb=" N TRP Z 67 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE Z 72 " --> pdb=" O TRP Z 67 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL Z 103 " --> pdb=" O LEU Z 79 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL Z 81 " --> pdb=" O ILE Z 101 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE Z 101 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N CYS Z 100 " --> pdb=" O ILE Z 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA Z 187 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL Z 104 " --> pdb=" O LEU Z 185 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU Z 185 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLY Z 201 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN Z 64 " --> pdb=" O GLY Z 201 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU Z 203 " --> pdb=" O ASN Z 64 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA Z 66 " --> pdb=" O LEU Z 203 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'f' and resid 41 through 42 removed outlier: 3.917A pdb=" N ILE f 51 " --> pdb=" O HIS f 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 77 through 78 Processing sheet with id=AD7, first strand: chain 'f' and resid 148 through 151 Processing sheet with id=AD8, first strand: chain 'd' and resid 84 through 95 removed outlier: 6.058A pdb=" N ASP d 85 " --> pdb=" O GLY d 112 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLY d 112 " --> pdb=" O ASP d 85 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU d 87 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE d 110 " --> pdb=" O LEU d 87 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU d 89 " --> pdb=" O PHE d 108 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG d 102 " --> pdb=" O LYS d 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 165 through 168 removed outlier: 3.748A pdb=" N GLY d 167 " --> pdb=" O VAL d 174 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 72 through 74 removed outlier: 3.820A pdb=" N PHE e 128 " --> pdb=" O GLY e 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 72 through 74 removed outlier: 3.820A pdb=" N PHE e 128 " --> pdb=" O GLY e 73 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL e 125 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N THR e 105 " --> pdb=" O VAL e 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 20 through 22 removed outlier: 4.041A pdb=" N ARG g 20 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN g 27 " --> pdb=" O CYS g 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'g' and resid 38 through 39 Processing sheet with id=AE5, first strand: chain 'g' and resid 42 through 44 removed outlier: 6.816A pdb=" N ASN g 43 " --> pdb=" O ASN g 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 65 through 66 Processing sheet with id=AE7, first strand: chain 'i' and resid 43 through 45 removed outlier: 4.432A pdb=" N VAL i 121 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N CYS i 62 " --> pdb=" O ILE i 89 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL i 91 " --> pdb=" O CYS i 62 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU i 64 " --> pdb=" O VAL i 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'j' and resid 137 through 139 removed outlier: 3.792A pdb=" N TYR j 147 " --> pdb=" O LYS j 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'P' and resid 36 through 38 removed outlier: 7.171A pdb=" N PHE P 51 " --> pdb=" O VAL P 117 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL P 117 " --> pdb=" O PHE P 51 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU P 53 " --> pdb=" O VAL P 115 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL P 115 " --> pdb=" O LEU P 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY P 55 " --> pdb=" O ASN P 113 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL P 111 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 73 through 79 Processing sheet with id=AF3, first strand: chain 'P' and resid 163 through 165 Processing sheet with id=AF4, first strand: chain 'k' and resid 94 through 95 removed outlier: 3.635A pdb=" N ILE k 95 " --> pdb=" O ASP m 202 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'l' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'l' and resid 57 through 60 removed outlier: 3.693A pdb=" N LEU l 58 " --> pdb=" O LEU l 79 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'm' and resid 35 through 37 removed outlier: 3.690A pdb=" N GLY m 35 " --> pdb=" O ARG m 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'm' and resid 132 through 138 Processing sheet with id=AF9, first strand: chain 'm' and resid 170 through 176 removed outlier: 3.546A pdb=" N LEU m 176 " --> pdb=" O GLY m 179 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'n' and resid 23 through 26 Processing sheet with id=AG2, first strand: chain 'h' and resid 96 through 98 Processing sheet with id=AG3, first strand: chain 'h' and resid 176 through 178 1212 hydrogen bonds defined for protein. 3426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1161 hydrogen bonds 1896 hydrogen bond angles 0 basepair planarities 468 basepair parallelities 895 stacking parallelities Total time for adding SS restraints: 64.84 Time building geometry restraints manager: 33.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11310 1.34 - 1.46: 40048 1.46 - 1.59: 35044 1.59 - 1.71: 1281 1.71 - 1.83: 317 Bond restraints: 88000 Sorted by residual: bond pdb=" N9 G E 734 " pdb=" C4 G E 734 " ideal model delta sigma weight residual 1.375 1.267 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" CA GLU L 124 " pdb=" C GLU L 124 " ideal model delta sigma weight residual 1.524 1.493 0.031 7.00e-03 2.04e+04 1.95e+01 bond pdb=" C2' U E1082 " pdb=" C1' U E1082 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.50e-02 4.44e+03 1.94e+01 bond pdb=" N9 A E 724 " pdb=" C4 A E 724 " ideal model delta sigma weight residual 1.374 1.286 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CA HIS Y 34 " pdb=" CB HIS Y 34 " ideal model delta sigma weight residual 1.522 1.553 -0.030 7.00e-03 2.04e+04 1.89e+01 ... (remaining 87995 not shown) Histogram of bond angle deviations from ideal: 81.23 - 98.02: 92 98.02 - 114.81: 68363 114.81 - 131.61: 59954 131.61 - 148.40: 157 148.40 - 165.19: 2 Bond angle restraints: 128568 Sorted by residual: angle pdb=" C3' C E 774 " pdb=" O3' C E 774 " pdb=" P A E 775 " ideal model delta sigma weight residual 120.20 165.19 -44.99 1.50e+00 4.44e-01 9.00e+02 angle pdb=" C3' C E1187 " pdb=" O3' C E1187 " pdb=" P C E1188 " ideal model delta sigma weight residual 120.20 160.37 -40.17 1.50e+00 4.44e-01 7.17e+02 angle pdb=" C3' A E 703 " pdb=" O3' A E 703 " pdb=" P A E 704 " ideal model delta sigma weight residual 120.20 148.22 -28.02 1.50e+00 4.44e-01 3.49e+02 angle pdb=" O3' U E 975 " pdb=" P U E 976 " pdb=" O5' U E 976 " ideal model delta sigma weight residual 104.00 131.48 -27.48 1.50e+00 4.44e-01 3.36e+02 angle pdb=" C3' A E 531 " pdb=" O3' A E 531 " pdb=" P G E 532 " ideal model delta sigma weight residual 120.20 146.52 -26.32 1.50e+00 4.44e-01 3.08e+02 ... (remaining 128563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 50712 35.91 - 71.82: 4475 71.82 - 107.73: 588 107.73 - 143.64: 29 143.64 - 179.55: 59 Dihedral angle restraints: 55863 sinusoidal: 41719 harmonic: 14144 Sorted by residual: dihedral pdb=" CA TYR r 121 " pdb=" C TYR r 121 " pdb=" N LEU r 122 " pdb=" CA LEU r 122 " ideal model delta harmonic sigma weight residual -180.00 -76.52 -103.48 0 5.00e+00 4.00e-02 4.28e+02 dihedral pdb=" CA LYS h 174 " pdb=" C LYS h 174 " pdb=" N VAL h 175 " pdb=" CA VAL h 175 " ideal model delta harmonic sigma weight residual 180.00 109.06 70.94 0 5.00e+00 4.00e-02 2.01e+02 dihedral pdb=" CA PRO c 62 " pdb=" C PRO c 62 " pdb=" N GLY c 63 " pdb=" CA GLY c 63 " ideal model delta harmonic sigma weight residual 180.00 117.36 62.64 0 5.00e+00 4.00e-02 1.57e+02 ... (remaining 55860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.977: 16025 0.977 - 1.954: 0 1.954 - 2.931: 0 2.931 - 3.908: 0 3.908 - 4.884: 4 Chirality restraints: 16029 Sorted by residual: chirality pdb=" C3' A E1903 " pdb=" C4' A E1903 " pdb=" O3' A E1903 " pdb=" C2' A E1903 " both_signs ideal model delta sigma weight residual False -2.48 2.41 -4.88 2.00e-01 2.50e+01 5.96e+02 chirality pdb=" C3' U E 325 " pdb=" C4' U E 325 " pdb=" O3' U E 325 " pdb=" C2' U E 325 " both_signs ideal model delta sigma weight residual False -2.48 2.24 -4.71 2.00e-01 2.50e+01 5.55e+02 chirality pdb=" C1' U E 702 " pdb=" O4' U E 702 " pdb=" C2' U E 702 " pdb=" N1 U E 702 " both_signs ideal model delta sigma weight residual False 2.45 -2.19 4.64 2.00e-01 2.50e+01 5.38e+02 ... (remaining 16026 not shown) Planarity restraints: 8845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G E 734 " 0.399 2.00e-02 2.50e+03 2.55e-01 1.95e+03 pdb=" N9 G E 734 " 0.068 2.00e-02 2.50e+03 pdb=" C8 G E 734 " 0.131 2.00e-02 2.50e+03 pdb=" N7 G E 734 " -0.088 2.00e-02 2.50e+03 pdb=" C5 G E 734 " -0.278 2.00e-02 2.50e+03 pdb=" C6 G E 734 " 0.064 2.00e-02 2.50e+03 pdb=" O6 G E 734 " 0.217 2.00e-02 2.50e+03 pdb=" N1 G E 734 " 0.159 2.00e-02 2.50e+03 pdb=" C2 G E 734 " -0.045 2.00e-02 2.50e+03 pdb=" N2 G E 734 " 0.233 2.00e-02 2.50e+03 pdb=" N3 G E 734 " -0.507 2.00e-02 2.50e+03 pdb=" C4 G E 734 " -0.352 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 746 " 0.281 2.00e-02 2.50e+03 2.14e-01 1.25e+03 pdb=" N9 A E 746 " 0.054 2.00e-02 2.50e+03 pdb=" C8 A E 746 " 0.134 2.00e-02 2.50e+03 pdb=" N7 A E 746 " -0.075 2.00e-02 2.50e+03 pdb=" C5 A E 746 " -0.278 2.00e-02 2.50e+03 pdb=" C6 A E 746 " 0.016 2.00e-02 2.50e+03 pdb=" N6 A E 746 " 0.099 2.00e-02 2.50e+03 pdb=" N1 A E 746 " 0.266 2.00e-02 2.50e+03 pdb=" C2 A E 746 " 0.155 2.00e-02 2.50e+03 pdb=" N3 A E 746 " -0.300 2.00e-02 2.50e+03 pdb=" C4 A E 746 " -0.352 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E1873 " -0.227 2.00e-02 2.50e+03 1.98e-01 1.18e+03 pdb=" N9 G E1873 " -0.053 2.00e-02 2.50e+03 pdb=" C8 G E1873 " 0.183 2.00e-02 2.50e+03 pdb=" N7 G E1873 " 0.216 2.00e-02 2.50e+03 pdb=" C5 G E1873 " 0.073 2.00e-02 2.50e+03 pdb=" C6 G E1873 " -0.064 2.00e-02 2.50e+03 pdb=" O6 G E1873 " -0.065 2.00e-02 2.50e+03 pdb=" N1 G E1873 " -0.364 2.00e-02 2.50e+03 pdb=" C2 G E1873 " -0.056 2.00e-02 2.50e+03 pdb=" N2 G E1873 " 0.428 2.00e-02 2.50e+03 pdb=" N3 G E1873 " -0.063 2.00e-02 2.50e+03 pdb=" C4 G E1873 " -0.009 2.00e-02 2.50e+03 ... (remaining 8842 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 8322 2.77 - 3.30: 74066 3.30 - 3.83: 159864 3.83 - 4.37: 189532 4.37 - 4.90: 273048 Nonbonded interactions: 704832 Sorted by model distance: nonbonded pdb=" N1 G E1852 " pdb=" N1 A E1866 " model vdw 2.237 2.600 nonbonded pdb=" N1 A E 711 " pdb=" N1 A E 746 " model vdw 2.335 3.200 nonbonded pdb=" N3 C E 259 " pdb=" N1 G E 954 " model vdw 2.353 2.600 nonbonded pdb=" N THR e 106 " pdb=" O THR e 106 " model vdw 2.389 2.496 nonbonded pdb=" N1 A E1088 " pdb=" N3 C E1166 " model vdw 2.409 3.200 ... (remaining 704827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 11.190 Check model and map are aligned: 0.870 Set scattering table: 0.580 Process input model: 213.380 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 232.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.108 88000 Z= 1.089 Angle : 2.042 44.990 128568 Z= 1.233 Chirality : 0.130 4.884 16029 Planarity : 0.022 0.255 8845 Dihedral : 22.328 179.550 46710 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 1.88 % Allowed : 8.52 % Favored : 89.59 % Rotamer: Outliers : 0.41 % Allowed : 2.20 % Favored : 97.40 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.32 % Twisted Proline : 1.65 % Twisted General : 0.94 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.09), residues: 4833 helix: -4.17 (0.08), residues: 1336 sheet: -2.27 (0.15), residues: 759 loop : -2.21 (0.10), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.144 0.014 TRP o 69 HIS 0.006 0.001 HIS b 132 PHE 0.097 0.010 PHE Q 46 TYR 0.166 0.016 TYR a 107 ARG 0.007 0.001 ARG O 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1743 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1726 time to evaluate : 4.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 139 LYS cc_start: 0.5152 (mttp) cc_final: 0.4700 (ttpp) REVERT: r 111 LEU cc_start: 0.5231 (mt) cc_final: 0.4703 (mt) REVERT: u 37 VAL cc_start: 0.4597 (t) cc_final: 0.4389 (t) REVERT: u 41 PHE cc_start: 0.2870 (m-10) cc_final: 0.2267 (m-10) REVERT: L 198 HIS cc_start: 0.6446 (m90) cc_final: 0.6141 (m-70) REVERT: L 231 SER cc_start: 0.6800 (m) cc_final: 0.6153 (t) REVERT: M 88 ASP cc_start: 0.6810 (t70) cc_final: 0.6487 (t0) REVERT: Q 130 ILE cc_start: 0.7666 (mt) cc_final: 0.7159 (mt) REVERT: R 12 SER cc_start: 0.8154 (m) cc_final: 0.7936 (p) REVERT: R 34 ILE cc_start: 0.8510 (mt) cc_final: 0.8307 (mt) REVERT: S 64 LEU cc_start: 0.7038 (mt) cc_final: 0.6555 (mt) REVERT: S 74 LEU cc_start: 0.7160 (mt) cc_final: 0.6899 (mt) REVERT: T 55 VAL cc_start: 0.7400 (t) cc_final: 0.6670 (p) REVERT: T 72 TYR cc_start: 0.5517 (m-80) cc_final: 0.5185 (m-80) REVERT: T 77 PHE cc_start: 0.6562 (m-80) cc_final: 0.6321 (m-80) REVERT: U 53 ILE cc_start: 0.5102 (tp) cc_final: 0.4780 (tt) REVERT: V 32 ASP cc_start: 0.6589 (t70) cc_final: 0.6346 (t70) REVERT: V 63 SER cc_start: 0.7589 (p) cc_final: 0.7000 (t) REVERT: V 65 TYR cc_start: 0.5516 (t80) cc_final: 0.5267 (t80) REVERT: V 125 VAL cc_start: 0.6208 (t) cc_final: 0.5681 (t) REVERT: W 191 THR cc_start: 0.7883 (p) cc_final: 0.7629 (m) REVERT: W 226 ASP cc_start: 0.4767 (t70) cc_final: 0.3522 (t0) REVERT: Z 17 LYS cc_start: 0.7609 (mttt) cc_final: 0.6339 (ttpt) REVERT: Z 36 THR cc_start: 0.7782 (m) cc_final: 0.7347 (m) REVERT: Z 83 TYR cc_start: 0.8343 (t80) cc_final: 0.7972 (t80) REVERT: Z 92 ARG cc_start: 0.7550 (mtm110) cc_final: 0.6123 (tpt-90) REVERT: b 17 PRO cc_start: 0.5990 (Cg_endo) cc_final: 0.5674 (Cg_exo) REVERT: b 159 ASP cc_start: 0.6748 (m-30) cc_final: 0.6079 (p0) REVERT: f 26 CYS cc_start: 0.6139 (t) cc_final: 0.5823 (t) REVERT: f 127 VAL cc_start: 0.7544 (m) cc_final: 0.7218 (m) REVERT: d 52 GLU cc_start: 0.5054 (mt-10) cc_final: 0.4671 (mt-10) REVERT: d 56 THR cc_start: 0.4786 (p) cc_final: 0.3906 (t) REVERT: d 223 TYR cc_start: 0.7258 (m-10) cc_final: 0.7021 (m-10) REVERT: e 9 ASN cc_start: 0.8205 (t0) cc_final: 0.7601 (t0) REVERT: g 17 TYR cc_start: 0.7094 (p90) cc_final: 0.6295 (p90) REVERT: g 57 PHE cc_start: 0.6999 (m-80) cc_final: 0.6740 (m-10) REVERT: a 70 ILE cc_start: 0.6401 (pt) cc_final: 0.6100 (tt) REVERT: k 127 LYS cc_start: 0.5052 (mttm) cc_final: 0.4825 (ttpt) REVERT: l 77 TYR cc_start: 0.7036 (m-80) cc_final: 0.6740 (m-80) REVERT: m 92 VAL cc_start: 0.2077 (t) cc_final: 0.1839 (t) REVERT: m 93 ARG cc_start: 0.6134 (ttt180) cc_final: 0.5623 (ptp-170) REVERT: m 102 GLU cc_start: 0.4236 (mt-10) cc_final: 0.3964 (mt-10) REVERT: m 167 VAL cc_start: 0.7769 (t) cc_final: 0.7492 (m) REVERT: m 201 PRO cc_start: 0.5567 (Cg_exo) cc_final: 0.5046 (Cg_endo) outliers start: 17 outliers final: 2 residues processed: 1737 average time/residue: 0.9080 time to fit residues: 2519.7104 Evaluate side-chains 853 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 851 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 165 TRP Chi-restraints excluded: chain h residue 181 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 573 optimal weight: 5.9990 chunk 514 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 532 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 323 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 616 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 103 HIS p 280 GLN p 307 ASN r 83 GLN r 100 GLN ** t 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 HIS M 143 ASN O 18 GLN O 37 HIS O 69 ASN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS Q 180 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 155 ASN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 GLN Z 74 GLN b 123 HIS ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 121 GLN d 153 ASN ** d 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 9 ASN e 70 ASN j 88 HIS P 60 GLN P 241 GLN ** k 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 HIS m 77 HIS n 51 GLN ** n 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 98 HIS h 239 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 88000 Z= 0.252 Angle : 0.817 32.308 128568 Z= 0.417 Chirality : 0.042 0.438 16029 Planarity : 0.006 0.059 8845 Dihedral : 23.550 179.861 36783 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.32 % Favored : 94.14 % Rotamer: Outliers : 4.37 % Allowed : 14.89 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.34 % Twisted Proline : 1.65 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.10), residues: 4833 helix: -1.79 (0.12), residues: 1412 sheet: -1.50 (0.16), residues: 807 loop : -1.91 (0.10), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP o 29 HIS 0.010 0.002 HIS P 232 PHE 0.034 0.003 PHE n 17 TYR 0.044 0.002 TYR u 43 ARG 0.009 0.001 ARG e 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 954 time to evaluate : 4.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 55 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4828 (ttm) REVERT: u 16 LEU cc_start: 0.5226 (mt) cc_final: 0.4762 (mt) REVERT: L 231 SER cc_start: 0.6676 (m) cc_final: 0.6377 (t) REVERT: M 88 ASP cc_start: 0.7105 (t70) cc_final: 0.6835 (t0) REVERT: O 131 ARG cc_start: 0.5785 (mtp85) cc_final: 0.5325 (mmm160) REVERT: Q 47 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6728 (t-90) REVERT: Q 130 ILE cc_start: 0.7330 (mt) cc_final: 0.7020 (mt) REVERT: S 8 LEU cc_start: 0.8603 (mt) cc_final: 0.8393 (mt) REVERT: S 16 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7264 (mp0) REVERT: T 72 TYR cc_start: 0.5508 (m-80) cc_final: 0.5274 (m-80) REVERT: T 83 ILE cc_start: 0.7790 (mm) cc_final: 0.7533 (mt) REVERT: U 53 ILE cc_start: 0.5166 (tp) cc_final: 0.4849 (tt) REVERT: V 17 ASP cc_start: 0.6959 (t0) cc_final: 0.6688 (t0) REVERT: V 50 THR cc_start: 0.7651 (t) cc_final: 0.7342 (t) REVERT: V 63 SER cc_start: 0.7834 (p) cc_final: 0.7539 (t) REVERT: V 119 ILE cc_start: 0.7989 (pt) cc_final: 0.7378 (mt) REVERT: W 113 TYR cc_start: 0.7385 (m-80) cc_final: 0.7164 (m-80) REVERT: Z 17 LYS cc_start: 0.7229 (mttt) cc_final: 0.6987 (ttmm) REVERT: Z 36 THR cc_start: 0.8100 (m) cc_final: 0.7827 (m) REVERT: Z 83 TYR cc_start: 0.8385 (t80) cc_final: 0.8070 (t80) REVERT: Z 92 ARG cc_start: 0.7967 (mtm110) cc_final: 0.6962 (tpt170) REVERT: Z 164 MET cc_start: 0.6831 (tmm) cc_final: 0.6542 (mmp) REVERT: Z 174 LYS cc_start: 0.4399 (mmtt) cc_final: 0.3913 (mmtt) REVERT: b 98 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.7005 (mt) REVERT: b 99 THR cc_start: 0.7543 (t) cc_final: 0.7304 (m) REVERT: b 114 LYS cc_start: 0.7035 (tmmt) cc_final: 0.6833 (tptm) REVERT: b 142 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8111 (tp) REVERT: b 159 ASP cc_start: 0.6701 (m-30) cc_final: 0.6328 (p0) REVERT: f 139 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6756 (mt-10) REVERT: d 70 GLU cc_start: 0.6400 (mm-30) cc_final: 0.5977 (mm-30) REVERT: d 153 ASN cc_start: 0.3514 (OUTLIER) cc_final: 0.3292 (m-40) REVERT: e 9 ASN cc_start: 0.8506 (t0) cc_final: 0.8029 (t0) REVERT: e 18 GLU cc_start: 0.4988 (tm-30) cc_final: 0.4727 (tm-30) REVERT: k 70 GLN cc_start: 0.6656 (mm-40) cc_final: 0.6228 (tp40) REVERT: l 96 LYS cc_start: 0.5794 (mtmt) cc_final: 0.5573 (mtmm) REVERT: m 201 PRO cc_start: 0.5813 (Cg_exo) cc_final: 0.5418 (Cg_endo) REVERT: h 75 TRP cc_start: 0.1722 (t60) cc_final: 0.1327 (t60) REVERT: h 121 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6195 (t80) outliers start: 183 outliers final: 111 residues processed: 1058 average time/residue: 0.8199 time to fit residues: 1449.3022 Evaluate side-chains 855 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 738 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 121 ASN Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 289 MET Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 55 MET Chi-restraints excluded: chain r residue 83 GLN Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain u residue 31 LEU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 47 HIS Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 237 ILE Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 94 LYS Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 161 ARG Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 142 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 56 MET Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 63 VAL Chi-restraints excluded: chain e residue 102 VAL Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 58 ASP Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 98 SER Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain c residue 21 VAL Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain h residue 121 PHE Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 208 PHE Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 342 optimal weight: 50.0000 chunk 191 optimal weight: 10.0000 chunk 513 optimal weight: 20.0000 chunk 419 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 617 optimal weight: 40.0000 chunk 667 optimal weight: 20.0000 chunk 550 optimal weight: 30.0000 chunk 612 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 495 optimal weight: 20.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 12 HIS p 23 GLN p 298 ASN r 38 ASN r 83 GLN t 55 HIS ** u 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS Q 36 HIS Q 176 HIS Q 180 GLN Q 183 HIS T 75 GLN U 88 ASN V 106 GLN W 77 GLN W 97 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 103 HIS W 148 GLN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 193 ASN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 HIS Z 179 GLN ** b 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN b 64 ASN b 115 HIS ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 116 GLN ** d 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 60 HIS ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 ASN ** k 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 38 HIS m 77 HIS m 124 HIS ** m 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 51 GLN ** n 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 98 ASN ** c 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN h 77 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 88000 Z= 0.533 Angle : 1.077 35.765 128568 Z= 0.541 Chirality : 0.054 0.386 16029 Planarity : 0.008 0.082 8845 Dihedral : 24.019 178.795 36781 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.65 % Favored : 90.92 % Rotamer: Outliers : 7.30 % Allowed : 16.63 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 1.10 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.10), residues: 4833 helix: -1.83 (0.12), residues: 1425 sheet: -1.49 (0.16), residues: 821 loop : -2.39 (0.11), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP d 151 HIS 0.031 0.003 HIS Q 47 PHE 0.035 0.004 PHE W 114 TYR 0.047 0.004 TYR o 71 ARG 0.017 0.001 ARG m 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 780 time to evaluate : 4.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 121 ASN cc_start: 0.5672 (p0) cc_final: 0.5386 (p0) REVERT: r 11 GLN cc_start: 0.7019 (mt0) cc_final: 0.6049 (mp10) REVERT: r 61 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7332 (t) REVERT: r 83 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.6038 (mt0) REVERT: r 115 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6544 (m-10) REVERT: t 103 ILE cc_start: 0.5854 (tp) cc_final: 0.5630 (tp) REVERT: u 71 VAL cc_start: 0.6458 (t) cc_final: 0.6062 (p) REVERT: L 29 ARG cc_start: 0.7228 (mmt-90) cc_final: 0.7014 (mtm180) REVERT: L 42 MET cc_start: 0.7820 (tmm) cc_final: 0.7525 (tmm) REVERT: L 231 SER cc_start: 0.7102 (m) cc_final: 0.6436 (t) REVERT: L 246 VAL cc_start: 0.7176 (m) cc_final: 0.6657 (t) REVERT: M 88 ASP cc_start: 0.7253 (t70) cc_final: 0.6890 (t0) REVERT: O 30 LYS cc_start: 0.3243 (pptt) cc_final: 0.2858 (ttpp) REVERT: O 85 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8377 (tt) REVERT: Q 22 GLU cc_start: 0.7074 (mp0) cc_final: 0.6674 (mp0) REVERT: Q 124 VAL cc_start: 0.7039 (m) cc_final: 0.6405 (m) REVERT: R 35 ASP cc_start: 0.5825 (OUTLIER) cc_final: 0.5545 (t0) REVERT: T 55 VAL cc_start: 0.7120 (m) cc_final: 0.6543 (p) REVERT: U 48 GLN cc_start: 0.4874 (pt0) cc_final: 0.4482 (pt0) REVERT: U 53 ILE cc_start: 0.3949 (tp) cc_final: 0.3674 (tt) REVERT: V 17 ASP cc_start: 0.6250 (t0) cc_final: 0.5775 (t0) REVERT: W 66 TYR cc_start: 0.7260 (m-10) cc_final: 0.6924 (m-10) REVERT: X 106 LEU cc_start: 0.8394 (mt) cc_final: 0.8111 (mt) REVERT: X 131 ASP cc_start: 0.6896 (p0) cc_final: 0.6391 (p0) REVERT: Z 36 THR cc_start: 0.8481 (m) cc_final: 0.8227 (m) REVERT: Z 92 ARG cc_start: 0.7954 (mtm110) cc_final: 0.6996 (tpt170) REVERT: Z 113 TYR cc_start: 0.7622 (t80) cc_final: 0.7410 (t80) REVERT: Z 174 LYS cc_start: 0.5717 (mmtt) cc_final: 0.5169 (mmtm) REVERT: b 46 MET cc_start: 0.6117 (tpp) cc_final: 0.5829 (tpt) REVERT: b 94 TYR cc_start: 0.6030 (m-80) cc_final: 0.5733 (m-10) REVERT: b 142 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8353 (tp) REVERT: d 253 PHE cc_start: 0.5668 (t80) cc_final: 0.5432 (t80) REVERT: e 9 ASN cc_start: 0.8444 (t0) cc_final: 0.8067 (t0) REVERT: e 43 LYS cc_start: 0.7506 (mttt) cc_final: 0.7096 (mttp) REVERT: e 115 GLU cc_start: 0.5515 (tp30) cc_final: 0.5307 (tp30) REVERT: e 121 THR cc_start: 0.6959 (OUTLIER) cc_final: 0.6718 (t) REVERT: g 47 ASN cc_start: 0.5338 (m-40) cc_final: 0.5122 (t0) REVERT: a 46 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6432 (t) REVERT: P 75 SER cc_start: 0.8514 (t) cc_final: 0.8310 (p) REVERT: k 108 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.4676 (t80) REVERT: l 93 GLU cc_start: 0.5492 (mt-10) cc_final: 0.5256 (mt-10) REVERT: h 98 VAL cc_start: 0.3877 (t) cc_final: 0.3624 (p) REVERT: h 121 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6727 (t80) REVERT: h 187 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.4523 (t80) outliers start: 306 outliers final: 191 residues processed: 988 average time/residue: 0.7925 time to fit residues: 1325.3309 Evaluate side-chains 844 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 642 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 289 MET Chi-restraints excluded: chain p residue 306 ASP Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 54 ILE Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 83 GLN Chi-restraints excluded: chain r residue 115 TYR Chi-restraints excluded: chain r residue 145 THR Chi-restraints excluded: chain t residue 30 ASP Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 122 TYR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain u residue 31 LEU Chi-restraints excluded: chain u residue 37 VAL Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 100 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain O residue 21 GLU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 35 ASP Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 67 GLN Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 34 PHE Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 207 VAL Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 91 HIS Chi-restraints excluded: chain X residue 94 LYS Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 155 LEU Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 64 ASN Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 161 ARG Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 24 ASP Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 49 SER Chi-restraints excluded: chain b residue 60 THR Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 142 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 204 LEU Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 225 LEU Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 63 VAL Chi-restraints excluded: chain e residue 102 VAL Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 98 SER Chi-restraints excluded: chain k residue 108 TYR Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 157 ASP Chi-restraints excluded: chain l residue 33 MET Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 39 HIS Chi-restraints excluded: chain l residue 42 ASN Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 183 VAL Chi-restraints excluded: chain n residue 33 TRP Chi-restraints excluded: chain n residue 76 ASN Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 121 PHE Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 174 LYS Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 208 PHE Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 610 optimal weight: 20.0000 chunk 464 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 294 optimal weight: 0.0470 chunk 414 optimal weight: 5.9990 chunk 619 optimal weight: 30.0000 chunk 656 optimal weight: 30.0000 chunk 323 optimal weight: 2.9990 chunk 587 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 28 GLN r 83 GLN ** u 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 HIS O 37 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 193 ASN W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN b 6 ASN ** b 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN b 115 HIS ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 8 ASN a 92 GLN i 60 HIS P 35 ASN k 70 GLN k 129 GLN m 124 HIS m 163 HIS o 65 GLN o 101 ASN ** c 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 197 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 88000 Z= 0.226 Angle : 0.741 22.597 128568 Z= 0.383 Chirality : 0.045 2.333 16029 Planarity : 0.005 0.062 8845 Dihedral : 23.809 179.675 36781 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.14 % Favored : 92.43 % Rotamer: Outliers : 6.13 % Allowed : 19.28 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 1.10 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.11), residues: 4833 helix: -0.95 (0.13), residues: 1424 sheet: -1.22 (0.16), residues: 849 loop : -2.19 (0.11), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP u 83 HIS 0.028 0.002 HIS b 115 PHE 0.039 0.002 PHE n 17 TYR 0.038 0.002 TYR u 43 ARG 0.008 0.001 ARG i 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 761 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 11 GLN cc_start: 0.6328 (mt0) cc_final: 0.5690 (mp10) REVERT: r 115 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6553 (m-10) REVERT: r 148 TYR cc_start: 0.5813 (m-10) cc_final: 0.5523 (m-10) REVERT: t 73 ASP cc_start: 0.5402 (m-30) cc_final: 0.4482 (m-30) REVERT: L 231 SER cc_start: 0.6696 (m) cc_final: 0.6146 (t) REVERT: M 88 ASP cc_start: 0.6815 (t70) cc_final: 0.6369 (t0) REVERT: Q 124 VAL cc_start: 0.7019 (OUTLIER) cc_final: 0.6569 (m) REVERT: R 93 LYS cc_start: 0.5978 (tptm) cc_final: 0.5304 (tptm) REVERT: T 55 VAL cc_start: 0.6944 (m) cc_final: 0.6624 (p) REVERT: T 83 ILE cc_start: 0.8378 (mm) cc_final: 0.8118 (mt) REVERT: U 53 ILE cc_start: 0.4881 (tp) cc_final: 0.4594 (tt) REVERT: V 17 ASP cc_start: 0.6048 (t0) cc_final: 0.5422 (t0) REVERT: W 66 TYR cc_start: 0.7128 (m-10) cc_final: 0.6719 (m-10) REVERT: W 79 ASP cc_start: 0.3783 (OUTLIER) cc_final: 0.2943 (t70) REVERT: X 94 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7062 (mptt) REVERT: X 131 ASP cc_start: 0.6902 (p0) cc_final: 0.6406 (p0) REVERT: Z 36 THR cc_start: 0.8399 (m) cc_final: 0.8090 (m) REVERT: Z 53 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: Z 92 ARG cc_start: 0.7560 (mtm110) cc_final: 0.6701 (tpt170) REVERT: Z 174 LYS cc_start: 0.5375 (mmtt) cc_final: 0.4557 (mptt) REVERT: b 39 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6765 (mtp180) REVERT: b 142 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7888 (tp) REVERT: f 54 LEU cc_start: 0.7556 (mt) cc_final: 0.7110 (mt) REVERT: d 85 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5433 (m-30) REVERT: d 231 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.4963 (m-80) REVERT: d 253 PHE cc_start: 0.5586 (t80) cc_final: 0.5356 (t80) REVERT: e 9 ASN cc_start: 0.8384 (t0) cc_final: 0.8089 (t0) REVERT: e 130 TYR cc_start: 0.7083 (m-80) cc_final: 0.6812 (m-80) REVERT: P 75 SER cc_start: 0.8180 (t) cc_final: 0.7945 (p) REVERT: l 71 THR cc_start: 0.5076 (OUTLIER) cc_final: 0.4772 (p) REVERT: h 108 PHE cc_start: 0.3062 (OUTLIER) cc_final: 0.2785 (m-10) REVERT: h 121 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6902 (t80) REVERT: h 187 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.4242 (t80) REVERT: h 198 ARG cc_start: 0.5970 (ptt180) cc_final: 0.5452 (ptp90) outliers start: 257 outliers final: 174 residues processed: 941 average time/residue: 0.7551 time to fit residues: 1223.0366 Evaluate side-chains 852 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 665 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 69 PHE Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 289 MET Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 83 GLN Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 108 LYS Chi-restraints excluded: chain r residue 115 TYR Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 122 TYR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain t residue 134 ILE Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 43 TYR Chi-restraints excluded: chain u residue 46 CYS Chi-restraints excluded: chain u residue 98 HIS Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 191 GLU Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 65 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 78 CYS Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 79 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 94 LYS Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 143 CYS Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Z residue 53 PHE Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 161 ARG Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 49 SER Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 142 ILE Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 108 PHE Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 231 PHE Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 4 MET Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain i residue 133 LEU Chi-restraints excluded: chain j residue 100 TYR Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 154 ASP Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 98 SER Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 150 ILE Chi-restraints excluded: chain k residue 171 VAL Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 156 MET Chi-restraints excluded: chain m residue 188 MET Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 22 VAL Chi-restraints excluded: chain n residue 76 ASN Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 121 PHE Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 174 LYS Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 546 optimal weight: 20.0000 chunk 372 optimal weight: 9.9990 chunk 9 optimal weight: 40.0000 chunk 488 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 560 optimal weight: 20.0000 chunk 453 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 335 optimal weight: 0.2980 chunk 589 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 overall best weight: 12.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 83 GLN ** r 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 245 ASN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN Z 179 GLN b 64 ASN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 60 HIS ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 ASN m 124 HIS m 163 HIS ** c 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 88000 Z= 0.417 Angle : 0.908 25.682 128568 Z= 0.458 Chirality : 0.050 2.032 16029 Planarity : 0.007 0.072 8845 Dihedral : 24.030 179.728 36781 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.75 % Favored : 89.80 % Rotamer: Outliers : 7.52 % Allowed : 20.10 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 0.55 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 4833 helix: -1.28 (0.12), residues: 1442 sheet: -1.28 (0.17), residues: 801 loop : -2.42 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP u 83 HIS 0.019 0.002 HIS m 124 PHE 0.038 0.003 PHE n 17 TYR 0.035 0.003 TYR u 43 ARG 0.011 0.001 ARG m 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 699 time to evaluate : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 63 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.3490 (mp) REVERT: r 11 GLN cc_start: 0.6724 (mt0) cc_final: 0.6087 (mp10) REVERT: r 115 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: t 73 ASP cc_start: 0.5559 (m-30) cc_final: 0.4861 (m-30) REVERT: u 71 VAL cc_start: 0.6336 (t) cc_final: 0.5603 (p) REVERT: u 125 ARG cc_start: 0.1827 (OUTLIER) cc_final: 0.0868 (tmm-80) REVERT: L 84 MET cc_start: 0.7878 (tpp) cc_final: 0.7448 (tpp) REVERT: L 100 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: L 143 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8161 (mtt180) REVERT: L 231 SER cc_start: 0.6621 (m) cc_final: 0.6058 (t) REVERT: M 25 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.5977 (pttm) REVERT: M 88 ASP cc_start: 0.6930 (t70) cc_final: 0.6684 (t0) REVERT: O 31 THR cc_start: 0.5918 (m) cc_final: 0.5704 (p) REVERT: Q 60 ARG cc_start: 0.4776 (OUTLIER) cc_final: 0.1659 (ttt180) REVERT: Q 117 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8499 (t) REVERT: R 48 SER cc_start: 0.8569 (p) cc_final: 0.8139 (t) REVERT: R 115 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8297 (tt) REVERT: T 1 MET cc_start: 0.5145 (mtm) cc_final: 0.4877 (mtm) REVERT: T 83 ILE cc_start: 0.8541 (mm) cc_final: 0.8291 (mt) REVERT: U 53 ILE cc_start: 0.4953 (tp) cc_final: 0.4682 (tt) REVERT: V 17 ASP cc_start: 0.6212 (t0) cc_final: 0.5429 (t0) REVERT: V 21 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: W 66 TYR cc_start: 0.7238 (m-10) cc_final: 0.6651 (m-10) REVERT: W 79 ASP cc_start: 0.2928 (OUTLIER) cc_final: 0.2713 (t70) REVERT: W 144 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: X 78 ASP cc_start: 0.8103 (p0) cc_final: 0.7867 (p0) REVERT: X 131 ASP cc_start: 0.6951 (p0) cc_final: 0.6437 (p0) REVERT: Z 36 THR cc_start: 0.8717 (m) cc_final: 0.8475 (m) REVERT: Z 53 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: Z 92 ARG cc_start: 0.7617 (mtm110) cc_final: 0.6698 (tpt170) REVERT: Z 100 CYS cc_start: 0.8230 (m) cc_final: 0.7663 (p) REVERT: Z 174 LYS cc_start: 0.4957 (mmtt) cc_final: 0.4732 (mmtm) REVERT: b 142 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8306 (tp) REVERT: d 85 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5379 (m-30) REVERT: e 9 ASN cc_start: 0.8357 (t0) cc_final: 0.8095 (t0) REVERT: e 20 ARG cc_start: 0.6722 (ptp-170) cc_final: 0.6466 (ptp-170) REVERT: e 26 LEU cc_start: 0.8690 (tp) cc_final: 0.8452 (tt) REVERT: e 121 THR cc_start: 0.7369 (OUTLIER) cc_final: 0.6842 (t) REVERT: e 130 TYR cc_start: 0.7076 (m-80) cc_final: 0.6730 (m-80) REVERT: P 64 MET cc_start: 0.7869 (pmm) cc_final: 0.7668 (pmm) REVERT: P 150 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5911 (pp) REVERT: k 139 TYR cc_start: 0.4948 (m-10) cc_final: 0.4748 (m-10) REVERT: l 44 LYS cc_start: 0.2686 (ttpt) cc_final: 0.2379 (ttpt) REVERT: o 85 PRO cc_start: 0.5303 (Cg_endo) cc_final: 0.4921 (Cg_exo) REVERT: h 108 PHE cc_start: 0.3890 (OUTLIER) cc_final: 0.3206 (m-10) REVERT: h 187 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.4564 (t80) REVERT: h 198 ARG cc_start: 0.6430 (ptt180) cc_final: 0.6098 (ptp90) outliers start: 315 outliers final: 233 residues processed: 921 average time/residue: 0.7465 time to fit residues: 1186.3976 Evaluate side-chains 902 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 650 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain p residue 69 PHE Chi-restraints excluded: chain p residue 177 LEU Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 289 MET Chi-restraints excluded: chain p residue 306 ASP Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 83 GLN Chi-restraints excluded: chain r residue 115 TYR Chi-restraints excluded: chain t residue 23 THR Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 122 TYR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain t residue 134 ILE Chi-restraints excluded: chain u residue 37 VAL Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 98 HIS Chi-restraints excluded: chain u residue 101 SER Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain u residue 125 ARG Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 100 TYR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 191 GLU Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 128 GLU Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 27 LYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 65 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 78 CYS Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain V residue 21 TYR Chi-restraints excluded: chain V residue 34 PHE Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 79 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 144 PHE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 185 GLU Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 91 HIS Chi-restraints excluded: chain X residue 94 LYS Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 155 LEU Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 53 PHE Chi-restraints excluded: chain Z residue 64 ASN Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 24 ASP Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 60 THR Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 142 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 153 HIS Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 26 CYS Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 152 ASP Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain f residue 204 LEU Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 108 PHE Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 4 MET Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain i residue 133 LEU Chi-restraints excluded: chain j residue 100 TYR Chi-restraints excluded: chain j residue 106 ASN Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 154 ASP Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 92 ASP Chi-restraints excluded: chain k residue 142 GLU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 150 ILE Chi-restraints excluded: chain k residue 157 ASP Chi-restraints excluded: chain k residue 169 THR Chi-restraints excluded: chain k residue 171 VAL Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 76 ASN Chi-restraints excluded: chain n residue 88 PHE Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 98 VAL Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 174 LYS Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 220 optimal weight: 8.9990 chunk 591 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 656 optimal weight: 30.0000 chunk 545 optimal weight: 10.0000 chunk 304 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 83 GLN t 105 ASN L 198 HIS L 245 ASN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN ** b 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 HIS ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 241 GLN m 73 GLN m 124 HIS c 56 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 88000 Z= 0.252 Angle : 0.749 25.179 128568 Z= 0.384 Chirality : 0.044 2.005 16029 Planarity : 0.005 0.054 8845 Dihedral : 23.951 179.968 36781 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.32 % Favored : 91.25 % Rotamer: Outliers : 7.11 % Allowed : 21.43 % Favored : 71.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 0.55 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.11), residues: 4833 helix: -0.89 (0.13), residues: 1436 sheet: -1.16 (0.18), residues: 783 loop : -2.34 (0.11), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP u 83 HIS 0.015 0.001 HIS m 124 PHE 0.039 0.002 PHE n 17 TYR 0.035 0.002 TYR u 43 ARG 0.008 0.001 ARG m 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 712 time to evaluate : 4.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 63 LEU cc_start: 0.3778 (OUTLIER) cc_final: 0.3429 (mp) REVERT: r 11 GLN cc_start: 0.6585 (mt0) cc_final: 0.5967 (mp10) REVERT: r 115 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: t 73 ASP cc_start: 0.5176 (m-30) cc_final: 0.4792 (m-30) REVERT: u 71 VAL cc_start: 0.6041 (t) cc_final: 0.5583 (p) REVERT: u 125 ARG cc_start: 0.1847 (OUTLIER) cc_final: 0.0714 (tmm-80) REVERT: L 84 MET cc_start: 0.7838 (tpp) cc_final: 0.7291 (tpp) REVERT: L 100 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: L 143 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7853 (mtt180) REVERT: L 231 SER cc_start: 0.6715 (m) cc_final: 0.6183 (t) REVERT: M 88 ASP cc_start: 0.6824 (t70) cc_final: 0.6607 (t0) REVERT: Q 60 ARG cc_start: 0.4741 (OUTLIER) cc_final: 0.1798 (ttt180) REVERT: Q 117 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8468 (t) REVERT: R 40 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8130 (mp) REVERT: R 112 LYS cc_start: 0.6628 (mttt) cc_final: 0.6286 (mttm) REVERT: S 25 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6639 (tt) REVERT: U 53 ILE cc_start: 0.4830 (tp) cc_final: 0.4581 (tt) REVERT: V 17 ASP cc_start: 0.6127 (t0) cc_final: 0.5438 (t0) REVERT: V 21 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: W 66 TYR cc_start: 0.7162 (m-10) cc_final: 0.6888 (m-10) REVERT: W 79 ASP cc_start: 0.2937 (OUTLIER) cc_final: 0.2393 (t70) REVERT: W 234 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7355 (m-70) REVERT: X 19 HIS cc_start: 0.6539 (OUTLIER) cc_final: 0.5833 (m-70) REVERT: X 78 ASP cc_start: 0.8043 (p0) cc_final: 0.7818 (p0) REVERT: X 131 ASP cc_start: 0.6928 (p0) cc_final: 0.6257 (p0) REVERT: Z 36 THR cc_start: 0.8635 (m) cc_final: 0.8380 (m) REVERT: Z 53 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5442 (m-80) REVERT: Z 92 ARG cc_start: 0.7124 (mtm110) cc_final: 0.6347 (tpt170) REVERT: Z 100 CYS cc_start: 0.8310 (m) cc_final: 0.7616 (p) REVERT: Z 174 LYS cc_start: 0.5107 (mmtt) cc_final: 0.4809 (mmtm) REVERT: b 142 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (tp) REVERT: f 203 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: d 85 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.5868 (m-30) REVERT: d 163 MET cc_start: 0.8369 (ptm) cc_final: 0.8000 (ptm) REVERT: d 253 PHE cc_start: 0.6199 (t80) cc_final: 0.5722 (t80) REVERT: e 9 ASN cc_start: 0.8385 (t0) cc_final: 0.8127 (t0) REVERT: e 20 ARG cc_start: 0.6682 (ptp-170) cc_final: 0.6305 (mtt90) REVERT: e 26 LEU cc_start: 0.8971 (tp) cc_final: 0.8738 (tt) REVERT: e 36 LYS cc_start: 0.7425 (mmmt) cc_final: 0.7159 (tppt) REVERT: P 100 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8597 (pp) REVERT: k 169 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7611 (p) REVERT: m 196 GLU cc_start: 0.5475 (OUTLIER) cc_final: 0.4557 (tt0) REVERT: n 89 LEU cc_start: 0.3339 (OUTLIER) cc_final: 0.2945 (pp) REVERT: o 85 PRO cc_start: 0.5128 (Cg_endo) cc_final: 0.4795 (Cg_exo) REVERT: c 56 HIS cc_start: 0.3935 (m170) cc_final: 0.3722 (m170) REVERT: h 187 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.4490 (t80) REVERT: h 198 ARG cc_start: 0.6316 (ptt180) cc_final: 0.5811 (ptp90) outliers start: 298 outliers final: 213 residues processed: 926 average time/residue: 0.8006 time to fit residues: 1287.6286 Evaluate side-chains 887 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 652 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain p residue 69 PHE Chi-restraints excluded: chain p residue 177 LEU Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 204 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 269 ASP Chi-restraints excluded: chain p residue 289 MET Chi-restraints excluded: chain p residue 291 ILE Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain q residue 27 ASN Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 115 TYR Chi-restraints excluded: chain t residue 18 THR Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 105 ASN Chi-restraints excluded: chain t residue 122 TYR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain t residue 134 ILE Chi-restraints excluded: chain u residue 37 VAL Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 43 TYR Chi-restraints excluded: chain u residue 46 CYS Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 98 HIS Chi-restraints excluded: chain u residue 101 SER Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain u residue 125 ARG Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 100 TYR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 191 GLU Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain O residue 10 ASN Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 27 LYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 65 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain V residue 21 TYR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 106 GLN Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 79 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 185 GLU Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain W residue 234 HIS Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain X residue 94 LYS Chi-restraints excluded: chain X residue 99 ILE Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Z residue 53 PHE Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 163 TRP Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 49 SER Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 142 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 153 HIS Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 26 CYS Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 152 ASP Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain f residue 203 ASP Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 108 PHE Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain j residue 100 TYR Chi-restraints excluded: chain j residue 106 ASN Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 113 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 142 GLU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 150 ILE Chi-restraints excluded: chain k residue 169 THR Chi-restraints excluded: chain k residue 171 VAL Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 76 PHE Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 156 MET Chi-restraints excluded: chain m residue 196 GLU Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 98 VAL Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 152 PHE Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 633 optimal weight: 40.0000 chunk 74 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 chunk 479 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 553 optimal weight: 30.0000 chunk 366 optimal weight: 20.0000 chunk 654 optimal weight: 30.0000 chunk 409 optimal weight: 40.0000 chunk 398 optimal weight: 10.0000 chunk 302 optimal weight: 5.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 80 GLN r 83 GLN ** r 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 245 ASN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Z 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 42 ASN m 124 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 88000 Z= 0.285 Angle : 0.782 26.369 128568 Z= 0.399 Chirality : 0.045 1.970 16029 Planarity : 0.006 0.053 8845 Dihedral : 23.974 179.937 36781 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.87 % Favored : 89.76 % Rotamer: Outliers : 7.54 % Allowed : 21.91 % Favored : 70.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 0.55 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 4833 helix: -0.96 (0.13), residues: 1445 sheet: -1.10 (0.18), residues: 777 loop : -2.39 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP u 83 HIS 0.014 0.002 HIS m 124 PHE 0.039 0.002 PHE n 17 TYR 0.040 0.003 TYR u 43 ARG 0.010 0.001 ARG m 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 705 time to evaluate : 4.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 63 LEU cc_start: 0.3839 (OUTLIER) cc_final: 0.3430 (mp) REVERT: p 252 MET cc_start: 0.6055 (tmm) cc_final: 0.5764 (tmm) REVERT: r 11 GLN cc_start: 0.6667 (mt0) cc_final: 0.6098 (mp10) REVERT: r 64 ARG cc_start: 0.4659 (OUTLIER) cc_final: 0.2749 (mpt180) REVERT: r 115 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: t 73 ASP cc_start: 0.5299 (m-30) cc_final: 0.4671 (m-30) REVERT: u 71 VAL cc_start: 0.6189 (t) cc_final: 0.5822 (p) REVERT: L 84 MET cc_start: 0.7966 (tpp) cc_final: 0.7300 (tpp) REVERT: L 100 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: L 143 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7910 (mtt180) REVERT: L 231 SER cc_start: 0.6744 (m) cc_final: 0.6176 (t) REVERT: M 25 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.6064 (pttm) REVERT: M 88 ASP cc_start: 0.6932 (t70) cc_final: 0.6618 (t0) REVERT: O 42 TRP cc_start: 0.6181 (OUTLIER) cc_final: 0.5894 (t60) REVERT: Q 60 ARG cc_start: 0.4739 (OUTLIER) cc_final: 0.1927 (ttt180) REVERT: Q 117 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8485 (t) REVERT: R 40 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8165 (mp) REVERT: S 25 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6906 (tt) REVERT: T 1 MET cc_start: 0.4884 (mtm) cc_final: 0.4425 (mtm) REVERT: T 41 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.4072 (t80) REVERT: U 53 ILE cc_start: 0.4830 (tp) cc_final: 0.4531 (tt) REVERT: V 17 ASP cc_start: 0.6362 (t0) cc_final: 0.5593 (t0) REVERT: V 21 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6530 (m-10) REVERT: W 66 TYR cc_start: 0.7207 (m-10) cc_final: 0.6935 (m-10) REVERT: W 79 ASP cc_start: 0.3448 (OUTLIER) cc_final: 0.2560 (t70) REVERT: W 234 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.7440 (m-70) REVERT: X 78 ASP cc_start: 0.8074 (p0) cc_final: 0.7834 (p0) REVERT: Y 25 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7604 (ptt90) REVERT: Z 36 THR cc_start: 0.8660 (m) cc_final: 0.8424 (m) REVERT: Z 53 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5541 (m-80) REVERT: Z 92 ARG cc_start: 0.7254 (mtm110) cc_final: 0.6358 (tpt170) REVERT: Z 100 CYS cc_start: 0.8312 (m) cc_final: 0.7642 (p) REVERT: Z 174 LYS cc_start: 0.5209 (mmtt) cc_final: 0.4939 (mmtm) REVERT: b 115 HIS cc_start: 0.6247 (OUTLIER) cc_final: 0.5249 (m90) REVERT: b 142 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8371 (tp) REVERT: d 85 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6340 (m-30) REVERT: d 163 MET cc_start: 0.8426 (ptm) cc_final: 0.8196 (ptm) REVERT: d 237 TRP cc_start: 0.6846 (p90) cc_final: 0.6217 (p90) REVERT: d 253 PHE cc_start: 0.6014 (t80) cc_final: 0.5753 (t80) REVERT: e 9 ASN cc_start: 0.8278 (t0) cc_final: 0.8032 (t0) REVERT: e 26 LEU cc_start: 0.9057 (tp) cc_final: 0.8761 (tt) REVERT: e 36 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7306 (tppt) REVERT: e 60 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7557 (mmtt) REVERT: g 82 ILE cc_start: 0.5721 (mm) cc_final: 0.5427 (mt) REVERT: P 92 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8422 (tm-30) REVERT: P 100 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8687 (pp) REVERT: l 44 LYS cc_start: 0.2179 (ttpt) cc_final: 0.1828 (ttpt) REVERT: m 163 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7230 (p-80) REVERT: m 196 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.4692 (tt0) REVERT: n 89 LEU cc_start: 0.3244 (OUTLIER) cc_final: 0.2747 (pp) REVERT: o 85 PRO cc_start: 0.5425 (Cg_endo) cc_final: 0.5219 (Cg_exo) REVERT: c 56 HIS cc_start: 0.4380 (m170) cc_final: 0.4154 (m170) REVERT: h 187 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.4627 (t80) REVERT: h 198 ARG cc_start: 0.6400 (ptt180) cc_final: 0.5810 (ptp90) outliers start: 316 outliers final: 241 residues processed: 926 average time/residue: 0.7669 time to fit residues: 1218.5595 Evaluate side-chains 922 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 656 time to evaluate : 4.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain p residue 69 PHE Chi-restraints excluded: chain p residue 130 ASP Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 204 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 269 ASP Chi-restraints excluded: chain p residue 291 ILE Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain q residue 27 ASN Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 64 ARG Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 83 GLN Chi-restraints excluded: chain r residue 115 TYR Chi-restraints excluded: chain t residue 18 THR Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 122 TYR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 46 CYS Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 98 HIS Chi-restraints excluded: chain u residue 101 SER Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 100 TYR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 191 GLU Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain O residue 10 ASN Chi-restraints excluded: chain O residue 21 GLU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 42 TRP Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 27 LYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 41 PHE Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 21 TYR Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 79 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 185 GLU Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain W residue 234 HIS Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain X residue 91 HIS Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 155 LEU Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 53 PHE Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 24 ASP Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 60 THR Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 142 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 153 HIS Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 26 CYS Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain f residue 203 ASP Chi-restraints excluded: chain f residue 204 LEU Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 108 PHE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 87 GLU Chi-restraints excluded: chain e residue 102 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain j residue 100 TYR Chi-restraints excluded: chain j residue 106 ASN Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 113 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 154 ASP Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 142 GLU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 150 ILE Chi-restraints excluded: chain k residue 157 ASP Chi-restraints excluded: chain k residue 169 THR Chi-restraints excluded: chain k residue 171 VAL Chi-restraints excluded: chain l residue 42 ASN Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 156 MET Chi-restraints excluded: chain m residue 163 HIS Chi-restraints excluded: chain m residue 196 GLU Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 76 ASN Chi-restraints excluded: chain n residue 88 PHE Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 71 TYR Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 98 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 404 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 390 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 416 optimal weight: 7.9990 chunk 445 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 514 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 102 GLN ** r 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 105 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 245 ASN M 7 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 ASN ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 88000 Z= 0.254 Angle : 0.748 26.930 128568 Z= 0.382 Chirality : 0.044 1.932 16029 Planarity : 0.005 0.070 8845 Dihedral : 23.963 179.733 36781 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.25 % Favored : 90.40 % Rotamer: Outliers : 7.21 % Allowed : 22.72 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 0.55 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.11), residues: 4833 helix: -0.79 (0.13), residues: 1435 sheet: -1.00 (0.19), residues: 780 loop : -2.37 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP o 69 HIS 0.015 0.002 HIS m 124 PHE 0.043 0.002 PHE n 17 TYR 0.043 0.002 TYR o 71 ARG 0.012 0.001 ARG O 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 684 time to evaluate : 5.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 63 LEU cc_start: 0.3901 (OUTLIER) cc_final: 0.3514 (mp) REVERT: r 11 GLN cc_start: 0.6607 (mt0) cc_final: 0.6101 (mp10) REVERT: r 64 ARG cc_start: 0.4618 (OUTLIER) cc_final: 0.2724 (mpt180) REVERT: r 70 ARG cc_start: 0.4608 (tpp-160) cc_final: 0.4055 (tpt170) REVERT: r 149 ARG cc_start: 0.4427 (mmt180) cc_final: 0.3200 (mtm110) REVERT: t 73 ASP cc_start: 0.5202 (m-30) cc_final: 0.4616 (m-30) REVERT: u 71 VAL cc_start: 0.6832 (t) cc_final: 0.6579 (p) REVERT: L 84 MET cc_start: 0.8081 (tpp) cc_final: 0.7310 (tpp) REVERT: L 100 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: L 231 SER cc_start: 0.6494 (m) cc_final: 0.5951 (t) REVERT: M 25 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6134 (pttm) REVERT: M 88 ASP cc_start: 0.6775 (t70) cc_final: 0.6554 (t0) REVERT: O 42 TRP cc_start: 0.6161 (OUTLIER) cc_final: 0.5873 (t60) REVERT: O 189 ASN cc_start: 0.6376 (OUTLIER) cc_final: 0.5915 (t0) REVERT: Q 7 LEU cc_start: 0.5528 (mt) cc_final: 0.5077 (mt) REVERT: Q 60 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.2268 (ttt180) REVERT: Q 117 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8511 (t) REVERT: R 40 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8201 (mp) REVERT: R 112 LYS cc_start: 0.6664 (mttt) cc_final: 0.6240 (mttm) REVERT: R 115 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8305 (tt) REVERT: T 1 MET cc_start: 0.4903 (mtm) cc_final: 0.4442 (mtm) REVERT: T 41 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.4000 (t80) REVERT: U 103 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6838 (mt-10) REVERT: V 17 ASP cc_start: 0.6523 (t0) cc_final: 0.5779 (t0) REVERT: V 21 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6570 (m-10) REVERT: W 66 TYR cc_start: 0.7149 (m-10) cc_final: 0.6922 (m-10) REVERT: W 79 ASP cc_start: 0.3462 (OUTLIER) cc_final: 0.2559 (t70) REVERT: W 144 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: W 234 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.7381 (m-70) REVERT: X 19 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.6177 (m-70) REVERT: X 78 ASP cc_start: 0.8074 (p0) cc_final: 0.7851 (p0) REVERT: Y 25 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7641 (ptp90) REVERT: Z 36 THR cc_start: 0.8635 (m) cc_final: 0.8399 (m) REVERT: Z 53 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5495 (m-80) REVERT: Z 92 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6449 (tpt170) REVERT: Z 100 CYS cc_start: 0.8338 (m) cc_final: 0.7597 (p) REVERT: Z 174 LYS cc_start: 0.5163 (mmtt) cc_final: 0.4887 (mmtm) REVERT: b 115 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.5325 (m90) REVERT: b 142 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8412 (tp) REVERT: f 209 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: d 163 MET cc_start: 0.8420 (ptm) cc_final: 0.8200 (ptm) REVERT: d 237 TRP cc_start: 0.6800 (p90) cc_final: 0.6232 (p90) REVERT: d 253 PHE cc_start: 0.6056 (t80) cc_final: 0.5781 (t80) REVERT: e 9 ASN cc_start: 0.8359 (t0) cc_final: 0.8081 (t0) REVERT: e 26 LEU cc_start: 0.8988 (tp) cc_final: 0.8683 (tt) REVERT: e 121 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.6907 (t) REVERT: e 130 TYR cc_start: 0.7165 (m-80) cc_final: 0.6422 (m-80) REVERT: g 82 ILE cc_start: 0.5760 (mm) cc_final: 0.5464 (mt) REVERT: P 47 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.4785 (ttp-110) REVERT: P 92 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8392 (tm-30) REVERT: P 100 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8593 (pp) REVERT: k 116 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.4183 (mt) REVERT: k 134 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.4902 (tm-30) REVERT: l 44 LYS cc_start: 0.3695 (ttpt) cc_final: 0.3175 (ttpt) REVERT: l 96 LYS cc_start: 0.6711 (mtmt) cc_final: 0.6415 (mtmm) REVERT: m 126 MET cc_start: 0.5165 (mmm) cc_final: 0.4947 (mmm) REVERT: m 163 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7189 (p-80) REVERT: m 196 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.4756 (tt0) REVERT: n 89 LEU cc_start: 0.3220 (OUTLIER) cc_final: 0.2831 (pp) REVERT: o 85 PRO cc_start: 0.5480 (Cg_endo) cc_final: 0.5075 (Cg_exo) REVERT: c 56 HIS cc_start: 0.4268 (m170) cc_final: 0.4055 (m170) REVERT: h 187 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.4641 (t80) REVERT: h 198 ARG cc_start: 0.6403 (ptt180) cc_final: 0.5920 (ptp90) outliers start: 302 outliers final: 243 residues processed: 896 average time/residue: 0.8085 time to fit residues: 1258.3048 Evaluate side-chains 931 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 658 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain p residue 69 PHE Chi-restraints excluded: chain p residue 120 ASP Chi-restraints excluded: chain p residue 130 ASP Chi-restraints excluded: chain p residue 177 LEU Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 204 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 269 ASP Chi-restraints excluded: chain p residue 291 ILE Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain q residue 27 ASN Chi-restraints excluded: chain q residue 31 VAL Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 45 ARG Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 64 ARG Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain t residue 18 THR Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 105 ASN Chi-restraints excluded: chain t residue 122 TYR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 98 HIS Chi-restraints excluded: chain u residue 101 SER Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 100 TYR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 110 LYS Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 191 GLU Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain O residue 10 ASN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 42 TRP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 27 LYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 41 PHE Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain V residue 21 TYR Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 79 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 144 PHE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 185 GLU Chi-restraints excluded: chain W residue 207 VAL Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain W residue 234 HIS Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain X residue 91 HIS Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 155 LEU Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Z residue 53 PHE Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 64 ASN Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 163 TRP Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 60 THR Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 142 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 153 HIS Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 26 CYS Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 96 LEU Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 152 ASP Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain f residue 203 ASP Chi-restraints excluded: chain f residue 209 ASP Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 108 PHE Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 127 GLU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 225 LEU Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain e residue 87 GLU Chi-restraints excluded: chain e residue 102 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain j residue 100 TYR Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 47 ARG Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 113 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 142 GLU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 150 ILE Chi-restraints excluded: chain k residue 169 THR Chi-restraints excluded: chain k residue 171 VAL Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 156 MET Chi-restraints excluded: chain m residue 163 HIS Chi-restraints excluded: chain m residue 196 GLU Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 88 PHE Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 71 TYR Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 98 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 134 VAL Chi-restraints excluded: chain h residue 152 PHE Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 595 optimal weight: 20.0000 chunk 626 optimal weight: 30.0000 chunk 572 optimal weight: 30.0000 chunk 609 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 478 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 551 optimal weight: 30.0000 chunk 576 optimal weight: 50.0000 chunk 607 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 102 GLN ** r 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 245 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 GLN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 GLN ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 241 GLN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 88000 Z= 0.362 Angle : 0.857 27.374 128568 Z= 0.433 Chirality : 0.048 1.907 16029 Planarity : 0.006 0.063 8845 Dihedral : 24.129 178.498 36781 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.28 % Favored : 88.37 % Rotamer: Outliers : 7.49 % Allowed : 23.05 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 0.55 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.11), residues: 4833 helix: -1.05 (0.13), residues: 1439 sheet: -1.07 (0.19), residues: 772 loop : -2.51 (0.11), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP o 69 HIS 0.016 0.002 HIS m 124 PHE 0.041 0.003 PHE n 17 TYR 0.047 0.003 TYR t 104 ARG 0.015 0.001 ARG t 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 664 time to evaluate : 4.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 63 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.4157 (mp) REVERT: p 189 LEU cc_start: 0.4948 (tp) cc_final: 0.4722 (tt) REVERT: r 64 ARG cc_start: 0.4815 (OUTLIER) cc_final: 0.2886 (mpt180) REVERT: r 149 ARG cc_start: 0.5036 (mmt180) cc_final: 0.4671 (mmt-90) REVERT: u 71 VAL cc_start: 0.6890 (t) cc_final: 0.6463 (p) REVERT: L 16 MET cc_start: 0.6337 (ttm) cc_final: 0.5733 (ttm) REVERT: L 84 MET cc_start: 0.8148 (tpp) cc_final: 0.7441 (tpp) REVERT: L 100 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: L 231 SER cc_start: 0.6680 (m) cc_final: 0.6127 (t) REVERT: L 246 VAL cc_start: 0.7280 (m) cc_final: 0.6847 (t) REVERT: M 25 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5809 (pttm) REVERT: M 88 ASP cc_start: 0.6965 (t70) cc_final: 0.6655 (t0) REVERT: O 42 TRP cc_start: 0.6509 (OUTLIER) cc_final: 0.6174 (t60) REVERT: Q 60 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.1921 (ttt180) REVERT: Q 117 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8539 (t) REVERT: R 40 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8306 (mp) REVERT: R 115 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8420 (tt) REVERT: T 41 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.4520 (t80) REVERT: V 21 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: W 24 MET cc_start: 0.6019 (ptm) cc_final: 0.5308 (tmm) REVERT: W 66 TYR cc_start: 0.7319 (m-10) cc_final: 0.7058 (m-10) REVERT: W 144 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: W 228 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6418 (pp30) REVERT: W 234 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7565 (m-70) REVERT: X 78 ASP cc_start: 0.8166 (p0) cc_final: 0.7926 (p0) REVERT: Z 36 THR cc_start: 0.8690 (m) cc_final: 0.8472 (m) REVERT: Z 53 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5631 (m-80) REVERT: Z 92 ARG cc_start: 0.7395 (mtm110) cc_final: 0.6539 (tpt170) REVERT: Z 100 CYS cc_start: 0.8341 (m) cc_final: 0.7614 (p) REVERT: Z 174 LYS cc_start: 0.5506 (mmtt) cc_final: 0.5133 (mmtm) REVERT: b 98 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7621 (mt) REVERT: b 142 ILE cc_start: 0.8672 (tp) cc_final: 0.8376 (tp) REVERT: f 40 TYR cc_start: 0.7177 (m-80) cc_final: 0.6900 (m-80) REVERT: d 163 MET cc_start: 0.8508 (ptm) cc_final: 0.8275 (ptm) REVERT: d 237 TRP cc_start: 0.6893 (p90) cc_final: 0.6310 (p90) REVERT: d 253 PHE cc_start: 0.5637 (t80) cc_final: 0.5409 (t80) REVERT: e 9 ASN cc_start: 0.8292 (t0) cc_final: 0.8008 (t0) REVERT: e 121 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7171 (t) REVERT: g 82 ILE cc_start: 0.5981 (mm) cc_final: 0.5742 (mt) REVERT: P 47 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.4999 (ttp-110) REVERT: P 100 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8491 (pp) REVERT: k 116 LEU cc_start: 0.4434 (OUTLIER) cc_final: 0.4165 (mt) REVERT: k 134 GLU cc_start: 0.5671 (OUTLIER) cc_final: 0.5366 (tm-30) REVERT: l 96 LYS cc_start: 0.6839 (mtmt) cc_final: 0.6568 (mtmm) REVERT: m 163 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7148 (p-80) REVERT: m 196 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.4817 (tt0) REVERT: n 89 LEU cc_start: 0.3411 (OUTLIER) cc_final: 0.3037 (pp) REVERT: h 187 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.4753 (t80) outliers start: 314 outliers final: 261 residues processed: 884 average time/residue: 0.7613 time to fit residues: 1160.5690 Evaluate side-chains 925 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 639 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 15 TRP Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain p residue 69 PHE Chi-restraints excluded: chain p residue 120 ASP Chi-restraints excluded: chain p residue 130 ASP Chi-restraints excluded: chain p residue 177 LEU Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 269 ASP Chi-restraints excluded: chain p residue 291 ILE Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain q residue 27 ASN Chi-restraints excluded: chain q residue 31 VAL Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 45 ARG Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 64 ARG Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain t residue 18 THR Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 122 TYR Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 84 PHE Chi-restraints excluded: chain u residue 98 HIS Chi-restraints excluded: chain u residue 101 SER Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 100 TYR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 191 GLU Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 127 ASN Chi-restraints excluded: chain O residue 10 ASN Chi-restraints excluded: chain O residue 21 GLU Chi-restraints excluded: chain O residue 42 TRP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 27 LYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 41 PHE Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain V residue 21 TYR Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 144 PHE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 185 GLU Chi-restraints excluded: chain W residue 207 VAL Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain W residue 228 GLN Chi-restraints excluded: chain W residue 234 HIS Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain X residue 91 HIS Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 155 LEU Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 53 PHE Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 64 ASN Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 163 TRP Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 24 ASP Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 60 THR Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 153 HIS Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 26 CYS Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 96 LEU Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 152 ASP Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain f residue 203 ASP Chi-restraints excluded: chain f residue 204 LEU Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 108 PHE Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 4 MET Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain e residue 87 GLU Chi-restraints excluded: chain e residue 102 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain j residue 100 TYR Chi-restraints excluded: chain j residue 106 ASN Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 47 ARG Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 113 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 142 GLU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 150 ILE Chi-restraints excluded: chain k residue 169 THR Chi-restraints excluded: chain k residue 171 VAL Chi-restraints excluded: chain l residue 33 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 144 GLN Chi-restraints excluded: chain m residue 156 MET Chi-restraints excluded: chain m residue 163 HIS Chi-restraints excluded: chain m residue 196 GLU Chi-restraints excluded: chain n residue 17 PHE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 88 PHE Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 71 TYR Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 98 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 134 VAL Chi-restraints excluded: chain h residue 152 PHE Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 400 optimal weight: 50.0000 chunk 644 optimal weight: 30.0000 chunk 393 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 448 optimal weight: 30.0000 chunk 676 optimal weight: 10.0000 chunk 622 optimal weight: 30.0000 chunk 538 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 416 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 245 ASN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 ASN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 GLN ** Z 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.7440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 88000 Z= 0.255 Angle : 0.762 27.251 128568 Z= 0.388 Chirality : 0.044 1.924 16029 Planarity : 0.005 0.125 8845 Dihedral : 24.069 179.377 36781 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.10 % Favored : 90.50 % Rotamer: Outliers : 6.56 % Allowed : 24.32 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 0.55 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.11), residues: 4833 helix: -0.86 (0.13), residues: 1441 sheet: -1.09 (0.19), residues: 777 loop : -2.43 (0.11), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP o 69 HIS 0.016 0.001 HIS m 124 PHE 0.046 0.002 PHE n 17 TYR 0.050 0.002 TYR u 43 ARG 0.018 0.001 ARG L 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 669 time to evaluate : 4.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 189 LEU cc_start: 0.5197 (tp) cc_final: 0.4915 (tt) REVERT: r 64 ARG cc_start: 0.4601 (OUTLIER) cc_final: 0.2808 (mpt180) REVERT: r 124 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6210 (pt) REVERT: r 149 ARG cc_start: 0.5043 (mmt180) cc_final: 0.4773 (mmt-90) REVERT: u 71 VAL cc_start: 0.6965 (t) cc_final: 0.6481 (p) REVERT: L 16 MET cc_start: 0.6925 (ttm) cc_final: 0.6306 (ttm) REVERT: L 84 MET cc_start: 0.8096 (tpp) cc_final: 0.7874 (tpt) REVERT: L 100 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: L 231 SER cc_start: 0.6460 (m) cc_final: 0.5923 (t) REVERT: M 25 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6064 (pttm) REVERT: M 88 ASP cc_start: 0.6915 (t70) cc_final: 0.6551 (t0) REVERT: O 42 TRP cc_start: 0.6278 (OUTLIER) cc_final: 0.5948 (t60) REVERT: Q 60 ARG cc_start: 0.5029 (OUTLIER) cc_final: 0.4060 (ttp-170) REVERT: Q 117 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8562 (t) REVERT: R 40 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8271 (mp) REVERT: R 93 LYS cc_start: 0.6634 (tptm) cc_final: 0.6386 (tptm) REVERT: R 115 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8307 (tt) REVERT: T 41 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.4287 (t80) REVERT: V 21 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6483 (m-10) REVERT: W 24 MET cc_start: 0.5838 (ptm) cc_final: 0.5425 (tmm) REVERT: W 66 TYR cc_start: 0.7134 (m-10) cc_final: 0.6913 (m-10) REVERT: W 144 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: W 234 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.7551 (m-70) REVERT: X 78 ASP cc_start: 0.8169 (p0) cc_final: 0.7942 (p0) REVERT: Y 25 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7513 (ptt90) REVERT: Z 53 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: Z 92 ARG cc_start: 0.7449 (mtm110) cc_final: 0.6698 (tpt170) REVERT: Z 100 CYS cc_start: 0.8326 (m) cc_final: 0.7532 (p) REVERT: b 142 ILE cc_start: 0.8594 (tp) cc_final: 0.8300 (tp) REVERT: f 13 MET cc_start: 0.6938 (mmt) cc_final: 0.6701 (mmt) REVERT: f 40 TYR cc_start: 0.7232 (m-80) cc_final: 0.6947 (m-80) REVERT: d 237 TRP cc_start: 0.6828 (p90) cc_final: 0.6344 (p90) REVERT: e 9 ASN cc_start: 0.8249 (t0) cc_final: 0.7933 (t0) REVERT: e 55 ASP cc_start: 0.6286 (p0) cc_final: 0.5610 (m-30) REVERT: e 121 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7210 (t) REVERT: e 130 TYR cc_start: 0.7028 (m-80) cc_final: 0.6271 (m-80) REVERT: g 82 ILE cc_start: 0.6004 (mm) cc_final: 0.5740 (mt) REVERT: P 47 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.4822 (ttp-110) REVERT: P 100 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8364 (pp) REVERT: k 101 LEU cc_start: 0.6011 (mm) cc_final: 0.5775 (mm) REVERT: k 116 LEU cc_start: 0.4499 (OUTLIER) cc_final: 0.4265 (mt) REVERT: k 134 GLU cc_start: 0.5605 (OUTLIER) cc_final: 0.4882 (tm-30) REVERT: l 96 LYS cc_start: 0.6710 (mtmt) cc_final: 0.6475 (mtmm) REVERT: m 163 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6983 (p-80) REVERT: m 196 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4556 (tt0) REVERT: n 89 LEU cc_start: 0.3811 (OUTLIER) cc_final: 0.3563 (pp) REVERT: h 187 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.4712 (t80) REVERT: h 203 LYS cc_start: 0.6259 (mttt) cc_final: 0.5676 (mptt) outliers start: 275 outliers final: 235 residues processed: 862 average time/residue: 0.7571 time to fit residues: 1121.9917 Evaluate side-chains 895 residues out of total 4190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 636 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 15 TRP Chi-restraints excluded: chain p residue 69 PHE Chi-restraints excluded: chain p residue 120 ASP Chi-restraints excluded: chain p residue 130 ASP Chi-restraints excluded: chain p residue 177 LEU Chi-restraints excluded: chain p residue 191 ASP Chi-restraints excluded: chain p residue 202 VAL Chi-restraints excluded: chain p residue 209 SER Chi-restraints excluded: chain p residue 211 CYS Chi-restraints excluded: chain p residue 269 ASP Chi-restraints excluded: chain p residue 291 ILE Chi-restraints excluded: chain q residue 21 HIS Chi-restraints excluded: chain q residue 27 ASN Chi-restraints excluded: chain q residue 31 VAL Chi-restraints excluded: chain q residue 45 ARG Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 64 ARG Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 124 ILE Chi-restraints excluded: chain t residue 18 THR Chi-restraints excluded: chain t residue 45 HIS Chi-restraints excluded: chain t residue 93 THR Chi-restraints excluded: chain t residue 96 MET Chi-restraints excluded: chain t residue 130 TYR Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 98 HIS Chi-restraints excluded: chain u residue 101 SER Chi-restraints excluded: chain u residue 105 ASP Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 100 TYR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 191 GLU Chi-restraints excluded: chain L residue 204 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 GLN Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 127 ASN Chi-restraints excluded: chain O residue 10 ASN Chi-restraints excluded: chain O residue 21 GLU Chi-restraints excluded: chain O residue 42 TRP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 27 LYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 41 PHE Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain V residue 21 TYR Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 53 MET Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 98 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 144 PHE Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 155 ASN Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 185 GLU Chi-restraints excluded: chain W residue 207 VAL Chi-restraints excluded: chain W residue 211 ASP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain W residue 234 HIS Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 47 ILE Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain X residue 91 HIS Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 155 LEU Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 53 PHE Chi-restraints excluded: chain Z residue 64 ASN Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 163 TRP Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 189 ILE Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 122 HIS Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 153 HIS Chi-restraints excluded: chain b residue 154 HIS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 96 LEU Chi-restraints excluded: chain f residue 145 ILE Chi-restraints excluded: chain f residue 152 ASP Chi-restraints excluded: chain f residue 201 LYS Chi-restraints excluded: chain f residue 203 ASP Chi-restraints excluded: chain f residue 204 LEU Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 108 PHE Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain d residue 169 CYS Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 235 ASP Chi-restraints excluded: chain e residue 4 MET Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain e residue 102 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 70 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain i residue 73 TYR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain j residue 100 TYR Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 47 ARG Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 113 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 155 ASP Chi-restraints excluded: chain P residue 232 HIS Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 142 GLU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 144 SER Chi-restraints excluded: chain k residue 150 ILE Chi-restraints excluded: chain k residue 171 VAL Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 59 LYS Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 156 MET Chi-restraints excluded: chain m residue 163 HIS Chi-restraints excluded: chain m residue 196 GLU Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 88 PHE Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain o residue 27 HIS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 71 TYR Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain h residue 96 VAL Chi-restraints excluded: chain h residue 98 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain h residue 134 VAL Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 152 PHE Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain h residue 167 LEU Chi-restraints excluded: chain h residue 181 TYR Chi-restraints excluded: chain h residue 187 TYR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain h residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 427 optimal weight: 4.9990 chunk 573 optimal weight: 30.0000 chunk 165 optimal weight: 9.9990 chunk 496 optimal weight: 30.0000 chunk 79 optimal weight: 0.0370 chunk 149 optimal weight: 20.0000 chunk 539 optimal weight: 20.0000 chunk 225 optimal weight: 0.1980 chunk 554 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 overall best weight: 2.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 ASN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 107 HIS ** Z 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN b 8 ASN ** b 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 GLN P 35 ASN ** P 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.108921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.095751 restraints weight = 335492.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.096362 restraints weight = 206685.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.096433 restraints weight = 156272.198| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 88000 Z= 0.173 Angle : 0.693 26.883 128568 Z= 0.354 Chirality : 0.041 1.943 16029 Planarity : 0.005 0.080 8845 Dihedral : 23.899 179.651 36781 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.30 % Favored : 91.35 % Rotamer: Outliers : 4.87 % Allowed : 26.44 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.38 % Twisted Proline : 0.55 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.11), residues: 4833 helix: -0.62 (0.13), residues: 1444 sheet: -0.90 (0.19), residues: 783 loop : -2.25 (0.11), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP n 73 HIS 0.016 0.001 HIS m 124 PHE 0.045 0.002 PHE n 17 TYR 0.041 0.002 TYR o 71 ARG 0.028 0.001 ARG O 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18826.19 seconds wall clock time: 332 minutes 25.14 seconds (19945.14 seconds total)