Starting phenix.real_space_refine on Mon Mar 18 16:13:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a63_15204/03_2024/8a63_15204_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a63_15204/03_2024/8a63_15204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a63_15204/03_2024/8a63_15204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a63_15204/03_2024/8a63_15204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a63_15204/03_2024/8a63_15204_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a63_15204/03_2024/8a63_15204_updated.pdb" } resolution = 3.1 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= 0.002 sd= 0.009 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 2 6.06 5 P 3022 5.49 5 Mg 164 5.21 5 S 67 5.16 5 C 43591 2.51 5 N 16411 2.21 5 O 25132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 80": "OD1" <-> "OD2" Residue "O GLU 105": "OE1" <-> "OE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 47": "OD1" <-> "OD2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "S TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 97": "OD1" <-> "OD2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 44": "OD1" <-> "OD2" Residue "V GLU 114": "OE1" <-> "OE2" Residue "W ASP 30": "OD1" <-> "OD2" Residue "W ASP 85": "OD1" <-> "OD2" Residue "Z GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 88390 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 457 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "2" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 487 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "3" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "4" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 477 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "5" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 425 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "6" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 400 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "7" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 357 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "8" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 512 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "9" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "A" Number of atoms: 62459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2908, 62459 Classifications: {'RNA': 2908} Modifications used: {'rna2p_pur': 306, 'rna2p_pyr': 140, 'rna3p_pur': 1396, 'rna3p_pyr': 1066} Link IDs: {'rna2p': 446, 'rna3p': 2461} Chain breaks: 2 Chain: "B" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2430 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 11, 'rna3p_pur': 54, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 99} Chain: "G" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2108 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1582 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "I" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1563 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "J" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1365 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "K" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1271 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 10, 'TRANS': 154} Chain: "M" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1117 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1094 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "P" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "Q" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 983 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "R" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "S" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 905 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "T" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "U" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "V" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "W" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 731 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "X" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 723 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "Z" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 563 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 183 Unusual residues: {' MG': 161, 'PUT': 2, 'SPD': 1} Classifications: {'undetermined': 164} Link IDs: {None: 163} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2093 SG CYS 5 30 84.725 207.818 128.326 1.00144.18 S ATOM 2113 SG CYS 5 33 83.621 207.711 124.439 1.00161.42 S ATOM 2196 SG CYS 5 43 87.021 207.482 124.977 1.00152.79 S ATOM 2218 SG CYS 5 46 83.985 209.702 124.559 1.00168.23 S ATOM 3633 SG CYS 9 11 136.063 120.228 179.134 1.00 62.84 S ATOM 3657 SG CYS 9 14 132.705 121.642 177.259 1.00 59.66 S ATOM 3761 SG CYS 9 27 135.134 123.784 179.322 1.00 53.28 S Time building chain proxies: 35.18, per 1000 atoms: 0.40 Number of scatterers: 88390 At special positions: 0 Unit cell: (191.06, 234.52, 223.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 1 19.00 S 67 16.00 P 3022 15.00 Mg 164 11.99 O 25132 8.00 N 16411 7.00 C 43591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 6 9 " - pdb=" SG CYS 6 12 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 12 " - pdb=" SG CYS 6 36 " 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: 41.08 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 33 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 30 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 43 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 46 " pdb=" ZN 9 101 " pdb="ZN ZN 9 101 " - pdb=" ND1 HIS 9 32 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 14 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 11 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 27 " Number of angles added : 9 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 45 sheets defined 25.2% alpha, 18.9% beta 979 base pairs and 1609 stacking pairs defined. Time for finding SS restraints: 48.01 Creating SS restraints... Processing helix chain '1' and resid 51 through 54 No H-bonds generated for 'chain '1' and resid 51 through 54' Processing helix chain '2' and resid 4 through 8 Processing helix chain '2' and resid 11 through 34 Processing helix chain '2' and resid 40 through 60 removed outlier: 3.720A pdb=" N VAL 2 57 " --> pdb=" O LYS 2 54 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 26 Processing helix chain '3' and resid 41 through 49 Processing helix chain '5' and resid 10 through 18 Processing helix chain '7' and resid 9 through 16 Processing helix chain '7' and resid 18 through 22 Processing helix chain '7' and resid 25 through 37 Processing helix chain '8' and resid 8 through 11 No H-bonds generated for 'chain '8' and resid 8 through 11' Processing helix chain '8' and resid 38 through 45 Processing helix chain '8' and resid 52 through 62 removed outlier: 5.678A pdb=" N GLN 8 60 " --> pdb=" O LYS 8 56 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET 8 61 " --> pdb=" O ARG 8 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL 8 62 " --> pdb=" O ILE 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 30 through 32 No H-bonds generated for 'chain '9' and resid 30 through 32' Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 198 through 202 removed outlier: 4.270A pdb=" N GLU G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 265 through 269 removed outlier: 3.856A pdb=" N LYS G 268 " --> pdb=" O ASN G 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 63 through 72 removed outlier: 3.628A pdb=" N LYS H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'I' and resid 21 through 24 No H-bonds generated for 'chain 'I' and resid 21 through 24' Processing helix chain 'I' and resid 30 through 44 Processing helix chain 'I' and resid 103 through 120 Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 161 through 166 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 196 through 205 removed outlier: 3.525A pdb=" N VAL I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 removed outlier: 3.578A pdb=" N GLN J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 20 Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 42 through 44 No H-bonds generated for 'chain 'J' and resid 42 through 44' Processing helix chain 'J' and resid 47 through 61 removed outlier: 3.727A pdb=" N SER J 52 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL J 54 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU J 56 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 59 " --> pdb=" O GLU J 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR J 61 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 105 Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 119 through 121 No H-bonds generated for 'chain 'J' and resid 119 through 121' Processing helix chain 'J' and resid 163 through 173 Processing helix chain 'K' and resid 59 through 80 removed outlier: 3.688A pdb=" N GLY K 66 " --> pdb=" O ARG K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 149 Processing helix chain 'M' and resid 26 through 38 removed outlier: 5.898A pdb=" N SER M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 98 through 109 removed outlier: 3.842A pdb=" N MET M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 122 removed outlier: 3.641A pdb=" N LYS M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS M 122 " --> pdb=" O GLN M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' Processing helix chain 'N' and resid 104 through 109 Processing helix chain 'N' and resid 112 through 117 Processing helix chain 'O' and resid 23 through 25 No H-bonds generated for 'chain 'O' and resid 23 through 25' Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 57 through 60 No H-bonds generated for 'chain 'O' and resid 57 through 60' Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 93 through 99 Processing helix chain 'O' and resid 130 through 139 Processing helix chain 'P' and resid 44 through 58 removed outlier: 4.089A pdb=" N TYR P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 124 removed outlier: 4.050A pdb=" N LYS P 124 " --> pdb=" O LEU P 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 27 Processing helix chain 'Q' and resid 34 through 53 removed outlier: 4.560A pdb=" N LYS Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL Q 43 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 63 Processing helix chain 'Q' and resid 94 through 100 Processing helix chain 'Q' and resid 102 through 106 removed outlier: 3.772A pdb=" N TYR Q 106 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 102 through 106' Processing helix chain 'R' and resid 7 through 19 Processing helix chain 'R' and resid 69 through 87 Processing helix chain 'R' and resid 104 through 114 Processing helix chain 'S' and resid 3 through 12 removed outlier: 4.705A pdb=" N SER S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN S 12 " --> pdb=" O ILE S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 56 No H-bonds generated for 'chain 'S' and resid 54 through 56' Processing helix chain 'S' and resid 98 through 102 Processing helix chain 'T' and resid 9 through 21 removed outlier: 3.515A pdb=" N ILE T 17 " --> pdb=" O ARG T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 29 Processing helix chain 'T' and resid 32 through 72 removed outlier: 3.770A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 86 Processing helix chain 'T' and resid 92 through 101 Processing helix chain 'T' and resid 103 through 116 Processing helix chain 'V' and resid 19 through 29 removed outlier: 4.155A pdb=" N VAL V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU V 28 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE V 29 " --> pdb=" O VAL V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 42 Processing helix chain 'V' and resid 47 through 65 removed outlier: 4.511A pdb=" N ILE V 51 " --> pdb=" O SER V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 71 through 73 No H-bonds generated for 'chain 'V' and resid 71 through 73' Processing helix chain 'W' and resid 14 through 19 removed outlier: 3.564A pdb=" N ILE W 19 " --> pdb=" O GLU W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 46 Processing helix chain 'X' and resid 65 through 67 No H-bonds generated for 'chain 'X' and resid 65 through 67' Processing sheet with id= A, first strand: chain '1' and resid 13 through 18 Processing sheet with id= B, first strand: chain '1' and resid 33 through 38 Processing sheet with id= C, first strand: chain '3' and resid 34 through 37 Processing sheet with id= D, first strand: chain '4' and resid 44 through 48 removed outlier: 3.545A pdb=" N PHE 4 23 " --> pdb=" O PHE 4 14 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '5' and resid 27 through 29 Processing sheet with id= F, first strand: chain '6' and resid 17 through 21 removed outlier: 4.059A pdb=" N TYR 6 17 " --> pdb=" O LEU 6 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '9' and resid 15 through 19 Processing sheet with id= H, first strand: chain 'G' and resid 3 through 5 Processing sheet with id= I, first strand: chain 'G' and resid 34 through 37 removed outlier: 4.017A pdb=" N LEU G 37 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG G 60 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 101 through 105 removed outlier: 3.543A pdb=" N THR G 80 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN G 95 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL G 78 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 129 through 131 Processing sheet with id= L, first strand: chain 'G' and resid 181 through 185 removed outlier: 6.244A pdb=" N ARG G 175 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL G 164 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 168 through 171 removed outlier: 4.626A pdb=" N VAL H 113 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU H 199 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL H 27 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET H 12 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL H 25 " --> pdb=" O MET H 12 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN H 14 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE H 23 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS H 189 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE H 176 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 80 through 84 removed outlier: 6.337A pdb=" N GLY H 52 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL H 35 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 123 through 126 removed outlier: 6.388A pdb=" N LEU I 192 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 126 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE I 194 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 88 through 91 removed outlier: 7.149A pdb=" N VAL J 157 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE J 34 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL J 155 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE J 36 " --> pdb=" O ASP J 153 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP J 153 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL J 132 " --> pdb=" O MET J 152 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 16 through 20 removed outlier: 3.561A pdb=" N LYS K 35 " --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 42 through 45 removed outlier: 3.711A pdb=" N ASN K 51 " --> pdb=" O LYS K 44 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 130 through 135 Processing sheet with id= T, first strand: chain 'K' and resid 95 through 99 Processing sheet with id= U, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.362A pdb=" N PHE M 54 " --> pdb=" O TYR M 17 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE M 19 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE M 56 " --> pdb=" O ILE M 19 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 74 through 78 Processing sheet with id= W, first strand: chain 'N' and resid 7 through 9 removed outlier: 6.738A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 75 through 78 Processing sheet with id= Y, first strand: chain 'O' and resid 89 through 91 Processing sheet with id= Z, first strand: chain 'P' and resid 129 through 133 removed outlier: 3.747A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA P 36 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE P 102 " --> pdb=" O ALA P 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 40 through 43 removed outlier: 3.721A pdb=" N ALA P 89 " --> pdb=" O SER P 76 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR P 74 " --> pdb=" O GLU P 91 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP P 93 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS P 72 " --> pdb=" O TRP P 93 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Q' and resid 29 through 33 removed outlier: 6.048A pdb=" N ILE Q 131 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYS Q 118 " --> pdb=" O ILE Q 131 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLU Q 133 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE Q 116 " --> pdb=" O GLU Q 133 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 70 through 73 removed outlier: 6.803A pdb=" N VAL Q 92 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 93 through 95 removed outlier: 3.631A pdb=" N VAL R 33 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 83 through 88 removed outlier: 3.588A pdb=" N LYS S 83 " --> pdb=" O HIS S 29 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR S 25 " --> pdb=" O ILE S 87 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG S 37 " --> pdb=" O GLU S 34 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N GLU S 44 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE S 64 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR S 60 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG S 50 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR S 58 " --> pdb=" O ARG S 50 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'U' and resid 10 through 15 removed outlier: 3.577A pdb=" N PHE U 40 " --> pdb=" O ILE U 4 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU U 6 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL U 38 " --> pdb=" O GLU U 6 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'U' and resid 19 through 22 Processing sheet with id= AH, first strand: chain 'U' and resid 32 through 35 removed outlier: 6.364A pdb=" N LYS U 61 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE U 97 " --> pdb=" O LYS U 61 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 71 through 77 removed outlier: 4.197A pdb=" N TYR U 82 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 7 through 12 removed outlier: 6.608A pdb=" N SER V 113 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL V 76 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 87 through 92 Processing sheet with id= AL, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.942A pdb=" N GLU W 28 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR W 26 " --> pdb=" O PRO W 10 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'W' and resid 62 through 65 removed outlier: 3.705A pdb=" N TYR W 68 " --> pdb=" O MET W 65 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'X' and resid 20 through 22 removed outlier: 5.898A pdb=" N LYS X 8 " --> pdb=" O LEU X 71 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU X 70 " --> pdb=" O THR X 79 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU X 77 " --> pdb=" O ASP X 72 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'X' and resid 40 through 45 Processing sheet with id= AP, first strand: chain 'X' and resid 81 through 85 Processing sheet with id= AQ, first strand: chain 'X' and resid 23 through 27 removed outlier: 6.736A pdb=" N LEU X 34 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA X 26 " --> pdb=" O ARG X 32 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG X 32 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Z' and resid 59 through 61 Processing sheet with id= AS, first strand: chain 'Z' and resid 74 through 79 724 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2446 hydrogen bonds 3860 hydrogen bond angles 0 basepair planarities 979 basepair parallelities 1609 stacking parallelities Total time for adding SS restraints: 177.74 Time building geometry restraints manager: 44.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9960 1.33 - 1.45: 44338 1.45 - 1.58: 35883 1.58 - 1.70: 6040 1.70 - 1.82: 120 Bond restraints: 96341 Sorted by residual: bond pdb=" CE1 HIS G 15 " pdb=" NE2 HIS G 15 " ideal model delta sigma weight residual 1.321 1.371 -0.050 1.00e-02 1.00e+04 2.49e+01 bond pdb=" CE1 HIS U 83 " pdb=" NE2 HIS U 83 " ideal model delta sigma weight residual 1.321 1.370 -0.049 1.00e-02 1.00e+04 2.41e+01 bond pdb=" CE1 HIS O 35 " pdb=" NE2 HIS O 35 " ideal model delta sigma weight residual 1.321 1.369 -0.048 1.00e-02 1.00e+04 2.30e+01 bond pdb=" CE1 HIS M 124 " pdb=" NE2 HIS M 124 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.25e+01 bond pdb=" C GLY H 116 " pdb=" O GLY H 116 " ideal model delta sigma weight residual 1.243 1.285 -0.043 9.30e-03 1.16e+04 2.11e+01 ... (remaining 96336 not shown) Histogram of bond angle deviations from ideal: 87.94 - 97.28: 53 97.28 - 106.62: 19381 106.62 - 115.97: 66601 115.97 - 125.31: 46419 125.31 - 134.66: 12605 Bond angle restraints: 145059 Sorted by residual: angle pdb=" O3' A A 731 " pdb=" P U A 732 " pdb=" O5' U A 732 " ideal model delta sigma weight residual 104.00 87.94 16.06 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O3' C A1849 " pdb=" C3' C A1849 " pdb=" C2' C A1849 " ideal model delta sigma weight residual 113.70 98.73 14.97 1.50e+00 4.44e-01 9.97e+01 angle pdb=" C3' U A 605 " pdb=" O3' U A 605 " pdb=" P G A 606 " ideal model delta sigma weight residual 120.20 105.72 14.48 1.50e+00 4.44e-01 9.31e+01 angle pdb=" O3' A A2908 " pdb=" C3' A A2908 " pdb=" C2' A A2908 " ideal model delta sigma weight residual 109.50 123.08 -13.58 1.50e+00 4.44e-01 8.20e+01 angle pdb=" C3' C A1958 " pdb=" O3' C A1958 " pdb=" P U A1959 " ideal model delta sigma weight residual 120.20 106.81 13.39 1.50e+00 4.44e-01 7.97e+01 ... (remaining 145054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 54566 36.00 - 71.99: 6283 71.99 - 107.99: 717 107.99 - 143.98: 19 143.98 - 179.98: 39 Dihedral angle restraints: 61624 sinusoidal: 53189 harmonic: 8435 Sorted by residual: dihedral pdb=" C5' A A 548 " pdb=" C4' A A 548 " pdb=" C3' A A 548 " pdb=" O3' A A 548 " ideal model delta sinusoidal sigma weight residual 147.00 74.75 72.25 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' C A1148 " pdb=" C4' C A1148 " pdb=" C3' C A1148 " pdb=" O3' C A1148 " ideal model delta sinusoidal sigma weight residual 147.00 78.56 68.44 1 8.00e+00 1.56e-02 9.49e+01 dihedral pdb=" C4' C A1148 " pdb=" C3' C A1148 " pdb=" C2' C A1148 " pdb=" C1' C A1148 " ideal model delta sinusoidal sigma weight residual -35.00 30.78 -65.78 1 8.00e+00 1.56e-02 8.85e+01 ... (remaining 61621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 12221 0.114 - 0.228: 5471 0.228 - 0.342: 759 0.342 - 0.457: 172 0.457 - 0.571: 21 Chirality restraints: 18644 Sorted by residual: chirality pdb=" C3' A A2809 " pdb=" C4' A A2809 " pdb=" O3' A A2809 " pdb=" C2' A A2809 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" P U A 3 " pdb=" OP1 U A 3 " pdb=" OP2 U A 3 " pdb=" O5' U A 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" P C A1593 " pdb=" OP1 C A1593 " pdb=" OP2 C A1593 " pdb=" O5' C A1593 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.03e+00 ... (remaining 18641 not shown) Planarity restraints: 7086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 43 " -0.797 9.50e-02 1.11e+02 3.57e-01 7.87e+01 pdb=" NE ARG G 43 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG G 43 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 43 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 43 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 122 " -0.768 9.50e-02 1.11e+02 3.44e-01 7.22e+01 pdb=" NE ARG Q 122 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG Q 122 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 122 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 122 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 1 18 " -0.687 9.50e-02 1.11e+02 3.08e-01 5.82e+01 pdb=" NE ARG 1 18 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG 1 18 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 1 18 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG 1 18 " -0.018 2.00e-02 2.50e+03 ... (remaining 7083 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.41: 299 2.41 - 3.09: 59022 3.09 - 3.78: 207773 3.78 - 4.46: 314151 4.46 - 5.14: 412187 Nonbonded interactions: 993432 Sorted by model distance: nonbonded pdb=" OD1 ASN 5 32 " pdb=" SG CYS 5 46 " model vdw 1.730 3.400 nonbonded pdb=" OP1 A A2610 " pdb="MG MG A3149 " model vdw 1.739 2.170 nonbonded pdb=" OP1 U A 619 " pdb="MG MG A3034 " model vdw 1.799 2.170 nonbonded pdb=" OP1 A A2536 " pdb="MG MG A3034 " model vdw 1.831 2.170 nonbonded pdb=" OP2 G A2535 " pdb="MG MG A3084 " model vdw 1.924 2.170 ... (remaining 993427 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 17.710 Check model and map are aligned: 0.960 Set scattering table: 0.620 Process input model: 379.070 Find NCS groups from input model: 1.470 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 409.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.011 0.090 96341 Z= 0.664 Angle : 1.656 16.064 145059 Z= 1.092 Chirality : 0.121 0.571 18644 Planarity : 0.020 0.357 7086 Dihedral : 23.255 179.976 56204 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.89 % Allowed : 4.49 % Favored : 94.62 % Rotamer: Outliers : 1.80 % Allowed : 5.13 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.32 (0.13), residues: 2917 helix: -1.85 (0.15), residues: 762 sheet: -1.26 (0.18), residues: 620 loop : -1.41 (0.14), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP G 250 HIS 0.013 0.002 HIS X 64 PHE 0.028 0.003 PHE T 32 TYR 0.034 0.004 TYR 7 5 ARG 0.019 0.002 ARG O 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 653 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 29 ARG cc_start: 0.7301 (mtt-85) cc_final: 0.6358 (mtp180) REVERT: 2 47 ARG cc_start: 0.6849 (mtp180) cc_final: 0.6437 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7211 (mptm) cc_final: 0.6720 (mtmt) REVERT: 3 4 LEU cc_start: 0.7120 (mt) cc_final: 0.6904 (mm) REVERT: 3 9 LYS cc_start: 0.7651 (pttp) cc_final: 0.6818 (mmmm) REVERT: 3 10 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7382 (mmm160) REVERT: 3 21 LYS cc_start: 0.7624 (mttt) cc_final: 0.7369 (mtmt) REVERT: 5 36 TYR cc_start: 0.6863 (m-80) cc_final: 0.6212 (m-80) REVERT: 6 5 ILE cc_start: 0.6565 (mm) cc_final: 0.6195 (pt) REVERT: 8 49 MET cc_start: 0.8177 (mmm) cc_final: 0.7922 (mmm) REVERT: G 77 ARG cc_start: 0.6167 (ttp80) cc_final: 0.5524 (ttm110) REVERT: G 100 GLU cc_start: 0.5696 (tt0) cc_final: 0.5491 (tt0) REVERT: G 102 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6933 (mtt180) REVERT: G 124 ILE cc_start: 0.7711 (mm) cc_final: 0.7420 (mm) REVERT: H 29 GLU cc_start: 0.7576 (tt0) cc_final: 0.7311 (tp30) REVERT: H 40 THR cc_start: 0.7432 (p) cc_final: 0.7124 (t) REVERT: H 63 LYS cc_start: 0.7483 (mtpp) cc_final: 0.6932 (mtmt) REVERT: H 107 ILE cc_start: 0.6976 (mm) cc_final: 0.6623 (mp) REVERT: I 200 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6827 (tt0) REVERT: I 201 LYS cc_start: 0.7435 (tppp) cc_final: 0.7167 (tptp) REVERT: J 26 MET cc_start: 0.5057 (mmm) cc_final: 0.4451 (mmm) REVERT: J 83 MET cc_start: 0.4033 (mtm) cc_final: 0.3361 (mmm) REVERT: J 100 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5254 (mt) REVERT: J 115 ARG cc_start: 0.1577 (OUTLIER) cc_final: 0.1172 (ptm-80) REVERT: K 44 LYS cc_start: 0.4062 (mmtm) cc_final: 0.3571 (mmmt) REVERT: K 90 ILE cc_start: 0.6047 (mm) cc_final: 0.5537 (tp) REVERT: K 158 LYS cc_start: 0.6860 (mtmt) cc_final: 0.6604 (mtmm) REVERT: K 172 LYS cc_start: 0.6312 (mtpp) cc_final: 0.6111 (mttt) REVERT: K 173 GLU cc_start: 0.4339 (OUTLIER) cc_final: 0.4102 (tm-30) REVERT: M 44 GLN cc_start: 0.7384 (mp10) cc_final: 0.7028 (mt0) REVERT: M 62 LYS cc_start: 0.7892 (mppt) cc_final: 0.7472 (mmmt) REVERT: M 100 LYS cc_start: 0.7848 (tptp) cc_final: 0.7296 (ttmm) REVERT: M 118 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7512 (mm110) REVERT: N 9 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7731 (mttp) REVERT: N 17 ARG cc_start: 0.6404 (mmt90) cc_final: 0.6070 (mpt-90) REVERT: N 18 GLU cc_start: 0.7572 (tt0) cc_final: 0.7243 (tt0) REVERT: N 72 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7317 (mp10) REVERT: N 81 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: N 91 LYS cc_start: 0.7080 (mttp) cc_final: 0.6789 (mtmt) REVERT: N 112 MET cc_start: 0.7563 (mmm) cc_final: 0.7041 (mmp) REVERT: O 86 GLU cc_start: 0.6349 (tp30) cc_final: 0.5395 (mt-10) REVERT: P 26 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6233 (mt-10) REVERT: P 63 LYS cc_start: 0.6152 (mtpt) cc_final: 0.5837 (tptt) REVERT: Q 91 PRO cc_start: 0.6869 (Cg_endo) cc_final: 0.6445 (Cg_exo) REVERT: R 38 LYS cc_start: 0.7102 (tppp) cc_final: 0.6809 (mmmm) REVERT: R 83 ARG cc_start: 0.5577 (mtt180) cc_final: 0.5004 (mmt-90) REVERT: S 19 ASN cc_start: 0.6962 (m-40) cc_final: 0.6752 (m110) REVERT: S 29 HIS cc_start: 0.7826 (m-70) cc_final: 0.7451 (m-70) REVERT: S 31 LYS cc_start: 0.7066 (mttp) cc_final: 0.6767 (mtpt) REVERT: S 88 ARG cc_start: 0.6844 (ptp-110) cc_final: 0.6257 (ptp-170) REVERT: S 104 ARG cc_start: 0.7247 (mmp80) cc_final: 0.6898 (mmt180) REVERT: T 12 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7695 (tttp) REVERT: T 78 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6775 (mmtp) REVERT: T 80 MET cc_start: 0.6729 (mmm) cc_final: 0.6465 (mmm) REVERT: U 1 MET cc_start: 0.7121 (ttp) cc_final: 0.6370 (tpp) REVERT: U 12 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8017 (mp) REVERT: U 61 LYS cc_start: 0.7712 (pttt) cc_final: 0.7292 (mttm) REVERT: U 86 GLN cc_start: 0.7940 (tt0) cc_final: 0.7726 (tt0) REVERT: V 15 VAL cc_start: 0.8329 (t) cc_final: 0.8081 (p) REVERT: W 67 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.4653 (mtp180) REVERT: X 32 ARG cc_start: 0.6770 (mtp85) cc_final: 0.6257 (mtp180) REVERT: X 36 GLU cc_start: 0.5953 (tt0) cc_final: 0.5499 (pt0) REVERT: Z 52 LYS cc_start: 0.8196 (mtpm) cc_final: 0.7925 (mtpp) REVERT: Z 76 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7466 (tpp-160) REVERT: Z 85 LYS cc_start: 0.7563 (ttmt) cc_final: 0.6966 (tptt) outliers start: 45 outliers final: 6 residues processed: 684 average time/residue: 1.0572 time to fit residues: 1151.6927 Evaluate side-chains 429 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 416 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 25 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain W residue 67 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 495 optimal weight: 1.9990 chunk 444 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 300 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 460 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 533 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 41 ASN 2 17 GLN 3 17 GLN 5 32 ASN 6 45 HIS G 70 ASN H 14 GLN H 201 GLN ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN J 46 ASN N 4 GLN R 32 ASN R 58 ASN S 14 ASN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 96341 Z= 0.289 Angle : 0.732 9.703 145059 Z= 0.377 Chirality : 0.043 0.429 18644 Planarity : 0.006 0.091 7086 Dihedral : 23.953 179.568 50219 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.02 % Favored : 96.71 % Rotamer: Outliers : 2.20 % Allowed : 9.73 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.96 (0.14), residues: 2917 helix: -0.02 (0.17), residues: 783 sheet: -0.67 (0.19), residues: 622 loop : -0.87 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 250 HIS 0.008 0.002 HIS 8 31 PHE 0.017 0.002 PHE R 119 TYR 0.024 0.003 TYR 5 49 ARG 0.008 0.001 ARG N 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 452 time to evaluate : 3.646 Fit side-chains revert: symmetry clash REVERT: 1 13 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7569 (tpp-160) REVERT: 1 37 ARG cc_start: 0.6697 (mtp85) cc_final: 0.5879 (ttm170) REVERT: 2 29 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.6404 (mtp180) REVERT: 2 47 ARG cc_start: 0.6921 (mtp180) cc_final: 0.6637 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7160 (mptm) cc_final: 0.6577 (mtmt) REVERT: 3 21 LYS cc_start: 0.7938 (mttt) cc_final: 0.7563 (mtmt) REVERT: 3 33 SER cc_start: 0.8225 (m) cc_final: 0.7851 (p) REVERT: 3 58 GLU cc_start: 0.4693 (mm-30) cc_final: 0.4135 (pt0) REVERT: 5 28 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6116 (p0) REVERT: 5 32 ASN cc_start: 0.3054 (OUTLIER) cc_final: 0.2837 (m-40) REVERT: 5 36 TYR cc_start: 0.7182 (m-80) cc_final: 0.6421 (m-80) REVERT: 6 5 ILE cc_start: 0.6896 (mm) cc_final: 0.6310 (pt) REVERT: 6 6 THR cc_start: 0.7424 (t) cc_final: 0.7224 (m) REVERT: 6 14 ASP cc_start: 0.6290 (p0) cc_final: 0.5363 (t0) REVERT: 6 26 ASN cc_start: 0.6910 (m-40) cc_final: 0.6608 (m110) REVERT: G 216 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7327 (mmtm) REVERT: H 29 GLU cc_start: 0.7912 (tt0) cc_final: 0.7576 (tp30) REVERT: H 44 ASP cc_start: 0.7811 (m-30) cc_final: 0.7563 (m-30) REVERT: I 200 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6756 (tt0) REVERT: I 201 LYS cc_start: 0.7362 (tppp) cc_final: 0.7151 (tptp) REVERT: J 4 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7079 (mm) REVERT: J 17 MET cc_start: 0.6068 (tmm) cc_final: 0.5861 (tmm) REVERT: J 83 MET cc_start: 0.4413 (OUTLIER) cc_final: 0.3520 (mmp) REVERT: J 98 ASP cc_start: 0.5644 (m-30) cc_final: 0.5409 (m-30) REVERT: J 100 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5383 (mt) REVERT: J 175 MET cc_start: 0.3728 (tpp) cc_final: 0.3391 (mtp) REVERT: K 44 LYS cc_start: 0.3948 (mmtm) cc_final: 0.3472 (mmmt) REVERT: K 54 ARG cc_start: 0.4685 (ttp-170) cc_final: 0.4455 (ttp-170) REVERT: M 44 GLN cc_start: 0.7479 (mp10) cc_final: 0.7130 (mt0) REVERT: M 100 LYS cc_start: 0.8077 (tptp) cc_final: 0.7260 (mttp) REVERT: N 9 LYS cc_start: 0.8241 (ttpp) cc_final: 0.7662 (tptm) REVERT: N 17 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5827 (mmt180) REVERT: N 18 GLU cc_start: 0.7600 (tt0) cc_final: 0.7257 (tt0) REVERT: N 72 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7331 (mp10) REVERT: N 112 MET cc_start: 0.7656 (mmm) cc_final: 0.7232 (mmp) REVERT: O 86 GLU cc_start: 0.6194 (tp30) cc_final: 0.5147 (mt-10) REVERT: P 26 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6257 (mt-10) REVERT: P 29 PHE cc_start: 0.7318 (m-80) cc_final: 0.6981 (m-80) REVERT: P 31 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6637 (tp30) REVERT: P 63 LYS cc_start: 0.6525 (mtpt) cc_final: 0.6139 (tptt) REVERT: P 66 ILE cc_start: 0.8229 (mt) cc_final: 0.8008 (mt) REVERT: Q 91 PRO cc_start: 0.6859 (Cg_endo) cc_final: 0.6418 (Cg_exo) REVERT: Q 110 GLN cc_start: 0.6291 (mp10) cc_final: 0.6071 (mp10) REVERT: R 83 ARG cc_start: 0.5378 (mtt180) cc_final: 0.4933 (mmt180) REVERT: S 19 ASN cc_start: 0.7232 (m-40) cc_final: 0.6961 (m110) REVERT: S 29 HIS cc_start: 0.8232 (m-70) cc_final: 0.7719 (m90) REVERT: S 31 LYS cc_start: 0.7027 (mttp) cc_final: 0.6577 (mtpt) REVERT: S 88 ARG cc_start: 0.6979 (ptp-110) cc_final: 0.6467 (ptp-170) REVERT: S 104 ARG cc_start: 0.7114 (mmp80) cc_final: 0.6749 (mmt180) REVERT: S 111 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6955 (tptm) REVERT: T 12 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7445 (tttt) REVERT: T 78 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6975 (mmtp) REVERT: U 61 LYS cc_start: 0.7800 (pttt) cc_final: 0.7353 (mttm) REVERT: W 83 THR cc_start: 0.6478 (p) cc_final: 0.6178 (p) REVERT: X 32 ARG cc_start: 0.6680 (mtp85) cc_final: 0.6316 (mtp180) REVERT: X 36 GLU cc_start: 0.6626 (tt0) cc_final: 0.6053 (pt0) REVERT: Z 76 ARG cc_start: 0.7844 (mmt180) cc_final: 0.7578 (tpp-160) outliers start: 55 outliers final: 31 residues processed: 488 average time/residue: 0.9924 time to fit residues: 797.8357 Evaluate side-chains 418 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 380 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 28 ASN Chi-restraints excluded: chain 5 residue 32 ASN Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 31 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 296 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 443 optimal weight: 7.9990 chunk 362 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 534 optimal weight: 9.9990 chunk 576 optimal weight: 9.9990 chunk 475 optimal weight: 10.0000 chunk 529 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 428 optimal weight: 0.0170 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 40 ASN 4 6 HIS 5 41 HIS 9 34 GLN G 15 HIS G 226 ASN I 9 GLN J 172 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN V 95 GLN W 73 ASN X 39 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 96341 Z= 0.356 Angle : 0.744 10.603 145059 Z= 0.382 Chirality : 0.044 0.394 18644 Planarity : 0.007 0.103 7086 Dihedral : 24.027 179.678 50199 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.08 % Favored : 95.75 % Rotamer: Outliers : 3.20 % Allowed : 12.33 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.04 (0.14), residues: 2917 helix: -0.01 (0.18), residues: 775 sheet: -0.63 (0.19), residues: 608 loop : -1.01 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 1 29 HIS 0.010 0.002 HIS 8 31 PHE 0.019 0.003 PHE T 32 TYR 0.024 0.003 TYR 5 49 ARG 0.008 0.001 ARG 6 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 414 time to evaluate : 3.566 Fit side-chains REVERT: 1 13 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7586 (tpp-160) REVERT: 1 37 ARG cc_start: 0.6775 (mtp85) cc_final: 0.6108 (ttm170) REVERT: 2 29 ARG cc_start: 0.7226 (mtt-85) cc_final: 0.6415 (mtp180) REVERT: 2 47 ARG cc_start: 0.6953 (mtp180) cc_final: 0.6695 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7241 (mptm) cc_final: 0.6473 (mtpt) REVERT: 2 52 ARG cc_start: 0.7230 (mtt90) cc_final: 0.7015 (mtt90) REVERT: 3 9 LYS cc_start: 0.7703 (pttp) cc_final: 0.6858 (mmmm) REVERT: 3 21 LYS cc_start: 0.8054 (mttt) cc_final: 0.7563 (mtmt) REVERT: 3 24 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: 3 33 SER cc_start: 0.8236 (m) cc_final: 0.7908 (p) REVERT: 3 58 GLU cc_start: 0.4505 (mm-30) cc_final: 0.4206 (pt0) REVERT: 5 36 TYR cc_start: 0.7271 (m-80) cc_final: 0.6501 (m-80) REVERT: 6 5 ILE cc_start: 0.6897 (mm) cc_final: 0.6338 (pt) REVERT: 6 6 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.6867 (m) REVERT: 6 28 GLU cc_start: 0.5646 (pm20) cc_final: 0.5444 (pm20) REVERT: G 4 LYS cc_start: 0.7722 (ptmt) cc_final: 0.7053 (mmpt) REVERT: G 216 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7293 (mmtm) REVERT: H 29 GLU cc_start: 0.7947 (tt0) cc_final: 0.7690 (tp30) REVERT: H 47 GLU cc_start: 0.8220 (pt0) cc_final: 0.7951 (pt0) REVERT: H 71 LYS cc_start: 0.7391 (mmmm) cc_final: 0.7080 (mmmt) REVERT: I 112 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7564 (t) REVERT: I 120 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5289 (mp0) REVERT: J 17 MET cc_start: 0.6510 (tmm) cc_final: 0.6204 (tmm) REVERT: J 64 LYS cc_start: 0.4652 (ptpt) cc_final: 0.4247 (tttm) REVERT: J 83 MET cc_start: 0.5347 (OUTLIER) cc_final: 0.4317 (mmp) REVERT: J 100 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4721 (mt) REVERT: J 152 MET cc_start: 0.4339 (mmt) cc_final: 0.3653 (mtm) REVERT: K 35 LYS cc_start: 0.3335 (tptt) cc_final: 0.2995 (mmmt) REVERT: K 44 LYS cc_start: 0.3837 (mmtm) cc_final: 0.3249 (mmmt) REVERT: K 62 ARG cc_start: 0.6784 (mtm-85) cc_final: 0.6563 (mtp180) REVERT: K 83 TYR cc_start: 0.4479 (m-80) cc_final: 0.4264 (m-80) REVERT: K 173 GLU cc_start: 0.4294 (OUTLIER) cc_final: 0.4055 (tm-30) REVERT: M 100 LYS cc_start: 0.7999 (tptp) cc_final: 0.7174 (mttp) REVERT: N 9 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7573 (tptm) REVERT: N 17 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6258 (mmt180) REVERT: N 18 GLU cc_start: 0.7672 (tt0) cc_final: 0.7384 (tt0) REVERT: N 72 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7201 (mp10) REVERT: N 105 GLU cc_start: 0.7716 (mp0) cc_final: 0.7501 (mp0) REVERT: N 112 MET cc_start: 0.7579 (mmm) cc_final: 0.7358 (mmp) REVERT: P 29 PHE cc_start: 0.7295 (m-80) cc_final: 0.7031 (m-10) REVERT: P 31 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6834 (tp30) REVERT: P 63 LYS cc_start: 0.6536 (mtpt) cc_final: 0.6034 (tptt) REVERT: Q 91 PRO cc_start: 0.6973 (Cg_endo) cc_final: 0.6464 (Cg_exo) REVERT: R 83 ARG cc_start: 0.5315 (mtt180) cc_final: 0.4913 (mmt180) REVERT: R 87 LYS cc_start: 0.4502 (tppt) cc_final: 0.4223 (tptp) REVERT: S 104 ARG cc_start: 0.7188 (mmp80) cc_final: 0.6955 (mmt180) REVERT: T 12 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7511 (tttp) REVERT: T 78 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7050 (mmtp) REVERT: U 1 MET cc_start: 0.6966 (ttt) cc_final: 0.6712 (tpp) REVERT: U 61 LYS cc_start: 0.7947 (pttt) cc_final: 0.7281 (mttm) REVERT: X 32 ARG cc_start: 0.6589 (mtp85) cc_final: 0.6154 (mtp180) REVERT: X 69 MET cc_start: 0.7055 (mtp) cc_final: 0.6606 (mtt) REVERT: Z 76 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7556 (tpp-160) outliers start: 80 outliers final: 52 residues processed: 470 average time/residue: 0.9508 time to fit residues: 739.3690 Evaluate side-chains 439 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 378 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 24 GLN Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 8 residue 51 SER Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain X residue 39 ASN Chi-restraints excluded: chain Z residue 43 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 527 optimal weight: 0.5980 chunk 401 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 254 optimal weight: 30.0000 chunk 358 optimal weight: 6.9990 chunk 535 optimal weight: 10.0000 chunk 567 optimal weight: 0.5980 chunk 280 optimal weight: 10.0000 chunk 507 optimal weight: 7.9990 chunk 152 optimal weight: 30.0000 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 26 ASN G 70 ASN G 199 GLN H 87 ASN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN X 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 96341 Z= 0.314 Angle : 0.690 9.229 145059 Z= 0.357 Chirality : 0.042 0.370 18644 Planarity : 0.006 0.083 7086 Dihedral : 23.970 179.584 50199 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.25 % Favored : 95.61 % Rotamer: Outliers : 3.64 % Allowed : 14.74 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.03 (0.14), residues: 2917 helix: 0.05 (0.18), residues: 771 sheet: -0.62 (0.19), residues: 617 loop : -1.04 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 1 29 HIS 0.010 0.002 HIS 8 31 PHE 0.018 0.002 PHE T 32 TYR 0.015 0.002 TYR 4 9 ARG 0.009 0.001 ARG M 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 382 time to evaluate : 3.662 Fit side-chains REVERT: 1 13 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7597 (tpp-160) REVERT: 1 37 ARG cc_start: 0.6750 (mtp85) cc_final: 0.6103 (ttm170) REVERT: 2 29 ARG cc_start: 0.7346 (mtt-85) cc_final: 0.6536 (mtp180) REVERT: 2 47 ARG cc_start: 0.6994 (mtp180) cc_final: 0.6695 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7251 (mptm) cc_final: 0.6510 (mtpt) REVERT: 2 52 ARG cc_start: 0.7204 (mtt90) cc_final: 0.6913 (mtt90) REVERT: 3 9 LYS cc_start: 0.7753 (pttp) cc_final: 0.6843 (mmmm) REVERT: 3 21 LYS cc_start: 0.8166 (mttt) cc_final: 0.7695 (mtmt) REVERT: 3 33 SER cc_start: 0.8245 (m) cc_final: 0.7944 (p) REVERT: 5 23 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.6318 (mp10) REVERT: 6 6 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.6780 (m) REVERT: G 216 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7303 (mmtm) REVERT: H 29 GLU cc_start: 0.8149 (tt0) cc_final: 0.7862 (tp30) REVERT: H 47 GLU cc_start: 0.8202 (pt0) cc_final: 0.7923 (pt0) REVERT: H 71 LYS cc_start: 0.7313 (mmmm) cc_final: 0.7057 (mmmt) REVERT: I 120 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5380 (mp0) REVERT: I 127 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5892 (tt0) REVERT: J 17 MET cc_start: 0.6599 (tmm) cc_final: 0.6304 (tmm) REVERT: J 64 LYS cc_start: 0.4824 (ptpt) cc_final: 0.4081 (tttm) REVERT: J 83 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4466 (mmp) REVERT: J 100 LEU cc_start: 0.5398 (tt) cc_final: 0.4929 (pp) REVERT: J 128 TYR cc_start: 0.6724 (t80) cc_final: 0.6370 (t80) REVERT: J 133 ARG cc_start: 0.4060 (OUTLIER) cc_final: 0.3770 (mmm160) REVERT: J 152 MET cc_start: 0.4452 (mmt) cc_final: 0.3731 (mtm) REVERT: K 27 LYS cc_start: 0.4931 (mptt) cc_final: 0.4088 (tppt) REVERT: K 35 LYS cc_start: 0.3367 (tptt) cc_final: 0.2905 (mmmt) REVERT: K 44 LYS cc_start: 0.3966 (mmtm) cc_final: 0.3387 (mmmt) REVERT: K 57 ASP cc_start: 0.5070 (t0) cc_final: 0.4614 (m-30) REVERT: K 173 GLU cc_start: 0.4374 (OUTLIER) cc_final: 0.4136 (tm-30) REVERT: M 100 LYS cc_start: 0.7987 (tptp) cc_final: 0.7116 (mttp) REVERT: N 17 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6334 (mmt180) REVERT: N 18 GLU cc_start: 0.7640 (tt0) cc_final: 0.7355 (tt0) REVERT: N 72 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7186 (mp10) REVERT: N 81 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: N 105 GLU cc_start: 0.7712 (mp0) cc_final: 0.7448 (mp0) REVERT: P 31 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6832 (tp30) REVERT: P 63 LYS cc_start: 0.6510 (mtpt) cc_final: 0.6001 (tptt) REVERT: Q 91 PRO cc_start: 0.6843 (Cg_endo) cc_final: 0.6314 (Cg_exo) REVERT: Q 115 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8005 (ttm110) REVERT: R 71 ASP cc_start: 0.5785 (OUTLIER) cc_final: 0.5315 (t0) REVERT: R 83 ARG cc_start: 0.5247 (mtt180) cc_final: 0.4790 (mmt180) REVERT: R 87 LYS cc_start: 0.4609 (tppt) cc_final: 0.4320 (tptp) REVERT: R 113 ARG cc_start: 0.5942 (ttm-80) cc_final: 0.5269 (mtt-85) REVERT: S 104 ARG cc_start: 0.7283 (mmp80) cc_final: 0.6969 (mmt180) REVERT: T 78 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7046 (mmtp) REVERT: U 1 MET cc_start: 0.7179 (ttt) cc_final: 0.6770 (tpp) REVERT: U 61 LYS cc_start: 0.8022 (pttt) cc_final: 0.7304 (mttm) REVERT: W 65 MET cc_start: 0.7784 (ttm) cc_final: 0.7513 (tpp) REVERT: W 67 ARG cc_start: 0.5366 (ptp90) cc_final: 0.5120 (mtm-85) REVERT: X 32 ARG cc_start: 0.6333 (mtp85) cc_final: 0.5995 (mtp180) REVERT: X 69 MET cc_start: 0.7029 (mtp) cc_final: 0.6552 (mtt) REVERT: X 70 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.5959 (mt) REVERT: Z 76 ARG cc_start: 0.7850 (mmt180) cc_final: 0.7559 (tpp-160) REVERT: Z 78 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7689 (mt-10) outliers start: 91 outliers final: 55 residues processed: 451 average time/residue: 0.9605 time to fit residues: 712.3778 Evaluate side-chains 433 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 364 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 23 GLN Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 115 ARG Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Z residue 43 SER Chi-restraints excluded: chain Z residue 78 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 472 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 422 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 484 optimal weight: 6.9990 chunk 392 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 509 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 16 ASN ** 5 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN H 191 ASN J 172 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 96341 Z= 0.457 Angle : 0.846 10.348 145059 Z= 0.427 Chirality : 0.049 0.414 18644 Planarity : 0.007 0.109 7086 Dihedral : 24.192 179.264 50197 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.73 % Favored : 94.07 % Rotamer: Outliers : 4.77 % Allowed : 15.42 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.48 (0.14), residues: 2917 helix: -0.52 (0.17), residues: 774 sheet: -0.75 (0.20), residues: 601 loop : -1.28 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 93 HIS 0.014 0.002 HIS 8 31 PHE 0.022 0.003 PHE R 119 TYR 0.021 0.003 TYR 4 9 ARG 0.008 0.001 ARG T 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 384 time to evaluate : 3.691 Fit side-chains REVERT: 1 13 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7604 (tpp-160) REVERT: 1 37 ARG cc_start: 0.6785 (mtp85) cc_final: 0.6143 (ttm170) REVERT: 2 47 ARG cc_start: 0.6942 (mtp180) cc_final: 0.6637 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7320 (mptm) cc_final: 0.6584 (mtpt) REVERT: 2 52 ARG cc_start: 0.7212 (mtt90) cc_final: 0.6889 (mtt90) REVERT: 3 9 LYS cc_start: 0.7719 (pttp) cc_final: 0.6867 (mmmm) REVERT: 3 21 LYS cc_start: 0.8182 (mttt) cc_final: 0.7758 (mtmt) REVERT: 3 24 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: 3 33 SER cc_start: 0.8267 (m) cc_final: 0.7940 (p) REVERT: G 198 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: G 216 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7306 (mmtm) REVERT: H 29 GLU cc_start: 0.8138 (tt0) cc_final: 0.7857 (tp30) REVERT: H 47 GLU cc_start: 0.8246 (pt0) cc_final: 0.7977 (pt0) REVERT: H 71 LYS cc_start: 0.7174 (mmmm) cc_final: 0.6937 (mmmt) REVERT: I 95 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8096 (ptt180) REVERT: I 120 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5358 (mp0) REVERT: I 127 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5883 (tt0) REVERT: J 17 MET cc_start: 0.6492 (tmm) cc_final: 0.6187 (tmm) REVERT: J 64 LYS cc_start: 0.4474 (ptpt) cc_final: 0.3730 (tttm) REVERT: J 83 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.4594 (mmp) REVERT: J 102 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.5025 (mtmm) REVERT: J 110 ARG cc_start: 0.5771 (mtp85) cc_final: 0.4807 (mmm160) REVERT: J 133 ARG cc_start: 0.4092 (OUTLIER) cc_final: 0.3823 (mmm160) REVERT: J 152 MET cc_start: 0.4727 (mmt) cc_final: 0.3894 (mtm) REVERT: J 173 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5717 (mt) REVERT: K 27 LYS cc_start: 0.4859 (mptt) cc_final: 0.3903 (tppt) REVERT: K 44 LYS cc_start: 0.3956 (mmtm) cc_final: 0.3397 (mmmt) REVERT: K 57 ASP cc_start: 0.5413 (t0) cc_final: 0.4913 (m-30) REVERT: K 62 ARG cc_start: 0.6731 (mtp180) cc_final: 0.6302 (ttp-170) REVERT: K 173 GLU cc_start: 0.4322 (OUTLIER) cc_final: 0.4094 (tm-30) REVERT: M 100 LYS cc_start: 0.7975 (tptp) cc_final: 0.7149 (mttp) REVERT: N 17 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6515 (mmt180) REVERT: N 18 GLU cc_start: 0.7684 (tt0) cc_final: 0.7371 (tm-30) REVERT: N 72 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7069 (mp10) REVERT: N 81 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: N 105 GLU cc_start: 0.7670 (mp0) cc_final: 0.7397 (mp0) REVERT: P 31 GLU cc_start: 0.7683 (mt-10) cc_final: 0.6919 (tp30) REVERT: P 63 LYS cc_start: 0.6588 (mtpt) cc_final: 0.6058 (tptt) REVERT: Q 28 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8057 (mp0) REVERT: Q 53 LYS cc_start: 0.7113 (tptm) cc_final: 0.6601 (tptp) REVERT: Q 115 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8078 (ttm110) REVERT: R 43 GLN cc_start: 0.6905 (mt0) cc_final: 0.6547 (mt0) REVERT: R 71 ASP cc_start: 0.5578 (OUTLIER) cc_final: 0.5192 (t0) REVERT: R 83 ARG cc_start: 0.5207 (mtt180) cc_final: 0.4759 (mmt180) REVERT: R 87 LYS cc_start: 0.4594 (tppt) cc_final: 0.4301 (tptp) REVERT: S 41 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6597 (pt0) REVERT: S 104 ARG cc_start: 0.7271 (mmp80) cc_final: 0.7008 (mmt180) REVERT: S 112 GLU cc_start: 0.6324 (tt0) cc_final: 0.5630 (mp0) REVERT: T 78 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7115 (mmtp) REVERT: U 1 MET cc_start: 0.7026 (ttt) cc_final: 0.6560 (tpp) REVERT: U 61 LYS cc_start: 0.8020 (pttt) cc_final: 0.7208 (mttm) REVERT: V 64 GLU cc_start: 0.7052 (tt0) cc_final: 0.6567 (pt0) REVERT: W 65 MET cc_start: 0.7832 (ttm) cc_final: 0.7146 (tpp) REVERT: W 67 ARG cc_start: 0.5413 (ptp90) cc_final: 0.5108 (mtp180) REVERT: X 32 ARG cc_start: 0.6380 (mtp85) cc_final: 0.6110 (mtp180) REVERT: X 69 MET cc_start: 0.7106 (mtp) cc_final: 0.6652 (mtt) REVERT: X 70 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6195 (mt) outliers start: 119 outliers final: 75 residues processed: 475 average time/residue: 0.9717 time to fit residues: 763.9999 Evaluate side-chains 468 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 376 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 24 GLN Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 8 residue 51 SER Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 115 ARG Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Z residue 43 SER Chi-restraints excluded: chain Z residue 83 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 190 optimal weight: 10.0000 chunk 510 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 567 optimal weight: 4.9990 chunk 471 optimal weight: 0.9990 chunk 262 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 7.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN K 99 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 96341 Z= 0.409 Angle : 0.782 8.997 145059 Z= 0.397 Chirality : 0.046 0.398 18644 Planarity : 0.007 0.095 7086 Dihedral : 24.118 179.749 50195 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % Rotamer: Outliers : 4.45 % Allowed : 17.18 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.50 (0.14), residues: 2917 helix: -0.52 (0.17), residues: 770 sheet: -0.80 (0.20), residues: 602 loop : -1.28 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 93 HIS 0.011 0.002 HIS 8 31 PHE 0.020 0.003 PHE 2 30 TYR 0.019 0.003 TYR G 103 ARG 0.008 0.001 ARG T 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 378 time to evaluate : 3.805 Fit side-chains REVERT: 1 37 ARG cc_start: 0.6785 (mtp85) cc_final: 0.6087 (ttm170) REVERT: 2 47 ARG cc_start: 0.6947 (mtp180) cc_final: 0.6608 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7312 (mptm) cc_final: 0.6592 (mtpt) REVERT: 2 52 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6911 (mtt90) REVERT: 3 9 LYS cc_start: 0.7752 (pttp) cc_final: 0.6885 (mmmm) REVERT: 3 21 LYS cc_start: 0.8156 (mttt) cc_final: 0.7736 (mtmt) REVERT: 3 24 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: 3 33 SER cc_start: 0.8301 (m) cc_final: 0.7980 (p) REVERT: 5 23 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6411 (mp10) REVERT: 6 6 THR cc_start: 0.7191 (OUTLIER) cc_final: 0.6595 (m) REVERT: G 216 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7295 (mmtm) REVERT: H 29 GLU cc_start: 0.8168 (tt0) cc_final: 0.7868 (tp30) REVERT: H 71 LYS cc_start: 0.7167 (mmmm) cc_final: 0.6941 (mmmt) REVERT: H 85 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.5424 (t0) REVERT: I 95 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8091 (ptt180) REVERT: I 120 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5346 (mp0) REVERT: I 127 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5865 (tt0) REVERT: J 64 LYS cc_start: 0.4323 (ptpt) cc_final: 0.3622 (tttm) REVERT: J 83 MET cc_start: 0.5569 (OUTLIER) cc_final: 0.4481 (mmp) REVERT: J 102 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4928 (mtmm) REVERT: J 133 ARG cc_start: 0.4121 (OUTLIER) cc_final: 0.3868 (mmm160) REVERT: J 152 MET cc_start: 0.4803 (mmt) cc_final: 0.3937 (mtm) REVERT: K 27 LYS cc_start: 0.4795 (mptt) cc_final: 0.3907 (tppt) REVERT: K 44 LYS cc_start: 0.3921 (mmtm) cc_final: 0.3331 (mmmt) REVERT: K 57 ASP cc_start: 0.5370 (t0) cc_final: 0.4933 (m-30) REVERT: K 83 TYR cc_start: 0.4977 (m-80) cc_final: 0.4754 (m-80) REVERT: K 173 GLU cc_start: 0.4319 (OUTLIER) cc_final: 0.4101 (tm-30) REVERT: M 62 LYS cc_start: 0.8303 (mppt) cc_final: 0.8013 (mmmt) REVERT: M 100 LYS cc_start: 0.8005 (tptp) cc_final: 0.7305 (ttmm) REVERT: N 17 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6441 (mmt180) REVERT: N 18 GLU cc_start: 0.7662 (tt0) cc_final: 0.7376 (tm-30) REVERT: N 72 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7053 (mp10) REVERT: N 81 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: N 105 GLU cc_start: 0.7659 (mp0) cc_final: 0.7381 (mp0) REVERT: P 31 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6847 (tp30) REVERT: P 63 LYS cc_start: 0.6553 (mtpt) cc_final: 0.6061 (tptt) REVERT: P 130 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7595 (ttpt) REVERT: Q 28 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8107 (mp0) REVERT: Q 115 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: R 12 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.7021 (mmmm) REVERT: R 43 GLN cc_start: 0.7026 (mt0) cc_final: 0.6552 (mt0) REVERT: R 71 ASP cc_start: 0.5670 (OUTLIER) cc_final: 0.5304 (t0) REVERT: R 83 ARG cc_start: 0.5300 (mtt180) cc_final: 0.4738 (mmt180) REVERT: S 41 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6563 (pt0) REVERT: S 104 ARG cc_start: 0.7296 (mmp80) cc_final: 0.6987 (mmt180) REVERT: T 78 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7057 (mmtp) REVERT: U 61 LYS cc_start: 0.8023 (pttt) cc_final: 0.7171 (mttm) REVERT: V 64 GLU cc_start: 0.7069 (tt0) cc_final: 0.6579 (pt0) REVERT: W 65 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.6787 (tpt) REVERT: W 67 ARG cc_start: 0.5341 (ptp90) cc_final: 0.5090 (mtm-85) REVERT: X 8 LYS cc_start: 0.6617 (mmmt) cc_final: 0.6151 (tttt) REVERT: X 32 ARG cc_start: 0.6350 (mtp85) cc_final: 0.6113 (mtp180) REVERT: X 69 MET cc_start: 0.7223 (mtp) cc_final: 0.6767 (mtt) REVERT: X 70 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6195 (mt) REVERT: Z 83 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.5461 (t0) outliers start: 111 outliers final: 78 residues processed: 465 average time/residue: 0.9192 time to fit residues: 710.1385 Evaluate side-chains 470 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 370 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 35 LYS Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 24 GLN Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 23 GLN Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 130 LYS Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 115 ARG Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 ASN Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Z residue 43 SER Chi-restraints excluded: chain Z residue 83 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 547 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 478 optimal weight: 0.1980 chunk 317 optimal weight: 10.0000 chunk 565 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 172 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 96341 Z= 0.277 Angle : 0.673 10.751 145059 Z= 0.350 Chirality : 0.041 0.376 18644 Planarity : 0.006 0.082 7086 Dihedral : 24.066 178.571 50195 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Rotamer: Outliers : 4.33 % Allowed : 17.66 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.32 (0.14), residues: 2917 helix: -0.26 (0.18), residues: 772 sheet: -0.78 (0.20), residues: 609 loop : -1.19 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 48 HIS 0.009 0.001 HIS 8 31 PHE 0.017 0.002 PHE 2 30 TYR 0.018 0.002 TYR S 99 ARG 0.007 0.001 ARG M 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 380 time to evaluate : 3.587 Fit side-chains REVERT: 1 37 ARG cc_start: 0.6750 (mtp85) cc_final: 0.6102 (ttm170) REVERT: 2 47 ARG cc_start: 0.6933 (mtp180) cc_final: 0.6599 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7304 (mptm) cc_final: 0.6579 (mtpt) REVERT: 2 52 ARG cc_start: 0.7168 (mtt90) cc_final: 0.6869 (mtt90) REVERT: 3 9 LYS cc_start: 0.7764 (pttp) cc_final: 0.6874 (mmmm) REVERT: 3 21 LYS cc_start: 0.8164 (mttt) cc_final: 0.7768 (mtmt) REVERT: 3 24 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: 3 33 SER cc_start: 0.8317 (m) cc_final: 0.8012 (p) REVERT: 5 23 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.6427 (mp10) REVERT: 6 6 THR cc_start: 0.7202 (t) cc_final: 0.6717 (m) REVERT: G 216 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7307 (mmtm) REVERT: H 9 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7464 (ttmt) REVERT: H 29 GLU cc_start: 0.8130 (tt0) cc_final: 0.7856 (tp30) REVERT: H 71 LYS cc_start: 0.7138 (mmmm) cc_final: 0.6920 (mmmt) REVERT: H 85 ASP cc_start: 0.5602 (OUTLIER) cc_final: 0.5282 (t0) REVERT: I 95 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8061 (ptt180) REVERT: I 120 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5420 (mp0) REVERT: J 64 LYS cc_start: 0.4241 (ptpt) cc_final: 0.3669 (tttm) REVERT: J 83 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.4463 (mmp) REVERT: J 102 LYS cc_start: 0.5621 (OUTLIER) cc_final: 0.5032 (mtmm) REVERT: J 152 MET cc_start: 0.4837 (mmt) cc_final: 0.3965 (mtm) REVERT: K 27 LYS cc_start: 0.4779 (mptt) cc_final: 0.3871 (tppt) REVERT: K 44 LYS cc_start: 0.3914 (mmtm) cc_final: 0.3277 (mmmt) REVERT: K 57 ASP cc_start: 0.5262 (t0) cc_final: 0.4849 (m-30) REVERT: K 83 TYR cc_start: 0.4848 (m-80) cc_final: 0.4644 (m-80) REVERT: M 49 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7783 (tp) REVERT: M 100 LYS cc_start: 0.8031 (tptp) cc_final: 0.7319 (ttmm) REVERT: N 17 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6377 (mmt180) REVERT: N 18 GLU cc_start: 0.7641 (tt0) cc_final: 0.7386 (tt0) REVERT: N 72 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7087 (mp10) REVERT: N 81 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: N 105 GLU cc_start: 0.7659 (mp0) cc_final: 0.7385 (mp0) REVERT: P 31 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6808 (tp30) REVERT: P 63 LYS cc_start: 0.6509 (mtpt) cc_final: 0.6023 (tptt) REVERT: Q 28 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8110 (mp0) REVERT: Q 115 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7970 (ttm110) REVERT: R 43 GLN cc_start: 0.6998 (mt0) cc_final: 0.6532 (mt0) REVERT: R 71 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5410 (t0) REVERT: R 83 ARG cc_start: 0.5302 (mtt180) cc_final: 0.4742 (mmt180) REVERT: S 41 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6523 (pt0) REVERT: S 104 ARG cc_start: 0.7319 (mmp80) cc_final: 0.7040 (mmt180) REVERT: S 112 GLU cc_start: 0.6194 (tt0) cc_final: 0.5614 (mp0) REVERT: T 78 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7088 (mmtp) REVERT: U 1 MET cc_start: 0.7072 (ttt) cc_final: 0.6754 (tpp) REVERT: U 61 LYS cc_start: 0.8004 (pttt) cc_final: 0.7156 (mttm) REVERT: V 64 GLU cc_start: 0.7030 (tt0) cc_final: 0.6535 (pt0) REVERT: W 65 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6926 (tpt) REVERT: W 67 ARG cc_start: 0.5336 (ptp90) cc_final: 0.5053 (mtm-85) REVERT: X 8 LYS cc_start: 0.6600 (mmmt) cc_final: 0.6182 (tttt) REVERT: X 10 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6824 (tttt) REVERT: X 32 ARG cc_start: 0.6343 (mtp85) cc_final: 0.6034 (mtp180) REVERT: X 69 MET cc_start: 0.7140 (mtp) cc_final: 0.6678 (mtt) REVERT: X 70 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6183 (mt) REVERT: Z 76 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7495 (tpp-160) REVERT: Z 83 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.5434 (t0) outliers start: 108 outliers final: 72 residues processed: 463 average time/residue: 0.9467 time to fit residues: 727.3054 Evaluate side-chains 459 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 368 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 24 GLN Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 23 GLN Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 115 ARG Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 10 LYS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Z residue 43 SER Chi-restraints excluded: chain Z residue 83 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 350 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 172 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN T 52 GLN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 96341 Z= 0.442 Angle : 0.822 9.640 145059 Z= 0.414 Chirality : 0.048 0.437 18644 Planarity : 0.007 0.103 7086 Dihedral : 24.169 179.944 50195 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.90 % Favored : 93.97 % Rotamer: Outliers : 4.69 % Allowed : 17.78 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.57 (0.14), residues: 2917 helix: -0.53 (0.17), residues: 763 sheet: -0.86 (0.20), residues: 592 loop : -1.34 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 93 HIS 0.010 0.002 HIS 8 31 PHE 0.022 0.003 PHE 2 30 TYR 0.021 0.003 TYR 5 36 ARG 0.007 0.001 ARG T 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 377 time to evaluate : 3.632 Fit side-chains REVERT: 1 37 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6119 (ttm170) REVERT: 2 47 ARG cc_start: 0.7016 (mtp180) cc_final: 0.6631 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7275 (mptm) cc_final: 0.6635 (mtpt) REVERT: 3 9 LYS cc_start: 0.7764 (pttp) cc_final: 0.6889 (mmmm) REVERT: 3 21 LYS cc_start: 0.8192 (mttt) cc_final: 0.7760 (mtmt) REVERT: 3 24 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: 3 33 SER cc_start: 0.8312 (m) cc_final: 0.7991 (p) REVERT: 5 23 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6418 (mp10) REVERT: 6 6 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6607 (m) REVERT: G 216 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7300 (mmtm) REVERT: H 9 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7491 (ttmt) REVERT: H 29 GLU cc_start: 0.8161 (tt0) cc_final: 0.7880 (tp30) REVERT: H 71 LYS cc_start: 0.7134 (mmmm) cc_final: 0.6907 (mmmt) REVERT: H 85 ASP cc_start: 0.5847 (OUTLIER) cc_final: 0.5546 (t0) REVERT: I 95 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8102 (ptt180) REVERT: I 120 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5401 (mp0) REVERT: I 127 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5930 (tt0) REVERT: J 64 LYS cc_start: 0.4461 (ptpt) cc_final: 0.3822 (tttm) REVERT: J 83 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.4697 (mmp) REVERT: J 102 LYS cc_start: 0.5517 (OUTLIER) cc_final: 0.4992 (mtmm) REVERT: J 115 ARG cc_start: 0.2029 (OUTLIER) cc_final: 0.1299 (ptm-80) REVERT: J 152 MET cc_start: 0.4581 (mmt) cc_final: 0.3667 (mtm) REVERT: K 27 LYS cc_start: 0.4775 (mptt) cc_final: 0.3852 (tppt) REVERT: K 44 LYS cc_start: 0.3916 (mmtm) cc_final: 0.3242 (mtpp) REVERT: K 57 ASP cc_start: 0.5468 (t0) cc_final: 0.5021 (m-30) REVERT: K 83 TYR cc_start: 0.4862 (m-80) cc_final: 0.4637 (m-80) REVERT: K 173 GLU cc_start: 0.4272 (OUTLIER) cc_final: 0.4005 (tm-30) REVERT: M 49 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7792 (tp) REVERT: M 62 LYS cc_start: 0.8307 (mppt) cc_final: 0.8023 (mmmt) REVERT: M 100 LYS cc_start: 0.8018 (tptp) cc_final: 0.7307 (ttmm) REVERT: N 17 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6418 (mmt180) REVERT: N 18 GLU cc_start: 0.7681 (tt0) cc_final: 0.7393 (tm-30) REVERT: N 81 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: N 105 GLU cc_start: 0.7662 (mp0) cc_final: 0.7387 (mp0) REVERT: P 31 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6816 (tp30) REVERT: P 63 LYS cc_start: 0.6565 (mtpt) cc_final: 0.6071 (tptt) REVERT: Q 28 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8090 (mp0) REVERT: Q 115 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8065 (ttm170) REVERT: R 12 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6975 (mtpp) REVERT: R 43 GLN cc_start: 0.7034 (mt0) cc_final: 0.6819 (mt0) REVERT: R 71 ASP cc_start: 0.5679 (OUTLIER) cc_final: 0.5294 (t0) REVERT: R 83 ARG cc_start: 0.5212 (mtt180) cc_final: 0.4652 (mmt-90) REVERT: S 104 ARG cc_start: 0.7292 (mmp80) cc_final: 0.7005 (mmt180) REVERT: S 112 GLU cc_start: 0.6297 (tt0) cc_final: 0.5649 (mp0) REVERT: T 78 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7080 (mmtp) REVERT: U 1 MET cc_start: 0.7031 (ttt) cc_final: 0.6605 (tpp) REVERT: U 61 LYS cc_start: 0.8057 (pttt) cc_final: 0.7147 (mttm) REVERT: V 64 GLU cc_start: 0.7062 (tt0) cc_final: 0.6579 (pt0) REVERT: W 65 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7387 (tpp) REVERT: W 67 ARG cc_start: 0.5374 (ptp90) cc_final: 0.5101 (mtm-85) REVERT: X 8 LYS cc_start: 0.6660 (mmmt) cc_final: 0.6204 (tttt) REVERT: X 10 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6828 (tttt) REVERT: X 32 ARG cc_start: 0.6386 (mtp85) cc_final: 0.6073 (mtp180) REVERT: X 40 MET cc_start: 0.8221 (mmm) cc_final: 0.7859 (mmm) REVERT: X 69 MET cc_start: 0.7251 (mtp) cc_final: 0.6796 (mtt) REVERT: X 70 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6297 (mt) REVERT: Z 83 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.5518 (t0) outliers start: 117 outliers final: 86 residues processed: 469 average time/residue: 0.9509 time to fit residues: 740.8712 Evaluate side-chains 477 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 368 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 24 GLN Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 23 GLN Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 130 LYS Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 115 ARG Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 10 LYS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Z residue 43 SER Chi-restraints excluded: chain Z residue 83 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 514 optimal weight: 3.9990 chunk 542 optimal weight: 4.9990 chunk 494 optimal weight: 5.9990 chunk 527 optimal weight: 5.9990 chunk 541 optimal weight: 5.9990 chunk 317 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 414 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 476 optimal weight: 4.9990 chunk 498 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 41 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN N 109 ASN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 96341 Z= 0.250 Angle : 0.648 9.488 145059 Z= 0.336 Chirality : 0.039 0.379 18644 Planarity : 0.005 0.063 7086 Dihedral : 24.013 177.031 50195 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 4.08 % Allowed : 18.50 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.25 (0.14), residues: 2917 helix: -0.10 (0.18), residues: 764 sheet: -0.77 (0.20), residues: 612 loop : -1.19 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 48 HIS 0.008 0.001 HIS 8 31 PHE 0.016 0.002 PHE T 57 TYR 0.014 0.002 TYR 4 9 ARG 0.006 0.001 ARG Z 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 385 time to evaluate : 3.639 Fit side-chains REVERT: 1 37 ARG cc_start: 0.6775 (mtp85) cc_final: 0.6169 (ttm170) REVERT: 2 42 ARG cc_start: 0.7012 (tpt90) cc_final: 0.6792 (tpt90) REVERT: 2 47 ARG cc_start: 0.7018 (mtp180) cc_final: 0.6644 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7251 (mptm) cc_final: 0.6497 (mtpt) REVERT: 2 52 ARG cc_start: 0.7229 (mtt90) cc_final: 0.6891 (mtt90) REVERT: 3 9 LYS cc_start: 0.7762 (pttp) cc_final: 0.6864 (mmmm) REVERT: 3 21 LYS cc_start: 0.8147 (mttt) cc_final: 0.7751 (mtmt) REVERT: 3 33 SER cc_start: 0.8330 (m) cc_final: 0.8053 (p) REVERT: 5 23 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6408 (mp10) REVERT: 6 6 THR cc_start: 0.7173 (OUTLIER) cc_final: 0.6626 (m) REVERT: G 216 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7307 (mmtm) REVERT: H 29 GLU cc_start: 0.8123 (tt0) cc_final: 0.7838 (tp30) REVERT: I 95 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8037 (ptt180) REVERT: I 120 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5462 (mp0) REVERT: I 127 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5753 (tt0) REVERT: J 64 LYS cc_start: 0.4370 (ptpt) cc_final: 0.3853 (tttm) REVERT: J 83 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.4424 (mmp) REVERT: J 148 LYS cc_start: 0.3839 (tptp) cc_final: 0.3413 (tppt) REVERT: J 152 MET cc_start: 0.4720 (mmt) cc_final: 0.3832 (mtm) REVERT: K 27 LYS cc_start: 0.4828 (mptt) cc_final: 0.3900 (tppt) REVERT: K 44 LYS cc_start: 0.4024 (mmtm) cc_final: 0.3293 (mtpp) REVERT: K 57 ASP cc_start: 0.5326 (t0) cc_final: 0.4865 (m-30) REVERT: K 62 ARG cc_start: 0.6629 (mtp180) cc_final: 0.6294 (ttp-170) REVERT: K 173 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.4013 (tm-30) REVERT: M 44 GLN cc_start: 0.7736 (mp10) cc_final: 0.7140 (mt0) REVERT: M 49 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7723 (tp) REVERT: M 100 LYS cc_start: 0.7991 (tptp) cc_final: 0.7268 (ttmm) REVERT: N 17 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6450 (mmt180) REVERT: N 18 GLU cc_start: 0.7636 (tt0) cc_final: 0.7381 (tt0) REVERT: N 81 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: N 105 GLU cc_start: 0.7646 (mp0) cc_final: 0.7364 (mp0) REVERT: P 31 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6787 (tp30) REVERT: P 63 LYS cc_start: 0.6484 (mtpt) cc_final: 0.6001 (tptt) REVERT: Q 28 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8106 (mp0) REVERT: Q 115 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8110 (ttm110) REVERT: R 43 GLN cc_start: 0.7014 (mt0) cc_final: 0.6563 (mt0) REVERT: R 71 ASP cc_start: 0.5688 (OUTLIER) cc_final: 0.5384 (t0) REVERT: R 83 ARG cc_start: 0.5296 (mtt180) cc_final: 0.4718 (mmt-90) REVERT: S 104 ARG cc_start: 0.7284 (mmp80) cc_final: 0.7020 (mmt180) REVERT: S 112 GLU cc_start: 0.6212 (tt0) cc_final: 0.5600 (mp0) REVERT: T 78 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7084 (mmtp) REVERT: U 1 MET cc_start: 0.7089 (ttt) cc_final: 0.6776 (tpp) REVERT: U 61 LYS cc_start: 0.8003 (pttt) cc_final: 0.7107 (mttm) REVERT: V 64 GLU cc_start: 0.7060 (tt0) cc_final: 0.6550 (pt0) REVERT: W 65 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6939 (tpt) REVERT: W 67 ARG cc_start: 0.5228 (ptp90) cc_final: 0.5005 (mtm-85) REVERT: X 8 LYS cc_start: 0.6623 (mmmt) cc_final: 0.6192 (tttt) REVERT: X 32 ARG cc_start: 0.6328 (mtp85) cc_final: 0.6016 (mtp180) REVERT: X 69 MET cc_start: 0.7183 (mtp) cc_final: 0.6731 (mtt) REVERT: X 78 PRO cc_start: 0.7366 (Cg_exo) cc_final: 0.7111 (Cg_endo) REVERT: Z 76 ARG cc_start: 0.7756 (mmt180) cc_final: 0.7487 (tpp-160) outliers start: 102 outliers final: 79 residues processed: 461 average time/residue: 0.9340 time to fit residues: 723.2548 Evaluate side-chains 465 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 372 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 23 GLN Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 115 ARG Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Z residue 43 SER Chi-restraints excluded: chain Z residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 525 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 557 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 387 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 538 optimal weight: 4.9990 chunk 465 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 96341 Z= 0.361 Angle : 0.741 10.377 145059 Z= 0.378 Chirality : 0.044 0.418 18644 Planarity : 0.006 0.083 7086 Dihedral : 24.084 178.990 50195 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.35 % Favored : 94.51 % Rotamer: Outliers : 4.16 % Allowed : 18.78 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.38 (0.14), residues: 2917 helix: -0.25 (0.18), residues: 759 sheet: -0.81 (0.20), residues: 593 loop : -1.27 (0.14), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 93 HIS 0.009 0.002 HIS 8 31 PHE 0.019 0.002 PHE 2 30 TYR 0.023 0.003 TYR 5 36 ARG 0.011 0.001 ARG N 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 371 time to evaluate : 3.602 Fit side-chains REVERT: 1 37 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6165 (ttm170) REVERT: 2 47 ARG cc_start: 0.7011 (mtp180) cc_final: 0.6632 (mtm-85) REVERT: 2 48 LYS cc_start: 0.7319 (mptm) cc_final: 0.6628 (mtpt) REVERT: 3 9 LYS cc_start: 0.7785 (pttp) cc_final: 0.6895 (mmmm) REVERT: 3 21 LYS cc_start: 0.8206 (mttt) cc_final: 0.7775 (mtmt) REVERT: 3 33 SER cc_start: 0.8297 (m) cc_final: 0.7999 (p) REVERT: 5 23 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.6414 (mp10) REVERT: 6 6 THR cc_start: 0.7156 (OUTLIER) cc_final: 0.6633 (m) REVERT: G 216 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7328 (mmtm) REVERT: H 9 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7491 (ttmt) REVERT: H 29 GLU cc_start: 0.8164 (tt0) cc_final: 0.7880 (tp30) REVERT: I 95 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8107 (ptt180) REVERT: I 120 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5401 (mp0) REVERT: I 127 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5935 (tt0) REVERT: J 64 LYS cc_start: 0.4587 (ptpt) cc_final: 0.3924 (tttm) REVERT: J 83 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.4510 (mmp) REVERT: J 115 ARG cc_start: 0.1903 (OUTLIER) cc_final: 0.1241 (ptm-80) REVERT: J 148 LYS cc_start: 0.3912 (tptp) cc_final: 0.3404 (tppt) REVERT: J 152 MET cc_start: 0.4599 (mmt) cc_final: 0.3735 (mtm) REVERT: K 27 LYS cc_start: 0.4781 (mptt) cc_final: 0.3861 (tppt) REVERT: K 44 LYS cc_start: 0.4049 (mmtm) cc_final: 0.3301 (mtpp) REVERT: K 57 ASP cc_start: 0.5382 (t0) cc_final: 0.4960 (m-30) REVERT: K 173 GLU cc_start: 0.4212 (OUTLIER) cc_final: 0.3937 (tm-30) REVERT: M 49 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7794 (tp) REVERT: M 100 LYS cc_start: 0.8026 (tptp) cc_final: 0.7312 (ttmm) REVERT: N 17 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6472 (mmt180) REVERT: N 18 GLU cc_start: 0.7665 (tt0) cc_final: 0.7384 (tm-30) REVERT: N 81 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: N 105 GLU cc_start: 0.7632 (mp0) cc_final: 0.7341 (mp0) REVERT: P 31 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6812 (tp30) REVERT: P 63 LYS cc_start: 0.6508 (mtpt) cc_final: 0.6021 (tptt) REVERT: Q 28 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8092 (mp0) REVERT: Q 115 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8011 (ttm110) REVERT: R 12 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6827 (mmmm) REVERT: R 43 GLN cc_start: 0.7020 (mt0) cc_final: 0.6805 (mt0) REVERT: R 71 ASP cc_start: 0.5676 (OUTLIER) cc_final: 0.5337 (t0) REVERT: R 83 ARG cc_start: 0.5225 (mtt180) cc_final: 0.4673 (mmt-90) REVERT: S 104 ARG cc_start: 0.7333 (mmp80) cc_final: 0.7037 (mmt180) REVERT: S 112 GLU cc_start: 0.6251 (tt0) cc_final: 0.5640 (mp0) REVERT: T 78 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7087 (mmtp) REVERT: U 1 MET cc_start: 0.7067 (ttt) cc_final: 0.6681 (tpp) REVERT: U 61 LYS cc_start: 0.8033 (pttt) cc_final: 0.7122 (mttm) REVERT: V 64 GLU cc_start: 0.7046 (tt0) cc_final: 0.6551 (pt0) REVERT: W 65 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7421 (tpp) REVERT: W 67 ARG cc_start: 0.5362 (ptp90) cc_final: 0.5097 (mtm-85) REVERT: X 8 LYS cc_start: 0.6624 (mmmt) cc_final: 0.6179 (tttt) REVERT: X 32 ARG cc_start: 0.6360 (mtp85) cc_final: 0.6050 (mtp180) REVERT: X 69 MET cc_start: 0.7178 (mtp) cc_final: 0.6717 (mtt) outliers start: 104 outliers final: 81 residues processed: 454 average time/residue: 0.9311 time to fit residues: 700.8291 Evaluate side-chains 469 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 371 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 5 residue 23 GLN Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 CYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 12 GLU Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 130 LYS Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 115 ARG Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 78 LYS Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Z residue 43 SER Chi-restraints excluded: chain Z residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 285 optimal weight: 10.0000 chunk 369 optimal weight: 5.9990 chunk 496 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 429 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 466 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 478 optimal weight: 0.0770 chunk 59 optimal weight: 10.0000 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN O 27 ASN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106255 restraints weight = 136619.833| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.69 r_work: 0.3034 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 96341 Z= 0.207 Angle : 0.613 10.554 145059 Z= 0.320 Chirality : 0.038 0.374 18644 Planarity : 0.005 0.060 7086 Dihedral : 23.981 178.223 50195 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Rotamer: Outliers : 3.80 % Allowed : 19.38 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.11 (0.14), residues: 2917 helix: 0.09 (0.18), residues: 758 sheet: -0.71 (0.20), residues: 606 loop : -1.13 (0.14), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 48 HIS 0.008 0.001 HIS 8 31 PHE 0.014 0.002 PHE 2 30 TYR 0.015 0.002 TYR 5 36 ARG 0.009 0.000 ARG N 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15185.39 seconds wall clock time: 272 minutes 33.96 seconds (16353.96 seconds total)