Starting phenix.real_space_refine on Tue Feb 20 11:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syx_25544/02_2024/7syx_25544_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syx_25544/02_2024/7syx_25544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syx_25544/02_2024/7syx_25544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syx_25544/02_2024/7syx_25544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syx_25544/02_2024/7syx_25544_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syx_25544/02_2024/7syx_25544_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1961 5.49 5 Mg 1 5.21 5 S 209 5.16 5 C 47048 2.51 5 N 15904 2.21 5 O 21620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "H TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 39": "OD1" <-> "OD2" Residue "H TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 103": "OD1" <-> "OD2" Residue "H ASP 152": "OD1" <-> "OD2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 138": "OE1" <-> "OE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K ASP 158": "OD1" <-> "OD2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 32": "OD1" <-> "OD2" Residue "O ASP 83": "OD1" <-> "OD2" Residue "Q TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 114": "OE1" <-> "OE2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "Y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 39": "OE1" <-> "OE2" Residue "Z TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d ASP 54": "OD1" <-> "OD2" Residue "e PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 144": "OD1" <-> "OD2" Residue "h ASP 231": "OD1" <-> "OD2" Residue "x GLU 600": "OE1" <-> "OE2" Residue "x ASP 767": "OD1" <-> "OD2" Residue "x PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 852": "OE1" <-> "OE2" Residue "x GLU 910": "OE1" <-> "OE2" Residue "x GLU 924": "OE1" <-> "OE2" Residue "x GLU 994": "OE1" <-> "OE2" Residue "x PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 1154": "OE1" <-> "OE2" Residue "x PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 1210": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 86744 Number of models: 1 Model: "" Number of chains: 41 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 112, 'rna3p_pur': 754, 'rna3p_pyr': 688} Link IDs: {'rna2p': 254, 'rna3p': 1442} Chain breaks: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 798 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2073 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} bond proxies already assigned to first conformer: 1709 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 628 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "i" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "x" Number of atoms: 4965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4965 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 598} Chain: "z" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 4017 Classifications: {'RNA': 188} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 17, 'rna3p_pur': 79, 'rna3p_pyr': 74} Link IDs: {'rna2p': 35, 'rna3p': 152} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 70164 SG CYS b 23 93.234 130.493 134.297 1.00 24.89 S ATOM 70185 SG CYS b 26 96.877 131.069 136.876 1.00 23.63 S ATOM 70565 SG CYS b 74 94.930 128.233 135.460 1.00 26.37 S ATOM 70584 SG CYS b 77 95.380 129.441 137.511 1.00 26.76 S Time building chain proxies: 33.32, per 1000 atoms: 0.38 Number of scatterers: 86744 At special positions: 0 Unit cell: (240.35, 195.7, 262.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 209 16.00 P 1961 15.00 Mg 1 11.99 O 21620 8.00 N 15904 7.00 C 47048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS g 141 " - pdb=" SG CYS g 144 " distance=2.03 Simple disulfide: pdb=" SG CYS x 633 " - pdb=" SG CYS x 718 " distance=2.03 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: 31.98 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " Number of angles added : 6 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 62 sheets defined 28.5% alpha, 14.6% beta 510 base pairs and 1023 stacking pairs defined. Time for finding SS restraints: 31.45 Creating SS restraints... Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.992A pdb=" N GLN B 84 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ARG B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 86 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 87 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 168 through 186 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'C' and resid 24 through 27 removed outlier: 3.930A pdb=" N LYS C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 27' Processing helix chain 'C' and resid 58 through 61 No H-bonds generated for 'chain 'C' and resid 58 through 61' Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 158 through 177 removed outlier: 4.003A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 189 removed outlier: 3.642A pdb=" N ILE C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 148 through 160 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.526A pdb=" N LYS D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 265 through 276 removed outlier: 6.515A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 98 through 111 Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'F' and resid 16 through 18 No H-bonds generated for 'chain 'F' and resid 16 through 18' Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 58 through 66 removed outlier: 3.819A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 262 Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 68 through 76 Processing helix chain 'G' and resid 87 through 104 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 143 through 161 Processing helix chain 'G' and resid 169 through 182 removed outlier: 5.446A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 202 Processing helix chain 'H' and resid 21 through 24 Processing helix chain 'H' and resid 138 through 144 Processing helix chain 'H' and resid 182 through 236 Processing helix chain 'I' and resid 18 through 32 Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'I' and resid 66 through 74 removed outlier: 4.153A pdb=" N LYS I 70 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN I 73 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS I 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 86 removed outlier: 4.122A pdb=" N VAL I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 120 No H-bonds generated for 'chain 'I' and resid 118 through 120' Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 170 through 180 Processing helix chain 'J' and resid 107 through 116 Processing helix chain 'J' and resid 134 through 138 Processing helix chain 'J' and resid 143 through 152 Processing helix chain 'J' and resid 160 through 168 Processing helix chain 'J' and resid 193 through 206 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 40 through 61 Processing helix chain 'K' and resid 68 through 84 Processing helix chain 'K' and resid 102 through 106 Processing helix chain 'K' and resid 110 through 117 Processing helix chain 'K' and resid 123 through 131 Processing helix chain 'K' and resid 154 through 156 No H-bonds generated for 'chain 'K' and resid 154 through 156' Processing helix chain 'K' and resid 172 through 185 Processing helix chain 'L' and resid 5 through 17 Processing helix chain 'L' and resid 42 through 55 Processing helix chain 'L' and resid 73 through 82 Processing helix chain 'M' and resid 48 through 52 removed outlier: 4.150A pdb=" N GLU M 52 " --> pdb=" O GLU M 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 27 Processing helix chain 'N' and resid 36 through 43 Processing helix chain 'N' and resid 61 through 69 Processing helix chain 'N' and resid 82 through 85 removed outlier: 3.750A pdb=" N LEU N 85 " --> pdb=" O ASN N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 85' Processing helix chain 'N' and resid 119 through 128 Processing helix chain 'O' and resid 30 through 42 Processing helix chain 'O' and resid 47 through 57 Processing helix chain 'O' and resid 71 through 78 Processing helix chain 'O' and resid 86 through 102 Processing helix chain 'O' and resid 110 through 131 Processing helix chain 'O' and resid 143 through 145 No H-bonds generated for 'chain 'O' and resid 143 through 145' Processing helix chain 'P' and resid 65 through 67 No H-bonds generated for 'chain 'P' and resid 65 through 67' Processing helix chain 'P' and resid 71 through 88 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'Q' and resid 22 through 26 Processing helix chain 'Q' and resid 30 through 36 Processing helix chain 'Q' and resid 39 through 45 Processing helix chain 'Q' and resid 55 through 65 Processing helix chain 'Q' and resid 116 through 119 removed outlier: 3.550A pdb=" N PHE Q 119 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 116 through 119' Processing helix chain 'R' and resid 45 through 58 removed outlier: 4.622A pdb=" N TYR R 49 " --> pdb=" O THR R 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU R 53 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 78 through 99 removed outlier: 4.131A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 115 removed outlier: 4.311A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 119 No H-bonds generated for 'chain 'R' and resid 117 through 119' Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'S' and resid 28 through 37 Processing helix chain 'S' and resid 44 through 61 Processing helix chain 'S' and resid 77 through 81 Processing helix chain 'S' and resid 100 through 109 Processing helix chain 'T' and resid 30 through 32 No H-bonds generated for 'chain 'T' and resid 30 through 32' Processing helix chain 'T' and resid 40 through 47 removed outlier: 3.672A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 58 No H-bonds generated for 'chain 'T' and resid 56 through 58' Processing helix chain 'T' and resid 61 through 72 Processing helix chain 'T' and resid 81 through 83 No H-bonds generated for 'chain 'T' and resid 81 through 83' Processing helix chain 'T' and resid 100 through 117 Processing helix chain 'T' and resid 120 through 127 Processing helix chain 'U' and resid 6 through 8 No H-bonds generated for 'chain 'U' and resid 6 through 8' Processing helix chain 'U' and resid 11 through 25 removed outlier: 3.855A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 66 Processing helix chain 'U' and resid 72 through 76 Processing helix chain 'U' and resid 97 through 109 Processing helix chain 'U' and resid 125 through 142 Processing helix chain 'V' and resid 30 through 45 Processing helix chain 'V' and resid 95 through 102 Processing helix chain 'W' and resid 57 through 62 Processing helix chain 'W' and resid 65 through 76 Processing helix chain 'X' and resid 6 through 20 Processing helix chain 'X' and resid 32 through 43 Processing helix chain 'X' and resid 85 through 92 removed outlier: 3.522A pdb=" N ASN X 92 " --> pdb=" O TRP X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 118 Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 26 through 30 Processing helix chain 'Y' and resid 33 through 37 Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 37 through 47 Processing helix chain 'Z' and resid 79 through 84 Processing helix chain 'Z' and resid 88 through 93 Processing helix chain 'Z' and resid 104 through 115 Processing helix chain 'Z' and resid 120 through 125 removed outlier: 3.779A pdb=" N VAL Z 125 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 64 removed outlier: 4.309A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Proline residue: a 63 - end of helix Processing helix chain 'a' and resid 70 through 77 Processing helix chain 'a' and resid 81 through 93 Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 75 through 80 Processing helix chain 'c' and resid 12 through 17 Processing helix chain 'e' and resid 3 through 6 No H-bonds generated for 'chain 'e' and resid 3 through 6' Processing helix chain 'e' and resid 33 through 35 No H-bonds generated for 'chain 'e' and resid 33 through 35' Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'e' and resid 47 through 50 No H-bonds generated for 'chain 'e' and resid 47 through 50' Processing helix chain 'f' and resid 84 through 87 No H-bonds generated for 'chain 'f' and resid 84 through 87' Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 102 through 104 No H-bonds generated for 'chain 'g' and resid 102 through 104' Processing helix chain 'n' and resid 3 through 23 Processing helix chain 'x' and resid 600 through 619 removed outlier: 4.102A pdb=" N TYR x 604 " --> pdb=" O GLU x 600 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP x 605 " --> pdb=" O GLU x 601 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS x 606 " --> pdb=" O ARG x 602 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA x 607 " --> pdb=" O ALA x 603 " (cutoff:3.500A) Processing helix chain 'x' and resid 642 through 650 Processing helix chain 'x' and resid 654 through 657 No H-bonds generated for 'chain 'x' and resid 654 through 657' Processing helix chain 'x' and resid 673 through 678 Processing helix chain 'x' and resid 711 through 714 No H-bonds generated for 'chain 'x' and resid 711 through 714' Processing helix chain 'x' and resid 733 through 745 Processing helix chain 'x' and resid 770 through 773 No H-bonds generated for 'chain 'x' and resid 770 through 773' Processing helix chain 'x' and resid 779 through 799 Processing helix chain 'x' and resid 829 through 843 Processing helix chain 'x' and resid 959 through 965 Processing helix chain 'x' and resid 986 through 998 Processing helix chain 'x' and resid 1013 through 1022 Processing helix chain 'x' and resid 1027 through 1029 No H-bonds generated for 'chain 'x' and resid 1027 through 1029' Processing helix chain 'x' and resid 1041 through 1048 Processing helix chain 'x' and resid 1060 through 1082 Processing helix chain 'x' and resid 1186 through 1194 Processing helix chain 'x' and resid 1196 through 1199 Processing helix chain 'x' and resid 1202 through 1214 Processing sheet with id= A, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.580A pdb=" N GLN A 37 " --> pdb=" O MET A 50 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU A 48 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 49 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 57 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 90 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 78 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 121 through 123 removed outlier: 6.152A pdb=" N THR B 97 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 78 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 99 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.365A pdb=" N ILE B 159 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS B 148 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE B 161 " --> pdb=" O CYS B 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.515A pdb=" N ASP C 29 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 49 " --> pdb=" O ASP C 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 32 through 34 Processing sheet with id= F, first strand: chain 'C' and resid 66 through 70 removed outlier: 5.456A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 121 through 125 removed outlier: 3.537A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 137 through 144 removed outlier: 3.609A pdb=" N LYS D 142 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.854A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 86 through 90 removed outlier: 8.622A pdb=" N TYR E 87 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE E 48 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLU E 89 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE E 50 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 45 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 42 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU E 47 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE E 49 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU E 38 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.670A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS E 134 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 186 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 188 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 70 through 72 Processing sheet with id= M, first strand: chain 'F' and resid 121 through 125 removed outlier: 3.870A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 180 through 182 removed outlier: 6.582A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 126 through 131 removed outlier: 6.765A pdb=" N VAL F 140 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE F 129 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS F 138 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 123 through 127 Processing sheet with id= Q, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.540A pdb=" N VAL H 112 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG H 51 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR H 34 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.504A pdb=" N VAL H 73 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.789A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU H 162 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG H 170 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 55 through 57 removed outlier: 3.779A pdb=" N ASN H 56 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL H 108 " --> pdb=" O ASN H 56 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 47 through 51 removed outlier: 3.787A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS I 91 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE I 62 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL I 93 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL I 64 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE I 95 " --> pdb=" O VAL I 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 184 through 188 removed outlier: 4.468A pdb=" N ASP I 184 " --> pdb=" O ARG I 152 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.569A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 187 through 189 removed outlier: 6.586A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.986A pdb=" N HIS J 44 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA J 57 " --> pdb=" O HIS J 44 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL J 46 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR J 55 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.509A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 109 through 112 removed outlier: 3.636A pdb=" N VAL M 87 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS M 79 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG M 89 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL M 77 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 91 through 95 Processing sheet with id= AC, first strand: chain 'N' and resid 31 through 33 removed outlier: 3.647A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.414A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA P 92 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS P 31 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS P 94 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE P 33 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS P 96 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA P 35 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG P 98 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU P 130 " --> pdb=" O ILE P 95 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Q' and resid 76 through 78 removed outlier: 3.743A pdb=" N VAL Q 76 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 9 through 12 removed outlier: 3.511A pdb=" N THR R 20 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU R 31 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N VAL R 70 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N VAL R 72 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.752A pdb=" N VAL T 15 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 81 through 83 Processing sheet with id= AI, first strand: chain 'U' and resid 113 through 116 removed outlier: 3.555A pdb=" N GLY U 120 " --> pdb=" O ASP U 116 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 85 through 91 removed outlier: 3.637A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU V 91 " --> pdb=" O ILE V 20 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR V 23 " --> pdb=" O GLU V 113 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU V 113 " --> pdb=" O THR V 23 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 63 through 66 removed outlier: 3.504A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 32 through 37 removed outlier: 3.645A pdb=" N ILE W 55 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 24 through 27 removed outlier: 3.863A pdb=" N VAL X 25 " --> pdb=" O VAL X 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL X 63 " --> pdb=" O VAL X 25 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'X' and resid 71 through 74 removed outlier: 6.965A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Y' and resid 80 through 84 removed outlier: 3.632A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Z' and resid 5 through 10 removed outlier: 3.643A pdb=" N THR Z 6 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Z 28 " --> pdb=" O THR Z 6 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG Z 8 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP Z 26 " --> pdb=" O ARG Z 8 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE Z 75 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET Z 23 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY Z 73 " --> pdb=" O MET Z 23 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Z' and resid 13 through 15 Processing sheet with id= AR, first strand: chain 'a' and resid 98 through 101 removed outlier: 3.520A pdb=" N LYS a 98 " --> pdb=" O THR a 110 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL a 100 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'b' and resid 20 through 22 Processing sheet with id= AT, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.517A pdb=" N ILE b 36 " --> pdb=" O TYR b 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR b 73 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'c' and resid 32 through 36 Processing sheet with id= AV, first strand: chain 'd' and resid 55 through 58 removed outlier: 6.744A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 138 through 140 Processing sheet with id= AX, first strand: chain 'h' and resid 5 through 7 Processing sheet with id= AY, first strand: chain 'h' and resid 18 through 23 removed outlier: 6.696A pdb=" N ALA h 34 " --> pdb=" O THR h 19 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE h 21 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU h 32 " --> pdb=" O ILE h 21 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N THR h 23 " --> pdb=" O MET h 30 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N MET h 30 " --> pdb=" O THR h 23 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE h 41 " --> pdb=" O SER h 33 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG h 57 " --> pdb=" O MET h 42 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'h' and resid 66 through 71 removed outlier: 6.631A pdb=" N GLY h 81 " --> pdb=" O SER h 67 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL h 69 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU h 79 " --> pdb=" O VAL h 69 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE h 71 " --> pdb=" O PHE h 77 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE h 77 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP h 91 " --> pdb=" O THR h 97 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR h 97 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'h' and resid 129 through 132 removed outlier: 4.441A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'h' and resid 151 through 156 removed outlier: 6.782A pdb=" N CYS h 168 " --> pdb=" O SER h 152 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL h 154 " --> pdb=" O VAL h 166 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL h 166 " --> pdb=" O VAL h 154 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE h 165 " --> pdb=" O TRP h 177 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP h 177 " --> pdb=" O ILE h 165 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY h 169 " --> pdb=" O LEU h 173 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU h 173 " --> pdb=" O GLY h 169 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'h' and resid 195 through 200 removed outlier: 6.832A pdb=" N GLY h 210 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL h 198 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA h 208 " --> pdb=" O VAL h 198 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL h 200 " --> pdb=" O LEU h 206 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU h 206 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP h 220 " --> pdb=" O HIS h 226 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS h 226 " --> pdb=" O ASP h 220 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'h' and resid 239 through 241 removed outlier: 4.605A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP h 259 " --> pdb=" O LEU h 248 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE h 256 " --> pdb=" O LEU h 270 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'x' and resid 817 through 820 removed outlier: 4.583A pdb=" N SER x 817 " --> pdb=" O PHE x 749 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA x 721 " --> pdb=" O ILE x 750 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA x 752 " --> pdb=" O ALA x 721 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU x 723 " --> pdb=" O ALA x 752 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASN x 754 " --> pdb=" O LEU x 723 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL x 725 " --> pdb=" O ASN x 754 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU x 697 " --> pdb=" O ILE x 632 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL x 634 " --> pdb=" O LEU x 697 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE x 699 " --> pdb=" O VAL x 634 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'x' and resid 927 through 931 removed outlier: 3.659A pdb=" N VAL x 929 " --> pdb=" O VAL x 873 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY x 868 " --> pdb=" O LEU x 864 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE x 874 " --> pdb=" O VAL x 858 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL x 858 " --> pdb=" O ILE x 874 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'x' and resid 893 through 898 removed outlier: 3.843A pdb=" N GLY x 893 " --> pdb=" O GLY x 890 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR x 885 " --> pdb=" O ALA x 948 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA x 948 " --> pdb=" O THR x 885 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE x 887 " --> pdb=" O LEU x 946 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU x 946 " --> pdb=" O ILE x 887 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'x' and resid 902 through 904 removed outlier: 4.325A pdb=" N LEU x 902 " --> pdb=" O HIS x 920 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS x 920 " --> pdb=" O LEU x 902 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'x' and resid 980 through 983 Processing sheet with id= BJ, first strand: chain 'x' and resid 1179 through 1181 removed outlier: 6.943A pdb=" N LYS x1093 " --> pdb=" O VAL x1112 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL x1112 " --> pdb=" O LYS x1093 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER x1138 " --> pdb=" O LYS x1158 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU x1160 " --> pdb=" O VAL x1136 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL x1136 " --> pdb=" O GLU x1160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL x1131 " --> pdb=" O VAL x1125 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE x1133 " --> pdb=" O MET x1123 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N MET x1123 " --> pdb=" O ILE x1133 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1288 hydrogen bonds 2178 hydrogen bond angles 0 basepair planarities 510 basepair parallelities 1023 stacking parallelities Total time for adding SS restraints: 64.50 Time building geometry restraints manager: 34.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14190 1.33 - 1.45: 33700 1.45 - 1.58: 40317 1.58 - 1.70: 3912 1.70 - 1.82: 322 Bond restraints: 92441 Sorted by residual: bond pdb=" CG PRO Y 116 " pdb=" CD PRO Y 116 " ideal model delta sigma weight residual 1.503 1.207 0.296 3.40e-02 8.65e+02 7.57e+01 bond pdb=" N PRO Y 116 " pdb=" CD PRO Y 116 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.10e+01 bond pdb=" CA GLN F 67 " pdb=" C GLN F 67 " ideal model delta sigma weight residual 1.523 1.568 -0.045 1.41e-02 5.03e+03 1.02e+01 bond pdb=" CB PRO Y 116 " pdb=" CG PRO Y 116 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.01e+01 bond pdb=" CA ASN a 45 " pdb=" CB ASN a 45 " ideal model delta sigma weight residual 1.539 1.642 -0.103 4.88e-02 4.20e+02 4.41e+00 ... (remaining 92436 not shown) Histogram of bond angle deviations from ideal: 86.20 - 96.62: 3 96.62 - 107.03: 12641 107.03 - 117.45: 67709 117.45 - 127.87: 50322 127.87 - 138.29: 3521 Bond angle restraints: 134196 Sorted by residual: angle pdb=" N PRO Y 116 " pdb=" CD PRO Y 116 " pdb=" CG PRO Y 116 " ideal model delta sigma weight residual 103.20 86.20 17.00 1.50e+00 4.44e-01 1.28e+02 angle pdb=" CA PRO Y 116 " pdb=" N PRO Y 116 " pdb=" CD PRO Y 116 " ideal model delta sigma weight residual 112.00 97.10 14.90 1.40e+00 5.10e-01 1.13e+02 angle pdb=" N VAL x 956 " pdb=" CA VAL x 956 " pdb=" C VAL x 956 " ideal model delta sigma weight residual 113.53 104.99 8.54 9.80e-01 1.04e+00 7.59e+01 angle pdb=" CA PRO Y 116 " pdb=" CB PRO Y 116 " pdb=" CG PRO Y 116 " ideal model delta sigma weight residual 104.50 93.02 11.48 1.90e+00 2.77e-01 3.65e+01 angle pdb=" N PRO Y 116 " pdb=" CA PRO Y 116 " pdb=" C PRO Y 116 " ideal model delta sigma weight residual 112.47 123.17 -10.70 2.06e+00 2.36e-01 2.70e+01 ... (remaining 134191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 53558 35.79 - 71.57: 4742 71.57 - 107.36: 625 107.36 - 143.15: 11 143.15 - 178.93: 27 Dihedral angle restraints: 58963 sinusoidal: 42785 harmonic: 16178 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 25.42 174.58 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 8.26 -168.26 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' C 21206 " pdb=" C1' C 21206 " pdb=" N1 C 21206 " pdb=" C2 C 21206 " ideal model delta sinusoidal sigma weight residual 200.00 32.75 167.25 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 58960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 15339 0.076 - 0.152: 1145 0.152 - 0.227: 99 0.227 - 0.303: 19 0.303 - 0.379: 4 Chirality restraints: 16606 Sorted by residual: chirality pdb=" CA PRO Y 116 " pdb=" N PRO Y 116 " pdb=" C PRO Y 116 " pdb=" CB PRO Y 116 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB ILE x 666 " pdb=" CA ILE x 666 " pdb=" CG1 ILE x 666 " pdb=" CG2 ILE x 666 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE h 258 " pdb=" CA ILE h 258 " pdb=" CG1 ILE h 258 " pdb=" CG2 ILE h 258 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 16603 not shown) Planarity restraints: 9756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 21852 " 0.005 2.00e-02 2.50e+03 3.14e-02 2.21e+01 pdb=" N1 C 21852 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C 21852 " -0.075 2.00e-02 2.50e+03 pdb=" O2 C 21852 " 0.053 2.00e-02 2.50e+03 pdb=" N3 C 21852 " -0.007 2.00e-02 2.50e+03 pdb=" C4 C 21852 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C 21852 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C 21852 " 0.016 2.00e-02 2.50e+03 pdb=" C6 C 21852 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 79 " 0.018 2.00e-02 2.50e+03 2.21e-02 8.59e+00 pdb=" CG PHE c 79 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE c 79 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE c 79 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE c 79 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE c 79 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE c 79 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP h 132 " 0.017 2.00e-02 2.50e+03 1.73e-02 7.48e+00 pdb=" CG TRP h 132 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP h 132 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP h 132 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP h 132 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP h 132 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP h 132 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP h 132 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP h 132 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP h 132 " 0.001 2.00e-02 2.50e+03 ... (remaining 9753 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 3504 2.68 - 3.24: 69258 3.24 - 3.79: 153059 3.79 - 4.35: 199770 4.35 - 4.90: 289811 Nonbonded interactions: 715402 Sorted by model distance: nonbonded pdb="MG MG x1301 " pdb=" O3A GTP x1302 " model vdw 2.127 2.170 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.253 2.440 nonbonded pdb=" OP1 C 2 151 " pdb=" OG1 THR Z 120 " model vdw 2.269 2.440 nonbonded pdb=" O SER x1185 " pdb=" OG SER x1188 " model vdw 2.277 2.440 nonbonded pdb=" O2' U 21535 " pdb=" OD1 ASN G 82 " model vdw 2.278 2.440 ... (remaining 715397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 16.780 Check model and map are aligned: 0.950 Set scattering table: 0.590 Process input model: 234.320 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.220 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 262.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 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 : 0.003 0.296 92441 Z= 0.221 Angle : 0.778 17.003 134196 Z= 0.385 Chirality : 0.041 0.379 16606 Planarity : 0.006 0.081 9756 Dihedral : 21.841 178.934 48517 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -2.35 (0.10), residues: 5549 helix: -1.53 (0.10), residues: 1756 sheet: -0.70 (0.18), residues: 898 loop : -1.85 (0.10), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP h 132 HIS 0.026 0.001 HIS J 116 PHE 0.051 0.002 PHE c 79 TYR 0.036 0.002 TYR J 149 ARG 0.018 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 815 time to evaluate : 4.846 Fit side-chains revert: symmetry clash REVERT: B 195 TRP cc_start: 0.7066 (t60) cc_final: 0.6812 (t60) REVERT: C 94 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7817 (ttpt) REVERT: C 169 MET cc_start: 0.7100 (mtp) cc_final: 0.6885 (ptt) REVERT: F 66 MET cc_start: 0.5452 (ppp) cc_final: 0.4931 (ttm) REVERT: G 38 TYR cc_start: 0.7219 (m-10) cc_final: 0.6930 (m-80) REVERT: H 20 ASP cc_start: 0.6499 (t70) cc_final: 0.6240 (t0) REVERT: J 3 ILE cc_start: 0.7435 (mp) cc_final: 0.7205 (mt) REVERT: M 119 ASP cc_start: 0.6684 (t0) cc_final: 0.6471 (t0) REVERT: P 114 SER cc_start: 0.8799 (p) cc_final: 0.8553 (p) REVERT: R 118 THR cc_start: 0.7934 (p) cc_final: 0.7650 (m) REVERT: S 36 GLU cc_start: 0.7047 (tp30) cc_final: 0.6641 (tt0) REVERT: T 50 ILE cc_start: 0.4819 (tt) cc_final: 0.4569 (mt) REVERT: T 71 MET cc_start: 0.7679 (ptp) cc_final: 0.7410 (ptp) REVERT: U 129 ARG cc_start: 0.6553 (mtm110) cc_final: 0.5711 (mtm-85) REVERT: U 130 ASP cc_start: 0.6124 (t0) cc_final: 0.5815 (t0) REVERT: a 55 TYR cc_start: 0.6372 (t80) cc_final: 0.6162 (t80) REVERT: b 56 VAL cc_start: 0.6918 (t) cc_final: 0.6672 (t) REVERT: h 212 LYS cc_start: 0.7322 (ptmt) cc_final: 0.6444 (tptp) REVERT: x 698 ILE cc_start: 0.7693 (mt) cc_final: 0.7485 (mt) REVERT: x 852 GLU cc_start: 0.4033 (mm-30) cc_final: 0.3201 (pt0) REVERT: x 1069 LYS cc_start: 0.7440 (tmmt) cc_final: 0.7093 (tttp) REVERT: x 1174 PHE cc_start: 0.5421 (p90) cc_final: 0.5198 (p90) REVERT: x 1200 MET cc_start: 0.0922 (mmm) cc_final: -0.0798 (tpp) outliers start: 0 outliers final: 0 residues processed: 815 average time/residue: 0.7940 time to fit residues: 1107.2763 Evaluate side-chains 597 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 624 optimal weight: 10.0000 chunk 560 optimal weight: 9.9990 chunk 311 optimal weight: 0.5980 chunk 191 optimal weight: 0.1980 chunk 378 optimal weight: 10.0000 chunk 299 optimal weight: 4.9990 chunk 580 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 352 optimal weight: 8.9990 chunk 431 optimal weight: 0.0470 chunk 672 optimal weight: 20.0000 overall best weight: 2.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN E 179 GLN J 9 HIS J 111 GLN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN K 125 HIS L 73 ASN O 105 ASN ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN R 142 GLN V 85 HIS X 15 ASN Y 97 ASN h 64 HIS ** x 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 809 ASN ** x 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS x1116 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 92441 Z= 0.178 Angle : 0.551 12.177 134196 Z= 0.276 Chirality : 0.035 0.221 16606 Planarity : 0.005 0.058 9756 Dihedral : 22.577 177.107 36899 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.28 % Allowed : 9.78 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.45 (0.11), residues: 5549 helix: -0.09 (0.12), residues: 1761 sheet: -0.66 (0.17), residues: 931 loop : -1.62 (0.11), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 67 HIS 0.021 0.001 HIS x1025 PHE 0.020 0.002 PHE R 13 TYR 0.018 0.001 TYR c 41 ARG 0.009 0.000 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 636 time to evaluate : 4.873 Fit side-chains revert: symmetry clash REVERT: B 99 ILE cc_start: 0.8017 (mm) cc_final: 0.7797 (mm) REVERT: C 169 MET cc_start: 0.7591 (mtp) cc_final: 0.7150 (ptt) REVERT: E 17 PHE cc_start: 0.6627 (m-80) cc_final: 0.6366 (t80) REVERT: F 158 ASP cc_start: 0.7320 (m-30) cc_final: 0.6987 (t0) REVERT: F 189 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7674 (mt) REVERT: F 200 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7373 (mtp180) REVERT: H 20 ASP cc_start: 0.6676 (t70) cc_final: 0.6420 (t0) REVERT: J 3 ILE cc_start: 0.7167 (mp) cc_final: 0.6933 (mt) REVERT: M 119 ASP cc_start: 0.6679 (t0) cc_final: 0.6441 (t0) REVERT: R 7 LEU cc_start: 0.6597 (pp) cc_final: 0.5791 (tp) REVERT: S 36 GLU cc_start: 0.7279 (tp30) cc_final: 0.6852 (tt0) REVERT: S 58 MET cc_start: 0.7880 (mmt) cc_final: 0.7614 (mmm) REVERT: U 88 MET cc_start: 0.7894 (mmp) cc_final: 0.7544 (mmm) REVERT: U 116 ASP cc_start: 0.6625 (t70) cc_final: 0.5941 (t70) REVERT: U 130 ASP cc_start: 0.6282 (t0) cc_final: 0.5969 (t0) REVERT: h 229 THR cc_start: 0.7565 (m) cc_final: 0.7135 (p) REVERT: n 15 ARG cc_start: 0.6029 (mtm180) cc_final: 0.5364 (mtp85) REVERT: x 602 ARG cc_start: 0.6190 (mmt180) cc_final: 0.5936 (tpt170) REVERT: x 1017 MET cc_start: 0.6362 (tpp) cc_final: 0.6082 (tpp) outliers start: 62 outliers final: 46 residues processed: 667 average time/residue: 0.7881 time to fit residues: 909.4575 Evaluate side-chains 616 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 569 time to evaluate : 4.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 45 TRP Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 192 PHE Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain M residue 116 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 807 TYR Chi-restraints excluded: chain x residue 1157 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 373 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 559 optimal weight: 6.9990 chunk 457 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 673 optimal weight: 10.0000 chunk 727 optimal weight: 30.0000 chunk 599 optimal weight: 20.0000 chunk 667 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 540 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS E 179 GLN F 138 HIS G 51 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN L 50 GLN M 19 ASN M 108 ASN O 13 GLN O 105 ASN ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN Q 104 GLN R 142 GLN V 85 HIS X 56 HIS ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 GLN e 10 HIS ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 ASN ** h 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 704 HIS ** x 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS ** x1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 92441 Z= 0.273 Angle : 0.654 12.784 134196 Z= 0.326 Chirality : 0.039 0.230 16606 Planarity : 0.005 0.068 9756 Dihedral : 22.708 179.954 36899 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 2.80 % Allowed : 14.66 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.46 (0.11), residues: 5549 helix: 0.11 (0.12), residues: 1750 sheet: -0.94 (0.17), residues: 971 loop : -1.68 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 67 HIS 0.014 0.001 HIS x1025 PHE 0.021 0.002 PHE C 81 TYR 0.020 0.002 TYR x 807 ARG 0.008 0.001 ARG a 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 632 time to evaluate : 4.968 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.2679 (OUTLIER) cc_final: 0.2420 (m-30) REVERT: C 169 MET cc_start: 0.7656 (mtp) cc_final: 0.7228 (ptt) REVERT: D 174 ILE cc_start: 0.6560 (mp) cc_final: 0.6325 (tp) REVERT: E 17 PHE cc_start: 0.6684 (m-80) cc_final: 0.6220 (t80) REVERT: E 120 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5960 (m-80) REVERT: I 165 ASN cc_start: 0.6219 (p0) cc_final: 0.5964 (p0) REVERT: O 13 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: Q 54 HIS cc_start: 0.3920 (OUTLIER) cc_final: 0.3644 (t-170) REVERT: Q 93 MET cc_start: 0.5577 (tpt) cc_final: 0.5218 (tpt) REVERT: S 58 MET cc_start: 0.8037 (mmt) cc_final: 0.7803 (mmm) REVERT: S 105 MET cc_start: 0.6963 (tmm) cc_final: 0.6706 (tmm) REVERT: U 88 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7392 (mpp) REVERT: U 116 ASP cc_start: 0.6849 (t70) cc_final: 0.6320 (t70) REVERT: c 79 PHE cc_start: 0.5537 (p90) cc_final: 0.5278 (p90) REVERT: d 47 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7500 (pttm) REVERT: f 86 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7291 (ttt90) REVERT: n 15 ARG cc_start: 0.5913 (mtm180) cc_final: 0.5263 (mtp85) REVERT: x 602 ARG cc_start: 0.6618 (mmt180) cc_final: 0.6199 (tpt-90) REVERT: x 1076 LYS cc_start: 0.7227 (mtmm) cc_final: 0.6842 (mtmm) REVERT: x 1169 MET cc_start: 0.1750 (ppp) cc_final: 0.1454 (ppp) REVERT: x 1186 ARG cc_start: 0.6354 (mpp-170) cc_final: 0.5645 (mmm-85) outliers start: 136 outliers final: 102 residues processed: 715 average time/residue: 0.7813 time to fit residues: 969.6129 Evaluate side-chains 671 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 563 time to evaluate : 4.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 45 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 192 PHE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 29 MET Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 104 GLN Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 88 MET Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 2 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 51 ASN Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 807 TYR Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1123 MET Chi-restraints excluded: chain x residue 1154 GLU Chi-restraints excluded: chain x residue 1157 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 665 optimal weight: 6.9990 chunk 506 optimal weight: 5.9990 chunk 349 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 321 optimal weight: 1.9990 chunk 452 optimal weight: 6.9990 chunk 675 optimal weight: 10.0000 chunk 715 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 640 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN Q 103 ASN R 142 GLN ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 188 HIS ** x 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 92441 Z= 0.294 Angle : 0.657 14.538 134196 Z= 0.329 Chirality : 0.040 0.236 16606 Planarity : 0.005 0.070 9756 Dihedral : 22.753 179.272 36899 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.27 % Favored : 93.71 % Rotamer: Outliers : 4.38 % Allowed : 17.54 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.57 (0.11), residues: 5549 helix: 0.14 (0.12), residues: 1736 sheet: -1.11 (0.16), residues: 970 loop : -1.78 (0.11), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 67 HIS 0.018 0.001 HIS x1025 PHE 0.018 0.002 PHE h 113 TYR 0.018 0.002 TYR x 807 ARG 0.008 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 614 time to evaluate : 5.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 169 MET cc_start: 0.7701 (mtp) cc_final: 0.7229 (ptt) REVERT: D 92 GLU cc_start: 0.6941 (pm20) cc_final: 0.6701 (pm20) REVERT: E 1 MET cc_start: 0.2984 (OUTLIER) cc_final: 0.2653 (ttm) REVERT: E 17 PHE cc_start: 0.6635 (m-80) cc_final: 0.6229 (t80) REVERT: E 207 HIS cc_start: 0.5975 (OUTLIER) cc_final: 0.5765 (t-90) REVERT: G 38 TYR cc_start: 0.7665 (m-10) cc_final: 0.7122 (m-80) REVERT: G 117 ILE cc_start: 0.7917 (mt) cc_final: 0.7591 (mm) REVERT: I 18 GLU cc_start: 0.5637 (OUTLIER) cc_final: 0.5349 (pm20) REVERT: J 114 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5659 (mp0) REVERT: K 73 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: K 142 VAL cc_start: 0.8335 (t) cc_final: 0.8086 (m) REVERT: M 108 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7684 (m-40) REVERT: M 119 ASP cc_start: 0.7060 (t0) cc_final: 0.6669 (t0) REVERT: Q 54 HIS cc_start: 0.4076 (OUTLIER) cc_final: 0.3819 (t-170) REVERT: S 58 MET cc_start: 0.8045 (mmt) cc_final: 0.7738 (mmm) REVERT: S 76 GLU cc_start: 0.6259 (mt-10) cc_final: 0.5867 (tp30) REVERT: S 105 MET cc_start: 0.6811 (tmm) cc_final: 0.6438 (tmm) REVERT: T 11 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5846 (t70) REVERT: U 91 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7452 (m90) REVERT: U 116 ASP cc_start: 0.6820 (t70) cc_final: 0.6382 (t70) REVERT: X 105 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8212 (p) REVERT: Y 92 ASN cc_start: 0.7489 (m110) cc_final: 0.7266 (m110) REVERT: Z 22 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6669 (mt0) REVERT: f 86 ARG cc_start: 0.7933 (ttt180) cc_final: 0.7407 (ttt90) REVERT: n 15 ARG cc_start: 0.5906 (mtm180) cc_final: 0.5379 (mtp85) REVERT: x 602 ARG cc_start: 0.7330 (mmt180) cc_final: 0.7033 (tpt-90) REVERT: x 1076 LYS cc_start: 0.7411 (mtmm) cc_final: 0.7146 (mtmm) outliers start: 213 outliers final: 150 residues processed: 757 average time/residue: 0.8419 time to fit residues: 1116.1649 Evaluate side-chains 730 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 569 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 192 PHE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 29 MET Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 28 HIS Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 75 MET Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 91 HIS Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain X residue 2 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 72 CYS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 105 THR Chi-restraints excluded: chain Y residue 69 CYS Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Z residue 22 GLN Chi-restraints excluded: chain Z residue 78 SER Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 51 ASN Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 807 TYR Chi-restraints excluded: chain x residue 861 VAL Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1087 VAL Chi-restraints excluded: chain x residue 1132 ASP Chi-restraints excluded: chain x residue 1154 GLU Chi-restraints excluded: chain x residue 1157 VAL Chi-restraints excluded: chain x residue 1177 THR Chi-restraints excluded: chain x residue 1198 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 595 optimal weight: 2.9990 chunk 406 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 532 optimal weight: 8.9990 chunk 295 optimal weight: 1.9990 chunk 610 optimal weight: 8.9990 chunk 494 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 chunk 642 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS F 112 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN M 108 ASN O 13 GLN Q 35 GLN Q 53 GLN R 142 GLN Y 61 GLN ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 92441 Z= 0.174 Angle : 0.551 15.458 134196 Z= 0.277 Chirality : 0.035 0.237 16606 Planarity : 0.004 0.064 9756 Dihedral : 22.655 178.229 36899 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.66 % Allowed : 19.49 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.27 (0.11), residues: 5549 helix: 0.51 (0.13), residues: 1733 sheet: -1.02 (0.17), residues: 943 loop : -1.65 (0.11), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 67 HIS 0.016 0.001 HIS x1025 PHE 0.015 0.001 PHE U 21 TYR 0.014 0.001 TYR E 107 ARG 0.006 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 627 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ILE cc_start: 0.8052 (mm) cc_final: 0.7713 (mm) REVERT: C 169 MET cc_start: 0.7688 (mtp) cc_final: 0.7207 (ptt) REVERT: D 102 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8004 (mp) REVERT: E 1 MET cc_start: 0.3053 (OUTLIER) cc_final: 0.2777 (ttm) REVERT: E 17 PHE cc_start: 0.6650 (m-80) cc_final: 0.6275 (t80) REVERT: E 120 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: E 207 HIS cc_start: 0.5892 (OUTLIER) cc_final: 0.5677 (t70) REVERT: F 66 MET cc_start: 0.6089 (ppp) cc_final: 0.5562 (ttm) REVERT: G 37 ASP cc_start: 0.7297 (p0) cc_final: 0.6829 (p0) REVERT: G 38 TYR cc_start: 0.7599 (m-10) cc_final: 0.7319 (m-80) REVERT: J 114 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5565 (mp0) REVERT: L 28 HIS cc_start: 0.4504 (m-70) cc_final: 0.4299 (m-70) REVERT: M 92 TYR cc_start: 0.7963 (p90) cc_final: 0.7575 (p90) REVERT: M 119 ASP cc_start: 0.6814 (t0) cc_final: 0.6437 (t0) REVERT: O 3 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8070 (mmp-170) REVERT: Q 30 TYR cc_start: 0.3584 (OUTLIER) cc_final: 0.2772 (m-10) REVERT: S 58 MET cc_start: 0.8037 (mmt) cc_final: 0.7837 (mmm) REVERT: S 76 GLU cc_start: 0.6215 (mt-10) cc_final: 0.5888 (tm-30) REVERT: S 105 MET cc_start: 0.6666 (tmm) cc_final: 0.6367 (tmm) REVERT: T 11 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.5714 (t70) REVERT: T 43 VAL cc_start: 0.6784 (t) cc_final: 0.6391 (p) REVERT: T 72 GLN cc_start: 0.6536 (tp40) cc_final: 0.5488 (mt0) REVERT: U 91 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7550 (m90) REVERT: U 116 ASP cc_start: 0.6845 (t70) cc_final: 0.6339 (t70) REVERT: U 130 ASP cc_start: 0.6405 (t0) cc_final: 0.6116 (t0) REVERT: V 87 ARG cc_start: 0.6008 (mmt180) cc_final: 0.5794 (mpt90) REVERT: Z 22 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6078 (mp-120) REVERT: f 86 ARG cc_start: 0.7922 (ttt180) cc_final: 0.7283 (ttt90) REVERT: n 15 ARG cc_start: 0.5950 (mtm180) cc_final: 0.5344 (mtp85) REVERT: x 602 ARG cc_start: 0.7342 (mmt180) cc_final: 0.6978 (tpt-90) REVERT: x 829 MET cc_start: 0.6033 (mtt) cc_final: 0.5494 (mmm) outliers start: 178 outliers final: 118 residues processed: 742 average time/residue: 0.8094 time to fit residues: 1049.1522 Evaluate side-chains 711 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 584 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 108 CYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 91 HIS Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 69 CYS Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Z residue 22 GLN Chi-restraints excluded: chain Z residue 109 GLU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 298 LEU Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 859 MET Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1123 MET Chi-restraints excluded: chain x residue 1177 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 240 optimal weight: 7.9990 chunk 644 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 419 optimal weight: 30.0000 chunk 176 optimal weight: 1.9990 chunk 715 optimal weight: 0.0020 chunk 594 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 236 optimal weight: 30.0000 chunk 375 optimal weight: 6.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN E 179 GLN G 114 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN O 13 GLN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 ASN ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 92441 Z= 0.216 Angle : 0.583 15.644 134196 Z= 0.293 Chirality : 0.037 0.234 16606 Planarity : 0.005 0.066 9756 Dihedral : 22.655 179.970 36899 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.53 % Allowed : 19.35 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.27 (0.11), residues: 5549 helix: 0.54 (0.13), residues: 1727 sheet: -1.05 (0.17), residues: 948 loop : -1.66 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 67 HIS 0.018 0.001 HIS x1025 PHE 0.031 0.002 PHE F 99 TYR 0.020 0.001 TYR L 70 ARG 0.013 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 603 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 ARG cc_start: 0.3336 (ptt-90) cc_final: 0.3134 (ptt-90) REVERT: C 169 MET cc_start: 0.7692 (mtp) cc_final: 0.7359 (ptt) REVERT: D 102 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7982 (mp) REVERT: E 1 MET cc_start: 0.3005 (OUTLIER) cc_final: 0.2744 (ttm) REVERT: E 17 PHE cc_start: 0.6659 (m-80) cc_final: 0.6241 (t80) REVERT: E 120 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: F 102 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7108 (mt) REVERT: G 37 ASP cc_start: 0.7236 (p0) cc_final: 0.6718 (p0) REVERT: G 38 TYR cc_start: 0.7645 (m-10) cc_final: 0.7337 (m-80) REVERT: I 18 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.5087 (pm20) REVERT: J 114 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5627 (mp0) REVERT: M 65 ASN cc_start: 0.6773 (t0) cc_final: 0.6559 (t0) REVERT: M 119 ASP cc_start: 0.6886 (t0) cc_final: 0.6477 (t0) REVERT: O 3 ARG cc_start: 0.8404 (mmp80) cc_final: 0.8038 (mmp-170) REVERT: Q 30 TYR cc_start: 0.3548 (OUTLIER) cc_final: 0.2781 (m-10) REVERT: S 58 MET cc_start: 0.8000 (mmt) cc_final: 0.7659 (mmm) REVERT: S 105 MET cc_start: 0.6769 (tmm) cc_final: 0.6481 (tmm) REVERT: T 11 HIS cc_start: 0.6190 (OUTLIER) cc_final: 0.5784 (t70) REVERT: T 65 GLU cc_start: 0.7322 (tp30) cc_final: 0.7077 (tp30) REVERT: T 72 GLN cc_start: 0.6521 (tp40) cc_final: 0.5470 (mt0) REVERT: U 91 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7505 (m90) REVERT: U 116 ASP cc_start: 0.6726 (t70) cc_final: 0.6385 (t70) REVERT: Z 22 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6109 (mt0) REVERT: c 13 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.6066 (tp30) REVERT: f 86 ARG cc_start: 0.7895 (ttt180) cc_final: 0.7244 (ttt90) REVERT: h 269 GLU cc_start: 0.6531 (tp30) cc_final: 0.5782 (tp30) REVERT: n 15 ARG cc_start: 0.5844 (mtm180) cc_final: 0.5371 (mtp85) REVERT: x 602 ARG cc_start: 0.7195 (mmt180) cc_final: 0.6888 (tpt-90) REVERT: x 829 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5412 (mmm) REVERT: x 1186 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6288 (mmm160) outliers start: 220 outliers final: 171 residues processed: 750 average time/residue: 0.7589 time to fit residues: 995.7024 Evaluate side-chains 764 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 580 time to evaluate : 4.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 192 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 29 MET Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 19 ASN Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 28 HIS Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 108 CYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 91 HIS Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain X residue 2 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 90 GLN Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 69 CYS Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Z residue 22 GLN Chi-restraints excluded: chain Z residue 109 GLU Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 51 ASN Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 298 LEU Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 805 LEU Chi-restraints excluded: chain x residue 829 MET Chi-restraints excluded: chain x residue 859 MET Chi-restraints excluded: chain x residue 861 VAL Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 964 GLU Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1021 VAL Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1123 MET Chi-restraints excluded: chain x residue 1132 ASP Chi-restraints excluded: chain x residue 1154 GLU Chi-restraints excluded: chain x residue 1157 VAL Chi-restraints excluded: chain x residue 1177 THR Chi-restraints excluded: chain x residue 1186 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 690 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 407 optimal weight: 3.9990 chunk 522 optimal weight: 10.0000 chunk 405 optimal weight: 2.9990 chunk 602 optimal weight: 8.9990 chunk 399 optimal weight: 6.9990 chunk 713 optimal weight: 0.9990 chunk 446 optimal weight: 20.0000 chunk 434 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN E 179 GLN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS M 19 ASN M 108 ASN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 92441 Z= 0.222 Angle : 0.589 15.643 134196 Z= 0.295 Chirality : 0.037 0.294 16606 Planarity : 0.005 0.066 9756 Dihedral : 22.658 179.712 36899 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.90 % Allowed : 19.70 % Favored : 75.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.34 % 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: -1.31 (0.11), residues: 5549 helix: 0.48 (0.13), residues: 1744 sheet: -1.01 (0.17), residues: 948 loop : -1.71 (0.11), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 67 HIS 0.017 0.001 HIS x1025 PHE 0.028 0.002 PHE F 99 TYR 0.018 0.001 TYR L 70 ARG 0.006 0.000 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 603 time to evaluate : 4.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6773 (m) REVERT: C 169 MET cc_start: 0.7658 (mtp) cc_final: 0.7338 (ptt) REVERT: D 102 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7959 (mp) REVERT: E 1 MET cc_start: 0.3052 (OUTLIER) cc_final: 0.2781 (ttm) REVERT: E 17 PHE cc_start: 0.6609 (m-80) cc_final: 0.6243 (t80) REVERT: E 120 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: F 102 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7135 (mt) REVERT: G 37 ASP cc_start: 0.7247 (p0) cc_final: 0.6736 (p0) REVERT: G 38 TYR cc_start: 0.7725 (m-10) cc_final: 0.7440 (m-80) REVERT: I 18 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.5160 (pm20) REVERT: J 114 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5705 (mp0) REVERT: K 73 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: M 119 ASP cc_start: 0.6942 (t0) cc_final: 0.6506 (t0) REVERT: M 141 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7860 (t0) REVERT: N 85 LEU cc_start: 0.0485 (OUTLIER) cc_final: 0.0269 (pt) REVERT: Q 30 TYR cc_start: 0.3695 (OUTLIER) cc_final: 0.2954 (m-10) REVERT: S 105 MET cc_start: 0.6703 (tmm) cc_final: 0.6407 (tmm) REVERT: T 11 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5783 (t70) REVERT: T 43 VAL cc_start: 0.6452 (OUTLIER) cc_final: 0.5947 (p) REVERT: T 65 GLU cc_start: 0.7309 (tp30) cc_final: 0.7037 (tp30) REVERT: T 72 GLN cc_start: 0.6808 (tp40) cc_final: 0.5666 (mt0) REVERT: U 91 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7447 (m90) REVERT: U 110 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8188 (tt) REVERT: U 116 ASP cc_start: 0.6742 (t70) cc_final: 0.6395 (t70) REVERT: Y 87 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.6637 (m-40) REVERT: Z 22 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6114 (mt0) REVERT: c 13 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6078 (tp30) REVERT: f 86 ARG cc_start: 0.7917 (ttt180) cc_final: 0.7275 (ttt90) REVERT: h 269 GLU cc_start: 0.6666 (tp30) cc_final: 0.5930 (tp30) REVERT: n 15 ARG cc_start: 0.5864 (mtm180) cc_final: 0.5436 (mtp85) REVERT: x 602 ARG cc_start: 0.7331 (mmt180) cc_final: 0.6998 (tpt-90) REVERT: x 829 MET cc_start: 0.5956 (mtt) cc_final: 0.5458 (mmm) REVERT: x 1186 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6304 (mmm160) REVERT: x 1200 MET cc_start: 0.2651 (tpp) cc_final: 0.2251 (mmm) outliers start: 238 outliers final: 184 residues processed: 770 average time/residue: 0.7730 time to fit residues: 1043.3096 Evaluate side-chains 783 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 580 time to evaluate : 5.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 28 HIS Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 108 CYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 91 HIS Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 2 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 90 GLN Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 69 CYS Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Z residue 22 GLN Chi-restraints excluded: chain Z residue 78 SER Chi-restraints excluded: chain Z residue 109 GLU Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 108 ARG Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 51 ASN Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 298 LEU Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain x residue 632 ILE Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 859 MET Chi-restraints excluded: chain x residue 861 VAL Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 964 GLU Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1117 VAL Chi-restraints excluded: chain x residue 1123 MET Chi-restraints excluded: chain x residue 1132 ASP Chi-restraints excluded: chain x residue 1137 THR Chi-restraints excluded: chain x residue 1154 GLU Chi-restraints excluded: chain x residue 1157 VAL Chi-restraints excluded: chain x residue 1177 THR Chi-restraints excluded: chain x residue 1186 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 441 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 214 optimal weight: 0.0020 chunk 140 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 453 optimal weight: 20.0000 chunk 485 optimal weight: 30.0000 chunk 352 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 560 optimal weight: 6.9990 overall best weight: 5.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 188 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 841 GLN x1025 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 92441 Z= 0.270 Angle : 0.640 15.025 134196 Z= 0.320 Chirality : 0.039 0.238 16606 Planarity : 0.005 0.068 9756 Dihedral : 22.718 178.288 36899 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.10 % Allowed : 20.05 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.44 (0.11), residues: 5549 helix: 0.35 (0.13), residues: 1741 sheet: -1.07 (0.17), residues: 955 loop : -1.77 (0.11), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 67 HIS 0.017 0.001 HIS x1025 PHE 0.026 0.002 PHE F 99 TYR 0.014 0.002 TYR L 70 ARG 0.010 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 589 time to evaluate : 5.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6811 (m) REVERT: C 169 MET cc_start: 0.7687 (mtp) cc_final: 0.7434 (ptt) REVERT: D 102 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7944 (mp) REVERT: E 1 MET cc_start: 0.3056 (OUTLIER) cc_final: 0.2823 (ttm) REVERT: E 17 PHE cc_start: 0.6665 (m-80) cc_final: 0.6300 (t80) REVERT: E 120 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.6241 (m-80) REVERT: E 179 GLN cc_start: 0.6773 (tp-100) cc_final: 0.6560 (tp40) REVERT: F 102 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7194 (mt) REVERT: G 37 ASP cc_start: 0.7290 (p0) cc_final: 0.6766 (p0) REVERT: G 38 TYR cc_start: 0.7771 (m-10) cc_final: 0.7487 (m-80) REVERT: I 18 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5183 (pm20) REVERT: J 114 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: K 73 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: K 142 VAL cc_start: 0.8410 (t) cc_final: 0.8102 (m) REVERT: L 85 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.3973 (tt) REVERT: M 119 ASP cc_start: 0.7039 (t0) cc_final: 0.6633 (t0) REVERT: M 141 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7937 (t0) REVERT: N 85 LEU cc_start: 0.0411 (OUTLIER) cc_final: 0.0137 (pt) REVERT: Q 30 TYR cc_start: 0.3662 (OUTLIER) cc_final: 0.3097 (m-10) REVERT: S 105 MET cc_start: 0.6814 (tmm) cc_final: 0.6604 (tmm) REVERT: T 11 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5847 (t70) REVERT: T 65 GLU cc_start: 0.7286 (tp30) cc_final: 0.6993 (tp30) REVERT: T 70 ILE cc_start: 0.6534 (mm) cc_final: 0.6083 (mt) REVERT: T 72 GLN cc_start: 0.6672 (tp40) cc_final: 0.5649 (mt0) REVERT: T 87 GLN cc_start: 0.6378 (mt0) cc_final: 0.6083 (mt0) REVERT: U 91 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7418 (m90) REVERT: U 110 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8231 (tt) REVERT: U 116 ASP cc_start: 0.6822 (t70) cc_final: 0.6528 (t70) REVERT: Y 87 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.6716 (m-40) REVERT: c 13 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6069 (tp30) REVERT: f 86 ARG cc_start: 0.8014 (ttt180) cc_final: 0.7357 (ttt90) REVERT: h 269 GLU cc_start: 0.6742 (tp30) cc_final: 0.6041 (tt0) REVERT: x 602 ARG cc_start: 0.7407 (mmt180) cc_final: 0.7077 (tpt-90) REVERT: x 829 MET cc_start: 0.5962 (mtt) cc_final: 0.5441 (mmm) REVERT: x 1088 PHE cc_start: 0.4084 (OUTLIER) cc_final: 0.3314 (m-10) REVERT: x 1196 PHE cc_start: 0.1058 (OUTLIER) cc_final: 0.0462 (t80) REVERT: x 1200 MET cc_start: 0.2865 (tpp) cc_final: 0.2509 (mmm) outliers start: 248 outliers final: 205 residues processed: 760 average time/residue: 0.7751 time to fit residues: 1029.9392 Evaluate side-chains 788 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 564 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 192 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 28 HIS Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 108 CYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 91 HIS Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 2 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 90 GLN Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 69 CYS Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Z residue 22 GLN Chi-restraints excluded: chain Z residue 78 SER Chi-restraints excluded: chain Z residue 109 GLU Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 108 ARG Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 51 ASN Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 298 LEU Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain x residue 632 ILE Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 805 LEU Chi-restraints excluded: chain x residue 859 MET Chi-restraints excluded: chain x residue 861 VAL Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 964 GLU Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1021 VAL Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1088 PHE Chi-restraints excluded: chain x residue 1117 VAL Chi-restraints excluded: chain x residue 1123 MET Chi-restraints excluded: chain x residue 1132 ASP Chi-restraints excluded: chain x residue 1137 THR Chi-restraints excluded: chain x residue 1154 GLU Chi-restraints excluded: chain x residue 1157 VAL Chi-restraints excluded: chain x residue 1177 THR Chi-restraints excluded: chain x residue 1196 PHE Chi-restraints excluded: chain x residue 1198 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 648 optimal weight: 20.0000 chunk 683 optimal weight: 6.9990 chunk 623 optimal weight: 2.9990 chunk 664 optimal weight: 5.9990 chunk 400 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 521 optimal weight: 5.9990 chunk 203 optimal weight: 0.0670 chunk 600 optimal weight: 9.9990 chunk 628 optimal weight: 20.0000 chunk 662 optimal weight: 20.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN ** h 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 92441 Z= 0.193 Angle : 0.574 15.338 134196 Z= 0.289 Chirality : 0.036 0.239 16606 Planarity : 0.004 0.066 9756 Dihedral : 22.664 178.862 36899 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.59 % Allowed : 21.04 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.30 (0.11), residues: 5549 helix: 0.51 (0.13), residues: 1740 sheet: -1.01 (0.17), residues: 933 loop : -1.71 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 67 HIS 0.018 0.001 HIS x1025 PHE 0.024 0.001 PHE F 99 TYR 0.015 0.001 TYR E 107 ARG 0.006 0.000 ARG x1186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 603 time to evaluate : 4.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6693 (m) REVERT: D 102 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7880 (mp) REVERT: E 1 MET cc_start: 0.2911 (OUTLIER) cc_final: 0.2662 (ttm) REVERT: E 17 PHE cc_start: 0.6645 (m-80) cc_final: 0.6252 (t80) REVERT: E 120 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6264 (m-80) REVERT: F 66 MET cc_start: 0.6104 (ppp) cc_final: 0.5658 (ttm) REVERT: F 102 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.6987 (mt) REVERT: G 37 ASP cc_start: 0.7246 (p0) cc_final: 0.6740 (p0) REVERT: G 38 TYR cc_start: 0.7775 (m-10) cc_final: 0.7515 (m-80) REVERT: I 18 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.5002 (pm20) REVERT: J 114 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5650 (mp0) REVERT: K 73 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: M 19 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6595 (t0) REVERT: M 119 ASP cc_start: 0.6880 (t0) cc_final: 0.6496 (t0) REVERT: Q 30 TYR cc_start: 0.3670 (OUTLIER) cc_final: 0.3091 (m-10) REVERT: S 105 MET cc_start: 0.6814 (tmm) cc_final: 0.6553 (tmm) REVERT: T 11 HIS cc_start: 0.6130 (OUTLIER) cc_final: 0.5722 (t70) REVERT: T 65 GLU cc_start: 0.7326 (tp30) cc_final: 0.7064 (tp30) REVERT: T 70 ILE cc_start: 0.6607 (mm) cc_final: 0.6177 (mt) REVERT: T 72 GLN cc_start: 0.6640 (tp40) cc_final: 0.5618 (mt0) REVERT: U 91 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7473 (m90) REVERT: U 116 ASP cc_start: 0.6732 (t70) cc_final: 0.6394 (t70) REVERT: V 87 ARG cc_start: 0.5882 (mmt-90) cc_final: 0.5599 (mmt-90) REVERT: W 70 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8434 (tt) REVERT: Y 87 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6646 (m-40) REVERT: Z 22 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.5778 (mt0) REVERT: c 13 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5921 (tp30) REVERT: f 86 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7327 (ttt90) REVERT: h 269 GLU cc_start: 0.6734 (tp30) cc_final: 0.6061 (tt0) REVERT: n 15 ARG cc_start: 0.5934 (mtm180) cc_final: 0.5335 (mtp85) REVERT: x 602 ARG cc_start: 0.7337 (mmt180) cc_final: 0.6872 (tpt-90) REVERT: x 829 MET cc_start: 0.5880 (mtt) cc_final: 0.5424 (mmm) REVERT: x 1186 ARG cc_start: 0.4498 (tpp80) cc_final: 0.4209 (mmm-85) REVERT: x 1196 PHE cc_start: 0.0802 (OUTLIER) cc_final: 0.0266 (t80) outliers start: 223 outliers final: 181 residues processed: 757 average time/residue: 0.7804 time to fit residues: 1032.4813 Evaluate side-chains 770 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 572 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 19 ASN Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 28 HIS Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 108 CYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 91 HIS Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain X residue 2 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 90 GLN Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 69 CYS Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Z residue 22 GLN Chi-restraints excluded: chain Z residue 109 GLU Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 108 ARG Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 51 ASN Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain x residue 632 ILE Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 805 LEU Chi-restraints excluded: chain x residue 859 MET Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 964 GLU Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1117 VAL Chi-restraints excluded: chain x residue 1123 MET Chi-restraints excluded: chain x residue 1132 ASP Chi-restraints excluded: chain x residue 1154 GLU Chi-restraints excluded: chain x residue 1157 VAL Chi-restraints excluded: chain x residue 1177 THR Chi-restraints excluded: chain x residue 1196 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 436 optimal weight: 7.9990 chunk 702 optimal weight: 1.9990 chunk 428 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 488 optimal weight: 4.9990 chunk 737 optimal weight: 40.0000 chunk 678 optimal weight: 4.9990 chunk 587 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 453 optimal weight: 8.9990 chunk 359 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN E 179 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x1025 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 92441 Z= 0.249 Angle : 0.627 14.852 134196 Z= 0.313 Chirality : 0.038 0.236 16606 Planarity : 0.005 0.067 9756 Dihedral : 22.687 178.333 36899 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.53 % Allowed : 21.28 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.43 (0.11), residues: 5549 helix: 0.39 (0.13), residues: 1736 sheet: -1.09 (0.16), residues: 964 loop : -1.78 (0.11), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 67 HIS 0.017 0.001 HIS x1025 PHE 0.026 0.002 PHE F 99 TYR 0.016 0.002 TYR E 107 ARG 0.006 0.001 ARG E 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11098 Ramachandran restraints generated. 5549 Oldfield, 0 Emsley, 5549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 590 time to evaluate : 5.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 GLU cc_start: 0.3070 (OUTLIER) cc_final: 0.2856 (mm-30) REVERT: C 130 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6639 (m) REVERT: D 102 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7917 (mp) REVERT: E 1 MET cc_start: 0.2927 (OUTLIER) cc_final: 0.2677 (ttm) REVERT: E 17 PHE cc_start: 0.6636 (m-80) cc_final: 0.6263 (t80) REVERT: E 67 ARG cc_start: 0.6281 (mmm160) cc_final: 0.5959 (mmm160) REVERT: E 120 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: F 102 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7042 (mt) REVERT: I 18 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.5127 (pm20) REVERT: J 114 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5601 (mp0) REVERT: K 73 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: L 85 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.3835 (tt) REVERT: M 19 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.6295 (t160) REVERT: M 119 ASP cc_start: 0.6988 (t0) cc_final: 0.6613 (t0) REVERT: N 85 LEU cc_start: 0.0588 (OUTLIER) cc_final: 0.0306 (pt) REVERT: Q 30 TYR cc_start: 0.3838 (OUTLIER) cc_final: 0.3271 (m-10) REVERT: S 105 MET cc_start: 0.6708 (tmm) cc_final: 0.6482 (tmm) REVERT: T 11 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5771 (t70) REVERT: T 65 GLU cc_start: 0.7331 (tp30) cc_final: 0.7075 (tp30) REVERT: T 70 ILE cc_start: 0.6587 (mm) cc_final: 0.6184 (mt) REVERT: T 72 GLN cc_start: 0.6627 (tp40) cc_final: 0.5620 (mt0) REVERT: T 87 GLN cc_start: 0.6406 (mt0) cc_final: 0.6098 (mt0) REVERT: U 91 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7401 (m90) REVERT: U 110 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8112 (tt) REVERT: U 116 ASP cc_start: 0.6784 (t0) cc_final: 0.6504 (t70) REVERT: V 87 ARG cc_start: 0.5871 (mmt-90) cc_final: 0.5498 (mmt-90) REVERT: W 70 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8468 (tt) REVERT: Y 87 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.6623 (m-40) REVERT: c 13 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5976 (tp30) REVERT: e 14 PHE cc_start: 0.7572 (p90) cc_final: 0.7304 (p90) REVERT: f 86 ARG cc_start: 0.8000 (ttt180) cc_final: 0.7372 (ttt90) REVERT: h 269 GLU cc_start: 0.6764 (tp30) cc_final: 0.6138 (tt0) REVERT: n 15 ARG cc_start: 0.5939 (mtm180) cc_final: 0.5172 (mtp85) REVERT: x 602 ARG cc_start: 0.7349 (mmt180) cc_final: 0.7029 (tpt-90) REVERT: x 829 MET cc_start: 0.5976 (mtt) cc_final: 0.5505 (mmm) REVERT: x 1186 ARG cc_start: 0.4729 (tpp80) cc_final: 0.3835 (mmm-85) REVERT: x 1196 PHE cc_start: 0.0661 (OUTLIER) cc_final: 0.0257 (t80) REVERT: x 1200 MET cc_start: 0.2732 (tpp) cc_final: 0.0799 (ttm) outliers start: 220 outliers final: 191 residues processed: 751 average time/residue: 0.7837 time to fit residues: 1028.8558 Evaluate side-chains 786 residues out of total 4857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 575 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 19 ASN Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 28 HIS Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 108 CYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 91 HIS Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 2 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 90 GLN Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 69 CYS Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Z residue 22 GLN Chi-restraints excluded: chain Z residue 109 GLU Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 108 ARG Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 51 ASN Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 632 ILE Chi-restraints excluded: chain x residue 757 ASP Chi-restraints excluded: chain x residue 805 LEU Chi-restraints excluded: chain x residue 835 LEU Chi-restraints excluded: chain x residue 859 MET Chi-restraints excluded: chain x residue 867 MET Chi-restraints excluded: chain x residue 871 ILE Chi-restraints excluded: chain x residue 964 GLU Chi-restraints excluded: chain x residue 981 VAL Chi-restraints excluded: chain x residue 1015 ASP Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1117 VAL Chi-restraints excluded: chain x residue 1123 MET Chi-restraints excluded: chain x residue 1137 THR Chi-restraints excluded: chain x residue 1154 GLU Chi-restraints excluded: chain x residue 1157 VAL Chi-restraints excluded: chain x residue 1177 THR Chi-restraints excluded: chain x residue 1196 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 466 optimal weight: 0.9990 chunk 625 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 541 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 163 optimal weight: 30.0000 chunk 587 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 603 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN x1025 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.142016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121381 restraints weight = 185708.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121139 restraints weight = 229535.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122046 restraints weight = 171951.471| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 92441 Z= 0.153 Angle : 0.544 15.087 134196 Z= 0.274 Chirality : 0.035 0.234 16606 Planarity : 0.004 0.064 9756 Dihedral : 22.597 179.176 36899 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.68 % Allowed : 22.29 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -1.18 (0.11), residues: 5549 helix: 0.62 (0.13), residues: 1741 sheet: -0.90 (0.17), residues: 935 loop : -1.65 (0.11), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 67 HIS 0.018 0.001 HIS x1025 PHE 0.023 0.001 PHE M 17 TYR 0.018 0.001 TYR e 7 ARG 0.004 0.000 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16160.30 seconds wall clock time: 287 minutes 50.83 seconds (17270.83 seconds total)