Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:25:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/12_2022/6khi_9989_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/12_2022/6khi_9989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/12_2022/6khi_9989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/12_2022/6khi_9989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/12_2022/6khi_9989_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/12_2022/6khi_9989_updated_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 388": "NH1" <-> "NH2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 512": "OE1" <-> "OE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F ARG 634": "NH1" <-> "NH2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 226": "NH1" <-> "NH2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H ARG 277": "NH1" <-> "NH2" Residue "H ARG 330": "NH1" <-> "NH2" Residue "H ARG 352": "NH1" <-> "NH2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "O ARG 44": "NH1" <-> "NH2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 72": "OE1" <-> "OE2" Residue "1 ARG 84": "NH1" <-> "NH2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 95": "OE1" <-> "OE2" Residue "1 GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32635 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2821 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "B" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3724 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3897 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "E" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "F" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4945 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 32, 'TRANS': 608} Chain breaks: 2 Chain: "G" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1278 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1537 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain: "J" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1307 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 11, 'TRANS': 148} Chain: "K" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1590 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 20, 'TRANS': 184} Chain: "L" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "N" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 11, 'TRANS': 136} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 469 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "V" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'DGD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCR': 2, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'LHG': 3, 'LMG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'LHG': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22426 SG CYS I 103 51.247 147.432 125.066 1.00 26.51 S ATOM 22470 SG CYS I 109 46.922 151.988 124.714 1.00 32.39 S ATOM 22175 SG CYS I 73 46.055 146.638 121.137 1.00 29.12 S ATOM 22451 SG CYS I 106 50.504 150.648 119.533 1.00 28.97 S ATOM 22122 SG CYS I 66 36.063 154.706 125.280 1.00 42.91 S ATOM 22144 SG CYS I 69 40.935 150.705 125.903 1.00 35.01 S ATOM 22103 SG CYS I 63 38.256 153.294 131.116 1.00 46.30 S ATOM 22504 SG CYS I 113 41.754 156.985 127.101 1.00 38.42 S ATOM 25530 SG CYS K 148 57.799 145.760 118.845 1.00 30.02 S ATOM 24806 SG CYS K 53 62.990 142.480 120.310 1.00 30.13 S ATOM 24800 SG CYS K 52 61.997 143.616 114.451 1.00 33.10 S ATOM 25304 SG CYS K 117 57.766 139.725 117.520 1.00 26.14 S ATOM 31484 SG CYS 1 41 32.927 160.609 122.910 1.00 83.69 S ATOM 31515 SG CYS 1 46 30.656 158.601 125.006 1.00 81.81 S ATOM 31534 SG CYS 1 49 27.912 161.206 121.565 1.00 94.03 S ATOM 31764 SG CYS 1 79 29.354 164.549 121.962 1.00100.16 S Time building chain proxies: 18.29, per 1000 atoms: 0.56 Number of scatterers: 32635 At special positions: 0 Unit cell: (168.48, 203.84, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 14 26.01 S 184 16.00 P 6 15.00 O 5743 8.00 N 5162 7.00 C 21526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 12.96 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 1 101 " pdb=" FE2 FES 1 101 " - pdb=" SG CYS 1 49 " pdb=" FE1 FES 1 101 " - pdb=" SG CYS 1 41 " pdb=" FE1 FES 1 101 " - pdb=" SG CYS 1 46 " pdb=" FE2 FES 1 101 " - pdb=" SG CYS 1 79 " pdb=" SF4 I 202 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 103 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 109 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 73 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 106 " pdb=" SF4 I 203 " pdb=" FE1 SF4 I 203 " - pdb=" SG CYS I 66 " pdb=" FE3 SF4 I 203 " - pdb=" SG CYS I 63 " pdb=" FE2 SF4 I 203 " - pdb=" SG CYS I 69 " pdb=" FE4 SF4 I 203 " - pdb=" SG CYS I 113 " pdb=" SF4 K 301 " pdb=" FE3 SF4 K 301 " - pdb=" SG CYS K 52 " pdb=" FE4 SF4 K 301 " - pdb=" SG CYS K 117 " pdb=" FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb=" FE1 SF4 K 301 " - pdb=" SG CYS K 148 " Number of angles added : 42 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 14 sheets defined 52.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 22 through 59 Proline residue: A 31 - end of helix removed outlier: 4.228A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Proline residue: A 76 - end of helix removed outlier: 4.125A pdb=" N LYS A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 84 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix removed outlier: 4.401A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 151 removed outlier: 3.836A pdb=" N ILE A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 4.554A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.668A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.811A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 removed outlier: 3.891A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 300 through 329 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'B' and resid 15 through 34 removed outlier: 3.847A pdb=" N THR B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 20 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 24 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.889A pdb=" N ARG B 41 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.711A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 110 through 127 removed outlier: 3.870A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 157 through 187 removed outlier: 3.675A pdb=" N ILE B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 208 through 223 removed outlier: 3.666A pdb=" N PHE B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 5.374A pdb=" N GLN B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP B 231 " --> pdb=" O PHE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.182A pdb=" N TYR B 236 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 263 removed outlier: 4.232A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 290 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.588A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 353 removed outlier: 3.833A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 370 through 384 Processing helix chain 'B' and resid 390 through 403 removed outlier: 4.396A pdb=" N GLY B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 removed outlier: 3.905A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 445 No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 457 through 476 removed outlier: 4.298A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 486 Processing helix chain 'C' and resid 19 through 42 removed outlier: 3.735A pdb=" N GLY C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 74 through 98 removed outlier: 3.970A pdb=" N ALA C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.615A pdb=" N PHE C 98 " --> pdb=" O TRP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 125 Processing helix chain 'D' and resid 6 through 18 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 32 through 56 removed outlier: 3.848A pdb=" N TRP D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 removed outlier: 4.021A pdb=" N TRP D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Proline residue: D 108 - end of helix Processing helix chain 'D' and resid 113 through 132 removed outlier: 4.403A pdb=" N GLY D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 4.312A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 162 through 188 removed outlier: 3.785A pdb=" N GLY D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 176 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.933A pdb=" N LYS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 238 No H-bonds generated for 'chain 'D' and resid 235 through 238' Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.832A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 271 through 296 removed outlier: 3.851A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 303 through 322 removed outlier: 4.169A pdb=" N ILE D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 357 removed outlier: 4.166A pdb=" N GLY D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 No H-bonds generated for 'chain 'D' and resid 368 through 371' Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 393 through 406 removed outlier: 3.826A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 441 removed outlier: 4.066A pdb=" N GLY D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Proline residue: D 431 - end of helix removed outlier: 4.076A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 479 Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 485 through 498 removed outlier: 5.421A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 27 through 51 removed outlier: 3.665A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.668A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'F' and resid 3 through 6 No H-bonds generated for 'chain 'F' and resid 3 through 6' Processing helix chain 'F' and resid 8 through 27 removed outlier: 3.680A pdb=" N ILE F 11 " --> pdb=" O ALA F 8 " (cutoff:3.500A) Proline residue: F 12 - end of helix Proline residue: F 15 - end of helix removed outlier: 4.050A pdb=" N ILE F 21 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL F 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 27 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 No H-bonds generated for 'chain 'F' and resid 30 through 33' Processing helix chain 'F' and resid 37 through 63 removed outlier: 4.288A pdb=" N GLY F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 117 removed outlier: 3.969A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 removed outlier: 3.782A pdb=" N LEU F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 162 removed outlier: 4.304A pdb=" N TRP F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 199 removed outlier: 3.811A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 191 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 removed outlier: 4.118A pdb=" N ASP F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 240 removed outlier: 4.120A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.740A pdb=" N MET F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 255' Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.892A pdb=" N HIS F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 279 removed outlier: 4.263A pdb=" N GLY F 273 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL F 274 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 284 No H-bonds generated for 'chain 'F' and resid 281 through 284' Processing helix chain 'F' and resid 288 through 308 Processing helix chain 'F' and resid 317 through 335 Processing helix chain 'F' and resid 339 through 348 Processing helix chain 'F' and resid 353 through 368 removed outlier: 3.885A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 392 through 402 removed outlier: 4.981A pdb=" N GLY F 401 " --> pdb=" O THR F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.776A pdb=" N GLU F 419 " --> pdb=" O TRP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 454 removed outlier: 4.208A pdb=" N LEU F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU F 437 " --> pdb=" O LEU F 433 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 440 " --> pdb=" O TRP F 436 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 492 Proline residue: F 489 - end of helix Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 504 Processing helix chain 'F' and resid 510 through 514 Processing helix chain 'F' and resid 532 through 555 removed outlier: 3.971A pdb=" N SER F 539 " --> pdb=" O ILE F 535 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY F 544 " --> pdb=" O SER F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 568 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 579 through 588 removed outlier: 3.548A pdb=" N PHE F 582 " --> pdb=" O LYS F 579 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP F 583 " --> pdb=" O TRP F 580 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU F 584 " --> pdb=" O TYR F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 619 removed outlier: 4.473A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 635 through 654 removed outlier: 3.823A pdb=" N SER F 653 " --> pdb=" O PHE F 649 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 654 " --> pdb=" O VAL F 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.945A pdb=" N THR G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 52 removed outlier: 3.979A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 70 through 76 Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.913A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 164 removed outlier: 3.970A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 57 removed outlier: 3.704A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 76 through 90 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 96 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 130 through 148 removed outlier: 4.223A pdb=" N PHE H 135 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG H 138 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU H 139 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA H 147 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 191 removed outlier: 4.652A pdb=" N VAL H 173 " --> pdb=" O TYR H 170 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR H 174 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS H 175 " --> pdb=" O TRP H 172 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU H 184 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.836A pdb=" N GLU H 191 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 204 Processing helix chain 'H' and resid 212 through 218 Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 258 through 282 removed outlier: 3.551A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 377 through 385 Processing helix chain 'I' and resid 4 through 29 Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 108 through 111 No H-bonds generated for 'chain 'I' and resid 108 through 111' Processing helix chain 'I' and resid 132 through 134 No H-bonds generated for 'chain 'I' and resid 132 through 134' Processing helix chain 'I' and resid 184 through 192 Processing helix chain 'J' and resid 46 through 54 Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.818A pdb=" N ALA K 59 " --> pdb=" O GLU K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 70 No H-bonds generated for 'chain 'K' and resid 68 through 70' Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 116 through 119 No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 152 through 166 Processing helix chain 'L' and resid 6 through 21 Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 41 through 53 Processing helix chain 'L' and resid 55 through 64 Proline residue: L 63 - end of helix Processing helix chain 'M' and resid 45 through 59 Processing helix chain 'M' and resid 67 through 87 Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 31 through 40 removed outlier: 3.593A pdb=" N LYS N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 55 through 58 No H-bonds generated for 'chain 'N' and resid 55 through 58' Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.714A pdb=" N LEU N 88 " --> pdb=" O VAL N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 122 removed outlier: 3.634A pdb=" N LEU N 116 " --> pdb=" O GLU N 112 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 146 No H-bonds generated for 'chain 'N' and resid 143 through 146' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'P' and resid 7 through 26 Proline residue: P 16 - end of helix Processing helix chain 'Q' and resid 18 through 41 Processing helix chain 'V' and resid 45 through 50 Processing helix chain 'V' and resid 52 through 58 Processing helix chain 'V' and resid 126 through 139 Processing helix chain '1' and resid 26 through 33 Processing helix chain '1' and resid 68 through 71 No H-bonds generated for 'chain '1' and resid 68 through 71' Processing helix chain '1' and resid 78 through 80 No H-bonds generated for 'chain '1' and resid 78 through 80' Processing helix chain '1' and resid 95 through 97 No H-bonds generated for 'chain '1' and resid 95 through 97' Processing sheet with id= A, first strand: chain 'F' and resid 69 through 76 removed outlier: 6.809A pdb=" N ILE F 83 " --> pdb=" O TRP F 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 27 through 30 Processing sheet with id= C, first strand: chain 'H' and resid 327 through 331 Processing sheet with id= D, first strand: chain 'I' and resid 56 through 58 Processing sheet with id= E, first strand: chain 'J' and resid 37 through 41 Processing sheet with id= F, first strand: chain 'J' and resid 60 through 62 Processing sheet with id= G, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.684A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'M' and resid 15 through 17 Processing sheet with id= I, first strand: chain 'N' and resid 19 through 22 Processing sheet with id= J, first strand: chain 'N' and resid 43 through 47 Processing sheet with id= K, first strand: chain 'O' and resid 9 through 11 Processing sheet with id= L, first strand: chain 'O' and resid 59 through 62 removed outlier: 6.098A pdb=" N LYS O 51 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL O 40 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 95 through 97 removed outlier: 6.673A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '1' and resid 16 through 20 removed outlier: 3.805A pdb=" N THR 1 16 " --> pdb=" O LEU 1 8 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS 1 87 " --> pdb=" O THR 1 7 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL 1 9 " --> pdb=" O CYS 1 87 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE 1 89 " --> pdb=" O VAL 1 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU 1 55 " --> pdb=" O LYS 1 88 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU 1 90 " --> pdb=" O LEU 1 53 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU 1 53 " --> pdb=" O LEU 1 90 " (cutoff:3.500A) 1413 hydrogen bonds defined for protein. 4002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.05 Time building geometry restraints manager: 14.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 13448 1.40 - 1.63: 19646 1.63 - 1.85: 315 1.85 - 2.07: 0 2.07 - 2.29: 40 Bond restraints: 33449 Sorted by residual: bond pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " ideal model delta sigma weight residual 1.840 1.616 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " ideal model delta sigma weight residual 1.840 1.618 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " ideal model delta sigma weight residual 1.840 1.621 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C25 BCR D 602 " pdb=" C26 BCR D 602 " ideal model delta sigma weight residual 1.347 1.557 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C25 BCR D 603 " pdb=" C26 BCR D 603 " ideal model delta sigma weight residual 1.347 1.554 -0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 33444 not shown) Histogram of bond angle deviations from ideal: 72.07 - 86.10: 42 86.10 - 100.14: 30 100.14 - 114.17: 20405 114.17 - 128.21: 24653 128.21 - 142.25: 330 Bond angle restraints: 45460 Sorted by residual: angle pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " pdb=" O7 SQD C 201 " ideal model delta sigma weight residual 111.32 73.52 37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " pdb=" O7 SQD D 601 " ideal model delta sigma weight residual 111.32 73.66 37.66 3.00e+00 1.11e-01 1.58e+02 angle pdb=" S1 FES 1 101 " pdb=" FE2 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.06 14.27 1.14e+00 7.69e-01 1.57e+02 angle pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " pdb=" O7 SQD L 101 " ideal model delta sigma weight residual 111.32 73.99 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S1 FES 1 101 " pdb=" FE1 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.10 14.23 1.20e+00 6.94e-01 1.41e+02 ... (remaining 45455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.24: 18295 25.24 - 50.48: 1088 50.48 - 75.72: 127 75.72 - 100.96: 20 100.96 - 126.20: 9 Dihedral angle restraints: 19539 sinusoidal: 7756 harmonic: 11783 Sorted by residual: dihedral pdb=" CA TYR H 72 " pdb=" C TYR H 72 " pdb=" N ALA H 73 " pdb=" CA ALA H 73 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP H 71 " pdb=" C ASP H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA PRO I 164 " pdb=" C PRO I 164 " pdb=" N ALA I 165 " pdb=" CA ALA I 165 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 19536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.933: 5208 0.933 - 1.867: 0 1.867 - 2.800: 0 2.800 - 3.734: 0 3.734 - 4.667: 1 Chirality restraints: 5209 Sorted by residual: chirality pdb=" C1 SQD D 601 " pdb=" C2 SQD D 601 " pdb=" O5 SQD D 601 " pdb=" O6 SQD D 601 " both_signs ideal model delta sigma weight residual False -2.39 2.28 -4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb=" FE1 SF4 K 301 " pdb=" S2 SF4 K 301 " pdb=" S3 SF4 K 301 " pdb=" S4 SF4 K 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE H 154 " pdb=" CA ILE H 154 " pdb=" CG1 ILE H 154 " pdb=" CG2 ILE H 154 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 5206 not shown) Planarity restraints: 5610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 603 " -0.279 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C17 BCR D 603 " 0.558 2.00e-02 2.50e+03 pdb=" C18 BCR D 603 " -0.290 2.00e-02 2.50e+03 pdb=" C19 BCR D 603 " -0.028 2.00e-02 2.50e+03 pdb=" C36 BCR D 603 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 602 " 0.491 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C11 BCR D 602 " -0.243 2.00e-02 2.50e+03 pdb=" C34 BCR D 602 " 0.110 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.047 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " -0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 BCR D 602 " -0.135 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" C13 BCR D 602 " 0.327 2.00e-02 2.50e+03 pdb=" C14 BCR D 602 " -0.419 2.00e-02 2.50e+03 pdb=" C15 BCR D 602 " 0.199 2.00e-02 2.50e+03 pdb=" C35 BCR D 602 " 0.028 2.00e-02 2.50e+03 ... (remaining 5607 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8008 2.79 - 3.31: 30089 3.31 - 3.84: 58724 3.84 - 4.37: 70745 4.37 - 4.90: 119169 Nonbonded interactions: 286735 Sorted by model distance: nonbonded pdb=" OH TYR C 75 " pdb=" O ALA E 75 " model vdw 2.257 2.440 nonbonded pdb=" O ALA B 39 " pdb=" OG1 THR B 43 " model vdw 2.276 2.440 nonbonded pdb=" O ALA D 322 " pdb=" OH TYR D 411 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASP H 359 " pdb=" OG SER H 391 " model vdw 2.287 2.440 nonbonded pdb=" OE1 GLN B 310 " pdb=" OH TYR B 332 " model vdw 2.290 2.440 ... (remaining 286730 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 14 7.16 5 P 6 5.49 5 S 184 5.16 5 C 21526 2.51 5 N 5162 2.21 5 O 5743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.030 Extract box with map and model: 16.400 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.300 Process input model: 86.520 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.008 0.224 33449 Z= 0.556 Angle : 1.252 37.802 45460 Z= 0.575 Chirality : 0.089 4.667 5209 Planarity : 0.012 0.309 5610 Dihedral : 16.083 126.196 12003 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.94 % Favored : 91.03 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.35 (0.10), residues: 4049 helix: -2.51 (0.08), residues: 2285 sheet: -2.96 (0.34), residues: 168 loop : -3.28 (0.13), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 592 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 600 average time/residue: 1.3721 time to fit residues: 986.1820 Evaluate side-chains 394 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 390 time to evaluate : 3.667 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.3290 time to fit residues: 5.3762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 315 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 365 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 339 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS B 296 GLN B 340 ASN B 404 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS E 2 GLN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS F 349 HIS F 570 GLN G 62 GLN G 71 ASN H 48 HIS H 205 GLN H 239 HIS K 80 GLN K 181 HIS L 70 GLN M 9 HIS M 37 ASN N 90 ASN S 64 GLN V 49 ASN V 86 GLN 1 70 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 33449 Z= 0.178 Angle : 0.636 8.738 45460 Z= 0.312 Chirality : 0.042 0.178 5209 Planarity : 0.005 0.072 5610 Dihedral : 10.515 144.344 4797 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.60 (0.12), residues: 4049 helix: -0.85 (0.10), residues: 2287 sheet: -2.65 (0.35), residues: 177 loop : -2.90 (0.14), residues: 1585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 443 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 37 residues processed: 495 average time/residue: 1.1959 time to fit residues: 725.2430 Evaluate side-chains 430 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 393 time to evaluate : 3.820 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 25 residues processed: 14 average time/residue: 0.7816 time to fit residues: 19.3947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 303 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 365 optimal weight: 2.9990 chunk 395 optimal weight: 0.0470 chunk 325 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 57 HIS K 80 GLN S 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 33449 Z= 0.186 Angle : 0.608 8.273 45460 Z= 0.300 Chirality : 0.042 0.164 5209 Planarity : 0.005 0.067 5610 Dihedral : 9.742 145.124 4797 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.13), residues: 4049 helix: -0.10 (0.11), residues: 2285 sheet: -2.55 (0.36), residues: 179 loop : -2.55 (0.15), residues: 1585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 426 time to evaluate : 3.697 Fit side-chains revert: symmetry clash outliers start: 114 outliers final: 48 residues processed: 496 average time/residue: 1.2235 time to fit residues: 745.0217 Evaluate side-chains 435 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 387 time to evaluate : 3.725 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 32 residues processed: 18 average time/residue: 0.4399 time to fit residues: 18.0313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 245 optimal weight: 0.5980 chunk 367 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 347 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS H 23 HIS K 80 GLN S 64 GLN V 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 33449 Z= 0.216 Angle : 0.620 15.509 45460 Z= 0.303 Chirality : 0.042 0.179 5209 Planarity : 0.004 0.065 5610 Dihedral : 9.285 143.792 4797 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.13), residues: 4049 helix: 0.21 (0.11), residues: 2290 sheet: -2.53 (0.35), residues: 185 loop : -2.39 (0.15), residues: 1574 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 392 time to evaluate : 3.383 Fit side-chains revert: symmetry clash outliers start: 119 outliers final: 55 residues processed: 475 average time/residue: 1.2399 time to fit residues: 722.6439 Evaluate side-chains 435 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 380 time to evaluate : 3.687 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 40 residues processed: 17 average time/residue: 0.6434 time to fit residues: 20.4137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 5 optimal weight: 0.0060 chunk 289 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 348 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN F 182 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 ASN H 23 HIS I 9 ASN M 100 ASN S 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 33449 Z= 0.330 Angle : 0.668 14.567 45460 Z= 0.328 Chirality : 0.044 0.196 5209 Planarity : 0.005 0.069 5610 Dihedral : 9.282 145.625 4797 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.13), residues: 4049 helix: 0.29 (0.11), residues: 2305 sheet: -2.54 (0.35), residues: 189 loop : -2.30 (0.15), residues: 1555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 396 time to evaluate : 3.701 Fit side-chains revert: symmetry clash outliers start: 133 outliers final: 76 residues processed: 487 average time/residue: 1.2064 time to fit residues: 721.9775 Evaluate side-chains 451 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 375 time to evaluate : 3.563 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 52 residues processed: 26 average time/residue: 0.5769 time to fit residues: 26.4942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 204 optimal weight: 0.0270 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 33449 Z= 0.192 Angle : 0.625 14.852 45460 Z= 0.306 Chirality : 0.042 0.220 5209 Planarity : 0.004 0.066 5610 Dihedral : 8.950 143.727 4797 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.13), residues: 4049 helix: 0.50 (0.11), residues: 2297 sheet: -2.23 (0.38), residues: 175 loop : -2.26 (0.15), residues: 1577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 399 time to evaluate : 3.852 Fit side-chains outliers start: 124 outliers final: 69 residues processed: 481 average time/residue: 1.1941 time to fit residues: 709.8041 Evaluate side-chains 447 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 378 time to evaluate : 3.926 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 55 residues processed: 16 average time/residue: 0.4956 time to fit residues: 17.2618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 327 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 387 optimal weight: 5.9990 chunk 242 optimal weight: 0.0570 chunk 236 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 HIS S 64 GLN V 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 33449 Z= 0.194 Angle : 0.621 13.156 45460 Z= 0.305 Chirality : 0.042 0.212 5209 Planarity : 0.004 0.067 5610 Dihedral : 8.730 142.433 4797 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 4049 helix: 0.68 (0.11), residues: 2276 sheet: -2.42 (0.34), residues: 194 loop : -2.12 (0.15), residues: 1579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 394 time to evaluate : 3.681 Fit side-chains outliers start: 101 outliers final: 64 residues processed: 471 average time/residue: 1.1769 time to fit residues: 684.5808 Evaluate side-chains 428 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 364 time to evaluate : 3.992 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 54 residues processed: 12 average time/residue: 0.4523 time to fit residues: 13.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 246 optimal weight: 0.3980 chunk 263 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 304 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN K 80 GLN S 64 GLN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 33449 Z= 0.179 Angle : 0.616 14.060 45460 Z= 0.302 Chirality : 0.042 0.214 5209 Planarity : 0.004 0.065 5610 Dihedral : 8.553 140.965 4797 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 4049 helix: 0.77 (0.11), residues: 2271 sheet: -2.30 (0.35), residues: 191 loop : -2.08 (0.15), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 390 time to evaluate : 3.543 Fit side-chains outliers start: 97 outliers final: 64 residues processed: 461 average time/residue: 1.1761 time to fit residues: 676.5137 Evaluate side-chains 426 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 362 time to evaluate : 3.614 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 50 residues processed: 15 average time/residue: 0.5731 time to fit residues: 17.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 338 optimal weight: 6.9990 chunk 361 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 283 optimal weight: 0.0870 chunk 110 optimal weight: 4.9990 chunk 326 optimal weight: 0.8980 chunk 341 optimal weight: 0.8980 chunk 359 optimal weight: 1.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN S 64 GLN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 33449 Z= 0.237 Angle : 0.647 17.544 45460 Z= 0.316 Chirality : 0.043 0.211 5209 Planarity : 0.004 0.067 5610 Dihedral : 8.575 141.717 4797 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 4049 helix: 0.74 (0.11), residues: 2288 sheet: -2.36 (0.36), residues: 175 loop : -2.03 (0.16), residues: 1586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 380 time to evaluate : 3.708 Fit side-chains outliers start: 84 outliers final: 55 residues processed: 450 average time/residue: 1.2206 time to fit residues: 679.9780 Evaluate side-chains 422 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 367 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 50 residues processed: 6 average time/residue: 0.3842 time to fit residues: 9.0277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 0.8980 chunk 381 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 400 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 318 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 246 optimal weight: 0.0970 chunk 195 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 170 HIS S 64 GLN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 33449 Z= 0.189 Angle : 0.636 15.672 45460 Z= 0.312 Chirality : 0.042 0.202 5209 Planarity : 0.004 0.066 5610 Dihedral : 8.428 139.704 4797 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 4049 helix: 0.86 (0.11), residues: 2266 sheet: -2.29 (0.37), residues: 175 loop : -2.01 (0.15), residues: 1608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 379 time to evaluate : 3.846 Fit side-chains outliers start: 68 outliers final: 56 residues processed: 439 average time/residue: 1.2032 time to fit residues: 651.5200 Evaluate side-chains 417 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 361 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 51 residues processed: 5 average time/residue: 0.8041 time to fit residues: 10.1627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN V 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080146 restraints weight = 70539.757| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.89 r_work: 0.3256 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 33449 Z= 0.258 Angle : 0.667 17.128 45460 Z= 0.326 Chirality : 0.043 0.210 5209 Planarity : 0.004 0.065 5610 Dihedral : 8.535 142.210 4797 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 4049 helix: 0.82 (0.11), residues: 2284 sheet: -2.37 (0.38), residues: 159 loop : -2.03 (0.15), residues: 1606 =============================================================================== Job complete usr+sys time: 11484.89 seconds wall clock time: 203 minutes 48.73 seconds (12228.73 seconds total)