Starting phenix.real_space_refine on Tue Jun 24 14:51:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkf_34851/06_2025/8hkf_34851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkf_34851/06_2025/8hkf_34851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hkf_34851/06_2025/8hkf_34851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkf_34851/06_2025/8hkf_34851.map" model { file = "/net/cci-nas-00/data/ceres_data/8hkf_34851/06_2025/8hkf_34851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkf_34851/06_2025/8hkf_34851.cif" } resolution = 2.66 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= 0.048 sd= 0.177 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: 6 Type Number sf(0) Gaussians K 16 8.98 5 Zn 4 6.06 5 S 212 5.16 5 C 18588 2.51 5 N 4772 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28700 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 7, ' ZN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A 777 94.964 62.616 128.258 1.00 76.38 S ATOM 4454 SG CYS A 778 98.806 62.321 128.069 1.00 80.73 S ATOM 4508 SG CYS A 785 97.164 65.665 128.995 1.00106.89 S ATOM 11618 SG CYS B 777 85.072 94.976 128.271 1.00 78.75 S ATOM 11624 SG CYS B 778 85.360 98.815 128.069 1.00 81.80 S ATOM 11678 SG CYS B 785 82.006 97.172 128.980 1.00108.36 S ATOM 18788 SG CYS C 777 52.631 85.104 128.346 1.00 76.11 S ATOM 18794 SG CYS C 778 48.797 85.346 128.094 1.00 82.44 S ATOM 18848 SG CYS C 785 50.465 81.992 128.989 1.00106.31 S ATOM 25958 SG CYS D 777 62.645 52.716 128.268 1.00 73.76 S ATOM 25964 SG CYS D 778 62.334 48.877 128.077 1.00 80.93 S ATOM 26018 SG CYS D 785 65.691 50.496 129.000 1.00108.52 S Time building chain proxies: 15.98, per 1000 atoms: 0.56 Number of scatterers: 28700 At special positions: 0 Unit cell: (148.72, 148.72, 142.48, 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) Zn 4 29.99 K 16 19.00 S 212 16.00 O 5108 8.00 N 4772 7.00 C 18588 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 778 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 778 " pdb=" ZN C1301 " pdb="ZN ZN C1301 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 778 " pdb=" ZN D1301 " pdb="ZN ZN D1301 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 778 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 785 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 20 sheets defined 54.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 110 through 137 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 removed outlier: 3.625A pdb=" N ALA A 178 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Proline residue: A 221 - end of helix removed outlier: 3.844A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.932A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 256 " --> pdb=" O MET A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix removed outlier: 3.506A pdb=" N GLU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.208A pdb=" N GLN A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.702A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.626A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.528A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.152A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.804A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 4.117A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.956A pdb=" N ASP A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1013 through 1017 removed outlier: 3.805A pdb=" N LEU A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.751A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 removed outlier: 3.696A pdb=" N ALA B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Proline residue: B 221 - end of helix removed outlier: 3.920A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Proline residue: B 230 - end of helix No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 256 removed outlier: 4.109A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.192A pdb=" N GLN B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 463 through 482 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.702A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.621A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.518A pdb=" N ARG B 780 " --> pdb=" O CYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.525A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 823 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.813A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 4.124A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.912A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.736A pdb=" N LEU B1017 " --> pdb=" O GLU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.557A pdb=" N ALA C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 219 through 228 removed outlier: 3.541A pdb=" N ILE C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 256 removed outlier: 4.127A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 395 through 400 removed outlier: 6.757A pdb=" N ARG C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.253A pdb=" N GLN C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.701A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 500 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.626A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.620A pdb=" N ARG C 780 " --> pdb=" O CYS C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.538A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.814A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 4.129A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.957A pdb=" N ASP C 976 " --> pdb=" O ILE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1013 through 1017 removed outlier: 3.753A pdb=" N LEU C1017 " --> pdb=" O GLU C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 111 through 137 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 removed outlier: 3.818A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 226 through 227 No H-bonds generated for 'chain 'D' and resid 226 through 227' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 240 through 256 removed outlier: 4.067A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.763A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.208A pdb=" N GLN D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.617A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 500 " --> pdb=" O LYS D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.629A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.507A pdb=" N ARG D 780 " --> pdb=" O CYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.531A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 822 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.815A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.135A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 removed outlier: 3.954A pdb=" N ASP D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1013 through 1017 removed outlier: 3.723A pdb=" N LEU D1017 " --> pdb=" O GLU D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.227A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.634A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.085A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 879 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.006A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.238A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.638A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AA9, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.101A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.991A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.228A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.638A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB5, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.112A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.984A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 433 removed outlier: 6.226A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.636A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC1, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.100A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D 879 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.978A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 3981 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: 11.62 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.15: 1 1.15 - 1.47: 16150 1.47 - 1.78: 12912 1.78 - 2.10: 280 2.10 - 2.41: 1 Bond restraints: 29344 Sorted by residual: bond pdb=" CG PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 1.503 0.840 0.663 3.40e-02 8.65e+02 3.80e+02 bond pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " ideal model delta sigma weight residual 1.492 2.412 -0.920 5.00e-02 4.00e+02 3.38e+02 bond pdb=" C ASP B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 1.336 1.559 -0.223 1.23e-02 6.61e+03 3.29e+02 bond pdb=" CG ARG C 232 " pdb=" CD ARG C 232 " ideal model delta sigma weight residual 1.520 1.287 0.233 3.00e-02 1.11e+03 6.04e+01 bond pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " ideal model delta sigma weight residual 1.808 1.586 0.222 3.30e-02 9.18e+02 4.55e+01 ... (remaining 29339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.20: 39802 21.20 - 42.41: 9 42.41 - 63.61: 0 63.61 - 84.82: 0 84.82 - 106.02: 1 Bond angle restraints: 39812 Sorted by residual: angle pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 106.10 0.08 106.02 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO B 139 " pdb=" N PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 112.00 84.71 27.29 1.40e+00 5.10e-01 3.80e+02 angle pdb=" N TRP C 146 " pdb=" CA TRP C 146 " pdb=" C TRP C 146 " ideal model delta sigma weight residual 112.86 134.82 -21.96 1.22e+00 6.72e-01 3.24e+02 angle pdb=" N TRP D 146 " pdb=" CA TRP D 146 " pdb=" C TRP D 146 " ideal model delta sigma weight residual 112.86 134.20 -21.34 1.22e+00 6.72e-01 3.06e+02 angle pdb=" C TRP D 146 " pdb=" CA TRP D 146 " pdb=" CB TRP D 146 " ideal model delta sigma weight residual 111.36 83.74 27.62 1.63e+00 3.76e-01 2.87e+02 ... (remaining 39807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 15898 20.44 - 40.88: 1353 40.88 - 61.32: 283 61.32 - 81.76: 49 81.76 - 102.20: 21 Dihedral angle restraints: 17604 sinusoidal: 6992 harmonic: 10612 Sorted by residual: dihedral pdb=" N PRO A 149 " pdb=" C PRO A 149 " pdb=" CA PRO A 149 " pdb=" CB PRO A 149 " ideal model delta harmonic sigma weight residual 115.10 134.13 -19.03 0 2.50e+00 1.60e-01 5.80e+01 dihedral pdb=" C PRO A 149 " pdb=" N PRO A 149 " pdb=" CA PRO A 149 " pdb=" CB PRO A 149 " ideal model delta harmonic sigma weight residual -120.70 -139.50 18.80 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" C TRP D 146 " pdb=" N TRP D 146 " pdb=" CA TRP D 146 " pdb=" CB TRP D 146 " ideal model delta harmonic sigma weight residual -122.60 -104.45 -18.15 0 2.50e+00 1.60e-01 5.27e+01 ... (remaining 17601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 4533 0.206 - 0.413: 10 0.413 - 0.619: 2 0.619 - 0.826: 2 0.826 - 1.032: 1 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CA PRO A 149 " pdb=" N PRO A 149 " pdb=" C PRO A 149 " pdb=" CB PRO A 149 " both_signs ideal model delta sigma weight residual False 2.72 1.69 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA PRO C 149 " pdb=" N PRO C 149 " pdb=" C PRO C 149 " pdb=" CB PRO C 149 " both_signs ideal model delta sigma weight residual False 2.72 1.91 0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 2.01 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4545 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 177 " 0.058 2.00e-02 2.50e+03 4.63e-02 5.35e+01 pdb=" CG TRP C 177 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 177 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 177 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 177 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP C 177 " -0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 177 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 177 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 177 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 148 " 0.095 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO C 149 " -0.247 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 148 " 0.095 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO D 149 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " 0.074 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.22: 36 2.22 - 2.95: 12769 2.95 - 3.68: 50386 3.68 - 4.41: 86113 4.41 - 5.14: 141623 Nonbonded interactions: 290927 Sorted by model distance: nonbonded pdb=" O TRP C 146 " pdb=" CD1 TRP C 146 " model vdw 1.494 3.260 nonbonded pdb=" O TRP C 146 " pdb=" CG TRP C 146 " model vdw 1.558 3.260 nonbonded pdb=" CD1 LEU B 802 " pdb=" CE1 TYR B 876 " model vdw 1.787 3.760 nonbonded pdb=" O TRP D 146 " pdb=" CG TRP D 146 " model vdw 1.806 3.260 nonbonded pdb=" CD1 LEU D 802 " pdb=" CE1 TYR D 876 " model vdw 1.820 3.760 ... (remaining 290922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 110 through 1205 or resid 1301 through 1304)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.710 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: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 68.170 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:15.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.009 0.920 29361 Z= 0.375 Angle : 0.967 106.020 39824 Z= 0.484 Chirality : 0.050 1.032 4548 Planarity : 0.006 0.143 4992 Dihedral : 16.149 102.196 10716 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 0.60 % Allowed : 22.14 % Favored : 77.26 % Cbeta Deviations : 0.20 % 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: -0.44 (0.13), residues: 3532 helix: -0.01 (0.12), residues: 1684 sheet: -0.37 (0.25), residues: 364 loop : -0.41 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP C 177 HIS 0.010 0.001 HIS C 291 PHE 0.035 0.002 PHE A 188 TYR 0.018 0.001 TYR C 403 ARG 0.013 0.001 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.20551 ( 1416) hydrogen bonds : angle 6.92595 ( 3981) metal coordination : bond 0.00205 ( 16) metal coordination : angle 0.36675 ( 12) covalent geometry : bond 0.00849 (29344) covalent geometry : angle 0.96744 (39812) Misc. bond : bond 0.41923 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 552 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7781 (ttt90) REVERT: B 168 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 294 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8165 (ttp80) REVERT: B 398 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7714 (ttt90) REVERT: C 950 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7337 (ttp80) REVERT: D 783 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7740 (pttp) REVERT: D 786 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8273 (mppt) REVERT: D 1018 TRP cc_start: 0.8221 (p-90) cc_final: 0.7967 (p-90) outliers start: 19 outliers final: 13 residues processed: 567 average time/residue: 1.4691 time to fit residues: 978.0551 Evaluate side-chains 536 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 522 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 925 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 8.9990 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 144 optimal weight: 0.1980 chunk 279 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 298 ASN A 470 GLN A 505 HIS A 632 ASN A 816 ASN ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 218 ASN B 270 GLN B 470 GLN B 505 HIS B 632 ASN B 816 ASN ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 357 GLN C 470 GLN C 505 HIS C 632 ASN C 816 ASN C1175 ASN D 156 ASN D 218 ASN D 251 ASN D 470 GLN D 505 HIS D 632 ASN D 816 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092415 restraints weight = 49710.742| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.20 r_work: 0.3098 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 29361 Z= 0.266 Angle : 0.697 12.136 39824 Z= 0.351 Chirality : 0.048 0.346 4548 Planarity : 0.008 0.300 4992 Dihedral : 5.341 59.422 3921 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 4.73 % Allowed : 18.46 % Favored : 76.81 % 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: 0.02 (0.14), residues: 3532 helix: 0.39 (0.12), residues: 1732 sheet: -0.44 (0.24), residues: 388 loop : -0.12 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 177 HIS 0.007 0.002 HIS A1046 PHE 0.017 0.002 PHE B 188 TYR 0.023 0.002 TYR B 403 ARG 0.010 0.001 ARG B1137 Details of bonding type rmsd hydrogen bonds : bond 0.05123 ( 1416) hydrogen bonds : angle 4.96411 ( 3981) metal coordination : bond 0.00457 ( 16) metal coordination : angle 1.54444 ( 12) covalent geometry : bond 0.00666 (29344) covalent geometry : angle 0.69659 (39812) Misc. bond : bond 0.00198 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 549 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8430 (p) cc_final: 0.8134 (m) REVERT: A 174 MET cc_start: 0.7490 (tpt) cc_final: 0.7153 (tpp) REVERT: A 200 LYS cc_start: 0.3797 (OUTLIER) cc_final: 0.3341 (ttpp) REVERT: A 317 TYR cc_start: 0.8820 (m-80) cc_final: 0.8568 (m-10) REVERT: A 347 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: A 353 TRP cc_start: 0.7207 (OUTLIER) cc_final: 0.6288 (t-100) REVERT: A 355 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: A 398 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7901 (ttt90) REVERT: A 538 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7380 (mmp80) REVERT: A 788 ASN cc_start: 0.8006 (p0) cc_final: 0.7705 (p0) REVERT: A 974 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: A 1137 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7173 (ttt-90) REVERT: B 200 LYS cc_start: 0.3475 (OUTLIER) cc_final: 0.3179 (tttm) REVERT: B 294 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8288 (ttp80) REVERT: B 398 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7860 (ttt90) REVERT: B 538 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7407 (mmp80) REVERT: B 565 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7653 (ttp-170) REVERT: C 133 ARG cc_start: 0.7917 (tmm-80) cc_final: 0.7715 (tmm-80) REVERT: C 190 GLU cc_start: 0.7057 (mp0) cc_final: 0.6497 (mp0) REVERT: C 283 PHE cc_start: 0.8646 (t80) cc_final: 0.8379 (t80) REVERT: C 788 ASN cc_start: 0.8176 (p0) cc_final: 0.7845 (p0) REVERT: C 829 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8394 (mmpt) REVERT: C 930 MET cc_start: 0.7179 (tpt) cc_final: 0.6957 (tpt) REVERT: C 974 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7998 (tmm) REVERT: C 1158 LYS cc_start: 0.8274 (mttt) cc_final: 0.7982 (mtmp) REVERT: D 117 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7103 (mm) REVERT: D 192 MET cc_start: 0.6240 (mtp) cc_final: 0.5797 (mtt) REVERT: D 538 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7423 (mmp80) REVERT: D 604 LYS cc_start: 0.8008 (pttt) cc_final: 0.7772 (pptt) REVERT: D 786 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8283 (mppt) REVERT: D 830 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8375 (mm-30) REVERT: D 974 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8054 (tmm) REVERT: D 1152 LEU cc_start: 0.8688 (tp) cc_final: 0.8483 (tp) outliers start: 149 outliers final: 45 residues processed: 625 average time/residue: 1.4418 time to fit residues: 1053.3786 Evaluate side-chains 584 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 524 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 PRO Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1137 ARG Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 894 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 974 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 279 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A 845 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 632 ASN B 845 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS C1147 GLN D 251 ASN D 632 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.127669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093154 restraints weight = 50152.461| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.01 r_work: 0.3150 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 29361 Z= 0.134 Angle : 0.585 10.339 39824 Z= 0.293 Chirality : 0.042 0.290 4548 Planarity : 0.006 0.150 4992 Dihedral : 5.589 165.316 3914 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.28 % Rotamer: Outliers : 3.18 % Allowed : 20.27 % Favored : 76.56 % 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: 0.54 (0.14), residues: 3532 helix: 0.91 (0.12), residues: 1688 sheet: -0.51 (0.26), residues: 364 loop : 0.13 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 177 HIS 0.005 0.001 HIS C 291 PHE 0.026 0.001 PHE D 283 TYR 0.038 0.001 TYR C 876 ARG 0.009 0.001 ARG B1137 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 1416) hydrogen bonds : angle 4.68762 ( 3981) metal coordination : bond 0.00145 ( 16) metal coordination : angle 1.05221 ( 12) covalent geometry : bond 0.00321 (29344) covalent geometry : angle 0.58515 (39812) Misc. bond : bond 0.00146 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 548 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8523 (p) cc_final: 0.8186 (m) REVERT: A 200 LYS cc_start: 0.3626 (OUTLIER) cc_final: 0.3407 (ttpp) REVERT: A 317 TYR cc_start: 0.8710 (m-80) cc_final: 0.8480 (m-10) REVERT: A 347 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: A 398 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7967 (ttt90) REVERT: A 426 SER cc_start: 0.8839 (t) cc_final: 0.8384 (p) REVERT: A 782 ASP cc_start: 0.7309 (m-30) cc_final: 0.7033 (m-30) REVERT: A 788 ASN cc_start: 0.7996 (p0) cc_final: 0.7715 (p0) REVERT: A 791 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: A 829 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8404 (mmtm) REVERT: A 1158 LYS cc_start: 0.8016 (mtmp) cc_final: 0.7770 (mtmm) REVERT: B 200 LYS cc_start: 0.3314 (OUTLIER) cc_final: 0.3087 (tttm) REVERT: B 398 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7962 (ttt180) REVERT: B 538 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7338 (mmt180) REVERT: B 600 ARG cc_start: 0.7093 (mmt180) cc_final: 0.6877 (mmt180) REVERT: B 829 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8210 (mmmm) REVERT: C 538 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7691 (mmp80) REVERT: C 788 ASN cc_start: 0.8094 (p0) cc_final: 0.7778 (p0) REVERT: C 829 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8399 (mmpt) REVERT: C 930 MET cc_start: 0.7025 (tpt) cc_final: 0.6739 (tpt) REVERT: C 1158 LYS cc_start: 0.8184 (mttt) cc_final: 0.7970 (mtmp) REVERT: D 117 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7043 (mm) REVERT: D 168 LEU cc_start: 0.8079 (tp) cc_final: 0.7736 (tt) REVERT: D 234 LEU cc_start: 0.8494 (tp) cc_final: 0.8171 (tp) REVERT: D 538 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7333 (mmp80) REVERT: D 604 LYS cc_start: 0.8050 (pttt) cc_final: 0.7803 (pptt) REVERT: D 783 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7787 (pttp) REVERT: D 786 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8263 (mppt) REVERT: D 829 LYS cc_start: 0.7762 (tmtt) cc_final: 0.7261 (tmtt) REVERT: D 830 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8368 (mm-30) REVERT: D 1158 LYS cc_start: 0.8073 (mtmp) cc_final: 0.7831 (mtmm) outliers start: 100 outliers final: 33 residues processed: 614 average time/residue: 1.5824 time to fit residues: 1143.8699 Evaluate side-chains 558 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 517 time to evaluate : 4.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 876 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 81 optimal weight: 0.0770 chunk 179 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 349 optimal weight: 9.9990 chunk 296 optimal weight: 0.0980 chunk 321 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 overall best weight: 1.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093715 restraints weight = 50125.473| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.13 r_work: 0.3132 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 29361 Z= 0.157 Angle : 0.595 11.273 39824 Z= 0.295 Chirality : 0.043 0.282 4548 Planarity : 0.005 0.144 4992 Dihedral : 5.642 178.971 3913 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 3.59 % Allowed : 20.46 % Favored : 75.95 % 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: 0.64 (0.14), residues: 3532 helix: 1.02 (0.12), residues: 1720 sheet: -0.49 (0.26), residues: 364 loop : 0.12 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 177 HIS 0.006 0.001 HIS C 291 PHE 0.023 0.002 PHE C 283 TYR 0.016 0.002 TYR D 553 ARG 0.010 0.001 ARG B1137 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1416) hydrogen bonds : angle 4.57638 ( 3981) metal coordination : bond 0.00134 ( 16) metal coordination : angle 1.03722 ( 12) covalent geometry : bond 0.00390 (29344) covalent geometry : angle 0.59516 (39812) Misc. bond : bond 0.00129 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 540 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.3835 (OUTLIER) cc_final: 0.3439 (ttpp) REVERT: A 317 TYR cc_start: 0.8665 (m-80) cc_final: 0.8425 (m-10) REVERT: A 351 TYR cc_start: 0.6774 (t80) cc_final: 0.6536 (t80) REVERT: A 355 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: A 398 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7932 (ttt90) REVERT: A 426 SER cc_start: 0.8837 (t) cc_final: 0.8397 (p) REVERT: A 427 GLN cc_start: 0.8093 (pp30) cc_final: 0.7861 (pp30) REVERT: A 538 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7286 (mmp80) REVERT: A 788 ASN cc_start: 0.8027 (p0) cc_final: 0.7756 (p0) REVERT: A 829 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8486 (mmtm) REVERT: A 1137 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7071 (ttp80) REVERT: A 1158 LYS cc_start: 0.8033 (mtmp) cc_final: 0.7776 (mtmm) REVERT: B 200 LYS cc_start: 0.3225 (OUTLIER) cc_final: 0.3001 (tttt) REVERT: B 398 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8017 (ttt180) REVERT: B 538 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7270 (mmp80) REVERT: B 600 ARG cc_start: 0.7118 (mmt180) cc_final: 0.6916 (mmt180) REVERT: B 830 GLU cc_start: 0.8575 (mp0) cc_final: 0.8338 (mp0) REVERT: B 1140 LEU cc_start: 0.8041 (tp) cc_final: 0.7617 (tp) REVERT: C 180 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: C 190 GLU cc_start: 0.7062 (mp0) cc_final: 0.6531 (mp0) REVERT: C 243 TRP cc_start: 0.6251 (m-10) cc_final: 0.5766 (m100) REVERT: C 250 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: C 346 PHE cc_start: 0.7413 (m-10) cc_final: 0.7137 (m-10) REVERT: C 382 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8297 (mmtt) REVERT: C 788 ASN cc_start: 0.8126 (p0) cc_final: 0.7808 (p0) REVERT: C 791 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7682 (mm-30) REVERT: C 829 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8356 (mmpt) REVERT: C 930 MET cc_start: 0.7083 (tpt) cc_final: 0.6690 (tpt) REVERT: C 1137 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7263 (ttp80) REVERT: C 1140 LEU cc_start: 0.8062 (tp) cc_final: 0.7726 (tp) REVERT: D 117 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6951 (mm) REVERT: D 168 LEU cc_start: 0.7937 (tp) cc_final: 0.7611 (tt) REVERT: D 234 LEU cc_start: 0.8272 (tp) cc_final: 0.7999 (tp) REVERT: D 308 CYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8023 (m) REVERT: D 538 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7315 (mmp80) REVERT: D 604 LYS cc_start: 0.8167 (pttt) cc_final: 0.7874 (pptt) REVERT: D 786 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8274 (mppt) REVERT: D 829 LYS cc_start: 0.7798 (tmtt) cc_final: 0.7270 (tmtt) REVERT: D 830 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: D 1158 LYS cc_start: 0.8044 (mtmp) cc_final: 0.7844 (mttt) outliers start: 113 outliers final: 55 residues processed: 608 average time/residue: 1.3540 time to fit residues: 967.3385 Evaluate side-chains 591 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 524 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 229 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 632 ASN B 845 HIS B1147 GLN ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.126852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092661 restraints weight = 50186.230| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.14 r_work: 0.3086 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 29361 Z= 0.197 Angle : 0.624 10.117 39824 Z= 0.310 Chirality : 0.045 0.276 4548 Planarity : 0.006 0.139 4992 Dihedral : 5.605 166.620 3913 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 4.07 % Allowed : 20.49 % Favored : 75.44 % 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: 0.65 (0.14), residues: 3532 helix: 1.07 (0.13), residues: 1712 sheet: -0.51 (0.27), residues: 364 loop : 0.07 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 177 HIS 0.006 0.002 HIS C 291 PHE 0.034 0.002 PHE C 188 TYR 0.016 0.002 TYR A1022 ARG 0.009 0.001 ARG A 948 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1416) hydrogen bonds : angle 4.54982 ( 3981) metal coordination : bond 0.00213 ( 16) metal coordination : angle 1.08555 ( 12) covalent geometry : bond 0.00491 (29344) covalent geometry : angle 0.62354 (39812) Misc. bond : bond 0.00704 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 544 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.3998 (OUTLIER) cc_final: 0.3683 (ttpp) REVERT: A 347 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: A 351 TYR cc_start: 0.6987 (t80) cc_final: 0.6705 (t80) REVERT: A 355 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: A 398 ARG cc_start: 0.8395 (ttp80) cc_final: 0.7997 (ttt90) REVERT: A 426 SER cc_start: 0.8841 (t) cc_final: 0.8437 (p) REVERT: A 427 GLN cc_start: 0.8125 (pp30) cc_final: 0.7909 (pp30) REVERT: A 538 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7410 (mmt90) REVERT: A 565 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8376 (ttt90) REVERT: A 783 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7317 (pttp) REVERT: A 788 ASN cc_start: 0.8059 (p0) cc_final: 0.7785 (p0) REVERT: A 829 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8406 (mmtm) REVERT: A 859 MET cc_start: 0.8844 (ttm) cc_final: 0.8513 (ttm) REVERT: A 892 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6178 (pp20) REVERT: B 200 LYS cc_start: 0.3294 (OUTLIER) cc_final: 0.3061 (tttt) REVERT: B 398 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8122 (ttt180) REVERT: B 538 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7285 (mmp80) REVERT: B 565 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7668 (ttp-170) REVERT: B 1140 LEU cc_start: 0.8017 (tp) cc_final: 0.7596 (tp) REVERT: B 1158 LYS cc_start: 0.8039 (mtmp) cc_final: 0.7807 (mtmm) REVERT: C 243 TRP cc_start: 0.6259 (m-10) cc_final: 0.5782 (m100) REVERT: C 250 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: C 346 PHE cc_start: 0.7443 (m-10) cc_final: 0.7157 (m-10) REVERT: C 348 GLU cc_start: 0.7909 (tp30) cc_final: 0.7641 (tp30) REVERT: C 538 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7666 (mmp80) REVERT: C 565 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8202 (ttt90) REVERT: C 788 ASN cc_start: 0.8121 (p0) cc_final: 0.7815 (p0) REVERT: C 829 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8339 (mmpt) REVERT: C 1140 LEU cc_start: 0.8075 (tp) cc_final: 0.7715 (tp) REVERT: C 1160 LEU cc_start: 0.8403 (mt) cc_final: 0.8188 (mt) REVERT: D 117 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7014 (mm) REVERT: D 168 LEU cc_start: 0.7928 (tp) cc_final: 0.7607 (tt) REVERT: D 169 TRP cc_start: 0.7985 (m100) cc_final: 0.7543 (m100) REVERT: D 234 LEU cc_start: 0.8196 (tp) cc_final: 0.7941 (tp) REVERT: D 308 CYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8053 (m) REVERT: D 538 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7346 (mmp80) REVERT: D 602 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6662 (p0) REVERT: D 604 LYS cc_start: 0.8196 (pttt) cc_final: 0.7879 (pptt) REVERT: D 783 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7818 (pttp) REVERT: D 786 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8259 (mppt) REVERT: D 830 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: D 1158 LYS cc_start: 0.8116 (mtmp) cc_final: 0.7907 (mttt) outliers start: 128 outliers final: 67 residues processed: 624 average time/residue: 1.3465 time to fit residues: 985.5615 Evaluate side-chains 614 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 531 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.0030 chunk 304 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 chunk 281 optimal weight: 30.0000 chunk 214 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 336 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093466 restraints weight = 50136.236| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.97 r_work: 0.3157 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 29361 Z= 0.121 Angle : 0.579 10.198 39824 Z= 0.285 Chirality : 0.042 0.258 4548 Planarity : 0.005 0.137 4992 Dihedral : 5.496 176.467 3913 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 3.30 % Allowed : 21.41 % Favored : 75.29 % 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: 0.88 (0.14), residues: 3532 helix: 1.27 (0.13), residues: 1700 sheet: -0.37 (0.27), residues: 360 loop : 0.17 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP C 177 HIS 0.005 0.001 HIS C 291 PHE 0.023 0.001 PHE C 188 TYR 0.020 0.001 TYR D 553 ARG 0.011 0.001 ARG C 948 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 1416) hydrogen bonds : angle 4.43926 ( 3981) metal coordination : bond 0.00141 ( 16) metal coordination : angle 0.97821 ( 12) covalent geometry : bond 0.00296 (29344) covalent geometry : angle 0.57915 (39812) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 530 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8504 (p) cc_final: 0.8215 (m) REVERT: A 200 LYS cc_start: 0.3847 (OUTLIER) cc_final: 0.3576 (ttpp) REVERT: A 334 MET cc_start: 0.8285 (tpp) cc_final: 0.8006 (mmt) REVERT: A 347 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6962 (mm-30) REVERT: A 351 TYR cc_start: 0.6950 (t80) cc_final: 0.6667 (t80) REVERT: A 354 MET cc_start: 0.7421 (mmm) cc_final: 0.7144 (mmm) REVERT: A 355 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 398 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8062 (ttt180) REVERT: A 426 SER cc_start: 0.8793 (t) cc_final: 0.8370 (p) REVERT: A 427 GLN cc_start: 0.8052 (pp30) cc_final: 0.7841 (pp30) REVERT: A 565 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8207 (ttt90) REVERT: A 783 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7384 (pttp) REVERT: A 788 ASN cc_start: 0.8004 (p0) cc_final: 0.7758 (p0) REVERT: A 829 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8455 (mmtm) REVERT: A 892 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6205 (pp20) REVERT: A 1158 LYS cc_start: 0.8055 (mtmp) cc_final: 0.7790 (mtmm) REVERT: B 200 LYS cc_start: 0.3209 (OUTLIER) cc_final: 0.2980 (tttt) REVERT: B 398 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8060 (ttt180) REVERT: B 538 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7324 (mmt180) REVERT: B 830 GLU cc_start: 0.8496 (mp0) cc_final: 0.8285 (mp0) REVERT: B 1140 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7653 (tp) REVERT: B 1158 LYS cc_start: 0.8000 (mtmp) cc_final: 0.7768 (mtmm) REVERT: C 170 VAL cc_start: 0.8525 (p) cc_final: 0.8059 (m) REVERT: C 180 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: C 193 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6478 (mt) REVERT: C 243 TRP cc_start: 0.6377 (m-10) cc_final: 0.5962 (m100) REVERT: C 250 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: C 346 PHE cc_start: 0.7468 (m-10) cc_final: 0.7193 (m-10) REVERT: C 538 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7650 (mmp80) REVERT: C 565 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8058 (ttt90) REVERT: C 788 ASN cc_start: 0.8149 (p0) cc_final: 0.7855 (p0) REVERT: C 791 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7635 (mm-30) REVERT: C 829 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8300 (mmpt) REVERT: C 1140 LEU cc_start: 0.8064 (tp) cc_final: 0.7745 (tp) REVERT: D 117 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7091 (mm) REVERT: D 168 LEU cc_start: 0.8052 (tp) cc_final: 0.7754 (tt) REVERT: D 180 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7707 (tp40) REVERT: D 308 CYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8098 (m) REVERT: D 565 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8072 (ttt90) REVERT: D 604 LYS cc_start: 0.8099 (pttt) cc_final: 0.7816 (pptt) REVERT: D 783 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7798 (pptt) REVERT: D 786 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8273 (mppt) REVERT: D 829 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7349 (tmtt) outliers start: 104 outliers final: 42 residues processed: 602 average time/residue: 1.4357 time to fit residues: 1013.1536 Evaluate side-chains 577 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 519 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 186 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 77 optimal weight: 0.0970 chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 305 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 293 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 632 ASN A 845 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.127312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093621 restraints weight = 49916.019| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.10 r_work: 0.3138 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 29361 Z= 0.152 Angle : 0.620 18.319 39824 Z= 0.300 Chirality : 0.043 0.252 4548 Planarity : 0.005 0.135 4992 Dihedral : 4.622 34.341 3909 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 3.27 % Allowed : 21.47 % Favored : 75.25 % 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: 0.86 (0.14), residues: 3532 helix: 1.26 (0.13), residues: 1696 sheet: -0.42 (0.28), residues: 364 loop : 0.17 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 177 HIS 0.007 0.001 HIS C 291 PHE 0.044 0.002 PHE C 188 TYR 0.015 0.002 TYR D 553 ARG 0.011 0.001 ARG B 948 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1416) hydrogen bonds : angle 4.43982 ( 3981) metal coordination : bond 0.00150 ( 16) metal coordination : angle 1.00213 ( 12) covalent geometry : bond 0.00377 (29344) covalent geometry : angle 0.61946 (39812) Misc. bond : bond 0.00562 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 532 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8417 (p) cc_final: 0.8119 (m) REVERT: A 200 LYS cc_start: 0.3773 (OUTLIER) cc_final: 0.3469 (ttpp) REVERT: A 334 MET cc_start: 0.8103 (tpp) cc_final: 0.7853 (mmt) REVERT: A 347 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6831 (mm-30) REVERT: A 355 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: A 382 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8424 (mmtt) REVERT: A 398 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8086 (ttt180) REVERT: A 426 SER cc_start: 0.8797 (t) cc_final: 0.8401 (p) REVERT: A 538 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7392 (mmt90) REVERT: A 565 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8247 (ttt90) REVERT: A 788 ASN cc_start: 0.8066 (p0) cc_final: 0.7826 (p0) REVERT: A 829 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8354 (mmtm) REVERT: A 892 GLU cc_start: 0.6581 (tm-30) cc_final: 0.6211 (pp20) REVERT: A 968 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7957 (mmp80) REVERT: B 398 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8082 (ttt180) REVERT: B 411 GLU cc_start: 0.7847 (tp30) cc_final: 0.7612 (mm-30) REVERT: B 538 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7277 (mmp80) REVERT: B 841 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8344 (tptp) REVERT: B 892 GLU cc_start: 0.5991 (tm-30) cc_final: 0.5412 (pp20) REVERT: B 1140 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7550 (tp) REVERT: B 1158 LYS cc_start: 0.7989 (mtmp) cc_final: 0.7754 (mtmm) REVERT: C 170 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7934 (m) REVERT: C 180 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: C 193 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6465 (mt) REVERT: C 224 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7316 (tt) REVERT: C 243 TRP cc_start: 0.6210 (m-10) cc_final: 0.5706 (m100) REVERT: C 250 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: C 252 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6206 (mtt) REVERT: C 346 PHE cc_start: 0.7461 (m-10) cc_final: 0.7180 (m-10) REVERT: C 348 GLU cc_start: 0.7937 (tp30) cc_final: 0.7576 (tp30) REVERT: C 538 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7667 (mmp80) REVERT: C 565 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8136 (ttt90) REVERT: C 788 ASN cc_start: 0.8171 (p0) cc_final: 0.7877 (p0) REVERT: C 791 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7675 (mm-30) REVERT: C 829 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8263 (mmpt) REVERT: C 1140 LEU cc_start: 0.8029 (tp) cc_final: 0.7724 (tp) REVERT: C 1160 LEU cc_start: 0.8368 (mt) cc_final: 0.8136 (mt) REVERT: D 117 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7069 (mm) REVERT: D 168 LEU cc_start: 0.7864 (tp) cc_final: 0.7653 (tt) REVERT: D 180 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7797 (tp40) REVERT: D 308 CYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7976 (m) REVERT: D 538 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7370 (mmp80) REVERT: D 565 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8173 (ttt90) REVERT: D 604 LYS cc_start: 0.8105 (pttt) cc_final: 0.7818 (pptt) REVERT: D 783 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7765 (pptt) REVERT: D 786 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8272 (mppt) REVERT: D 829 LYS cc_start: 0.7751 (tmtt) cc_final: 0.7380 (tptp) outliers start: 103 outliers final: 54 residues processed: 602 average time/residue: 1.3816 time to fit residues: 977.3326 Evaluate side-chains 599 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 523 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 248 optimal weight: 0.0980 chunk 335 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 332 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 845 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B1147 GLN ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.128132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094547 restraints weight = 50350.662| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.13 r_work: 0.3154 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 29361 Z= 0.120 Angle : 0.602 17.366 39824 Z= 0.289 Chirality : 0.042 0.245 4548 Planarity : 0.005 0.132 4992 Dihedral : 4.501 33.461 3909 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.52 % Favored : 97.40 % Rotamer: Outliers : 2.60 % Allowed : 22.08 % Favored : 75.32 % 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: 1.02 (0.14), residues: 3532 helix: 1.39 (0.13), residues: 1688 sheet: -0.27 (0.28), residues: 360 loop : 0.23 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 177 HIS 0.007 0.001 HIS C 291 PHE 0.019 0.001 PHE A 188 TYR 0.019 0.001 TYR D 553 ARG 0.014 0.001 ARG A 948 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 1416) hydrogen bonds : angle 4.37482 ( 3981) metal coordination : bond 0.00225 ( 16) metal coordination : angle 0.98981 ( 12) covalent geometry : bond 0.00293 (29344) covalent geometry : angle 0.60218 (39812) Misc. bond : bond 0.00185 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 535 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8514 (p) cc_final: 0.8271 (m) REVERT: A 200 LYS cc_start: 0.3724 (OUTLIER) cc_final: 0.3471 (ttpp) REVERT: A 252 MET cc_start: 0.6855 (tpt) cc_final: 0.6638 (mmm) REVERT: A 312 PHE cc_start: 0.8166 (m-10) cc_final: 0.7889 (m-10) REVERT: A 334 MET cc_start: 0.8200 (tpp) cc_final: 0.7994 (mmt) REVERT: A 347 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: A 351 TYR cc_start: 0.7005 (t80) cc_final: 0.6761 (t80) REVERT: A 355 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: A 398 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8090 (ttt180) REVERT: A 426 SER cc_start: 0.8776 (t) cc_final: 0.8359 (p) REVERT: A 565 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8252 (ttt90) REVERT: A 788 ASN cc_start: 0.8022 (p0) cc_final: 0.7804 (p0) REVERT: A 829 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8449 (mmtm) REVERT: A 892 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6279 (pp20) REVERT: A 1158 LYS cc_start: 0.8065 (mtmp) cc_final: 0.7801 (mtmm) REVERT: B 163 ASN cc_start: 0.8262 (m-40) cc_final: 0.7784 (p0) REVERT: B 174 MET cc_start: 0.7077 (tpp) cc_final: 0.6552 (tpp) REVERT: B 398 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8093 (ttt180) REVERT: B 411 GLU cc_start: 0.7756 (tp30) cc_final: 0.7465 (mm-30) REVERT: B 538 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7335 (mmt180) REVERT: B 841 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8340 (tptp) REVERT: B 892 GLU cc_start: 0.6047 (tm-30) cc_final: 0.5505 (pp20) REVERT: B 1140 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7490 (tp) REVERT: B 1158 LYS cc_start: 0.8030 (mtmp) cc_final: 0.7812 (mtmm) REVERT: C 170 VAL cc_start: 0.8390 (p) cc_final: 0.7903 (m) REVERT: C 180 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: C 193 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6353 (mt) REVERT: C 224 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7393 (tt) REVERT: C 243 TRP cc_start: 0.6355 (m-10) cc_final: 0.5948 (m100) REVERT: C 250 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: C 252 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6281 (mtt) REVERT: C 346 PHE cc_start: 0.7503 (m-10) cc_final: 0.7233 (m-10) REVERT: C 348 GLU cc_start: 0.7955 (tp30) cc_final: 0.7577 (tp30) REVERT: C 565 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8114 (ttt90) REVERT: C 788 ASN cc_start: 0.8144 (p0) cc_final: 0.7869 (p0) REVERT: C 791 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7670 (mm-30) REVERT: C 829 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8326 (mmpt) REVERT: C 1140 LEU cc_start: 0.7990 (tp) cc_final: 0.7720 (tp) REVERT: C 1160 LEU cc_start: 0.8393 (mt) cc_final: 0.8173 (mt) REVERT: D 117 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7281 (mm) REVERT: D 192 MET cc_start: 0.6225 (mtp) cc_final: 0.5520 (mpp) REVERT: D 193 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.4943 (mt) REVERT: D 308 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8101 (m) REVERT: D 354 MET cc_start: 0.7494 (mtp) cc_final: 0.7235 (mtt) REVERT: D 565 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8113 (ttt90) REVERT: D 604 LYS cc_start: 0.8064 (pttt) cc_final: 0.7832 (pptt) REVERT: D 786 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8234 (mppt) outliers start: 82 outliers final: 43 residues processed: 591 average time/residue: 1.3907 time to fit residues: 964.6848 Evaluate side-chains 577 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 517 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 101 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 335 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 331 optimal weight: 0.0670 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A1175 ASN B 218 ASN B 241 ASN B 632 ASN B 931 GLN ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS D1175 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092154 restraints weight = 50127.699| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.13 r_work: 0.3074 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 29361 Z= 0.228 Angle : 0.685 17.040 39824 Z= 0.331 Chirality : 0.047 0.255 4548 Planarity : 0.006 0.130 4992 Dihedral : 4.793 37.282 3909 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.89 % Rotamer: Outliers : 2.83 % Allowed : 22.20 % Favored : 74.97 % 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: 3532 helix: 1.14 (0.13), residues: 1724 sheet: -0.43 (0.27), residues: 364 loop : 0.03 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 177 HIS 0.008 0.002 HIS C 291 PHE 0.039 0.002 PHE C 188 TYR 0.024 0.002 TYR B 876 ARG 0.014 0.001 ARG A 948 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 1416) hydrogen bonds : angle 4.50189 ( 3981) metal coordination : bond 0.00356 ( 16) metal coordination : angle 1.13832 ( 12) covalent geometry : bond 0.00570 (29344) covalent geometry : angle 0.68522 (39812) Misc. bond : bond 0.00141 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 544 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.3894 (OUTLIER) cc_final: 0.3571 (ttpp) REVERT: A 312 PHE cc_start: 0.8326 (m-10) cc_final: 0.8058 (m-10) REVERT: A 334 MET cc_start: 0.8223 (tpp) cc_final: 0.8020 (mmt) REVERT: A 347 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: A 351 TYR cc_start: 0.7147 (t80) cc_final: 0.6902 (t80) REVERT: A 355 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: A 382 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8449 (mmtt) REVERT: A 398 ARG cc_start: 0.8403 (ttp80) cc_final: 0.7968 (ttt90) REVERT: A 426 SER cc_start: 0.8816 (t) cc_final: 0.8421 (p) REVERT: A 538 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7377 (mmt90) REVERT: A 565 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8375 (ttt90) REVERT: A 788 ASN cc_start: 0.8083 (p0) cc_final: 0.7831 (p0) REVERT: A 829 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8326 (mmtm) REVERT: A 892 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6329 (pp20) REVERT: B 398 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8151 (ttt180) REVERT: B 411 GLU cc_start: 0.7857 (tp30) cc_final: 0.7600 (mm-30) REVERT: B 538 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7278 (mmp80) REVERT: B 565 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7587 (ttp-170) REVERT: B 841 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8361 (tptp) REVERT: B 892 GLU cc_start: 0.6147 (tm-30) cc_final: 0.5518 (pt0) REVERT: B 1140 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7584 (tp) REVERT: B 1158 LYS cc_start: 0.8081 (mtmp) cc_final: 0.7839 (mtmm) REVERT: C 170 VAL cc_start: 0.8455 (p) cc_final: 0.7993 (m) REVERT: C 180 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: C 224 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7439 (tt) REVERT: C 250 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: C 252 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6245 (mtt) REVERT: C 345 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: C 346 PHE cc_start: 0.7565 (m-10) cc_final: 0.7320 (m-10) REVERT: C 348 GLU cc_start: 0.8007 (tp30) cc_final: 0.7695 (tp30) REVERT: C 565 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8273 (ttt90) REVERT: C 788 ASN cc_start: 0.8218 (p0) cc_final: 0.7927 (p0) REVERT: C 791 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7725 (mm-30) REVERT: C 829 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8336 (mmpt) REVERT: C 1160 LEU cc_start: 0.8435 (mt) cc_final: 0.8205 (mt) REVERT: D 117 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7267 (mm) REVERT: D 192 MET cc_start: 0.6242 (mtp) cc_final: 0.5549 (mpp) REVERT: D 308 CYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8193 (m) REVERT: D 411 GLU cc_start: 0.7773 (tp30) cc_final: 0.7572 (tp30) REVERT: D 538 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7334 (mmp80) REVERT: D 565 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8237 (ttt90) REVERT: D 604 LYS cc_start: 0.8140 (pttt) cc_final: 0.7848 (pptt) REVERT: D 786 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8274 (mppt) REVERT: D 829 LYS cc_start: 0.8391 (mmpt) cc_final: 0.7811 (tptp) REVERT: D 1142 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6993 (mtp180) outliers start: 89 outliers final: 50 residues processed: 600 average time/residue: 1.3799 time to fit residues: 972.0773 Evaluate side-chains 605 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 535 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 18 optimal weight: 6.9990 chunk 331 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 33 optimal weight: 0.0270 chunk 14 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 284 optimal weight: 0.9980 overall best weight: 1.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS D1147 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.126801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093182 restraints weight = 50258.027| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.10 r_work: 0.3131 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 29361 Z= 0.176 Angle : 0.655 16.958 39824 Z= 0.316 Chirality : 0.044 0.239 4548 Planarity : 0.008 0.430 4992 Dihedral : 4.972 96.639 3909 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 2.35 % Allowed : 23.09 % Favored : 74.56 % 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: 0.83 (0.14), residues: 3532 helix: 1.25 (0.13), residues: 1700 sheet: -0.41 (0.28), residues: 364 loop : 0.13 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 177 HIS 0.007 0.001 HIS C 291 PHE 0.030 0.002 PHE B 283 TYR 0.016 0.002 TYR B 403 ARG 0.036 0.001 ARG B1137 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1416) hydrogen bonds : angle 4.48112 ( 3981) metal coordination : bond 0.00234 ( 16) metal coordination : angle 1.00604 ( 12) covalent geometry : bond 0.00436 (29344) covalent geometry : angle 0.65440 (39812) Misc. bond : bond 0.00336 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 524 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8380 (p) cc_final: 0.8093 (m) REVERT: A 200 LYS cc_start: 0.3851 (OUTLIER) cc_final: 0.3533 (ttpp) REVERT: A 312 PHE cc_start: 0.8141 (m-10) cc_final: 0.7855 (m-10) REVERT: A 347 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: A 351 TYR cc_start: 0.7077 (t80) cc_final: 0.6823 (t80) REVERT: A 355 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: A 382 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8382 (mmtt) REVERT: A 398 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8105 (ttt180) REVERT: A 426 SER cc_start: 0.8767 (t) cc_final: 0.8378 (p) REVERT: A 565 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8299 (ttt90) REVERT: A 788 ASN cc_start: 0.8098 (p0) cc_final: 0.7859 (p0) REVERT: A 892 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6348 (pp20) REVERT: B 398 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8115 (ttt180) REVERT: B 411 GLU cc_start: 0.7780 (tp30) cc_final: 0.7483 (mm-30) REVERT: B 538 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7265 (mmp80) REVERT: B 565 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7547 (ttp-170) REVERT: B 841 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8337 (tptp) REVERT: B 892 GLU cc_start: 0.6156 (tm-30) cc_final: 0.5694 (pp20) REVERT: B 1140 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7564 (tp) REVERT: B 1158 LYS cc_start: 0.8010 (mtmp) cc_final: 0.7767 (mtmm) REVERT: C 170 VAL cc_start: 0.8250 (p) cc_final: 0.7781 (m) REVERT: C 180 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: C 213 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6760 (p) REVERT: C 224 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7432 (tt) REVERT: C 250 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: C 252 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.6071 (mtt) REVERT: C 346 PHE cc_start: 0.7522 (m-10) cc_final: 0.7271 (m-10) REVERT: C 348 GLU cc_start: 0.7936 (tp30) cc_final: 0.7632 (tp30) REVERT: C 565 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8208 (ttt90) REVERT: C 788 ASN cc_start: 0.8228 (p0) cc_final: 0.7949 (p0) REVERT: C 791 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 829 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8241 (mmpt) REVERT: C 830 GLU cc_start: 0.8549 (mp0) cc_final: 0.8343 (mm-30) REVERT: C 1160 LEU cc_start: 0.8385 (mt) cc_final: 0.8156 (mt) REVERT: D 117 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7210 (mm) REVERT: D 180 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7882 (tp40) REVERT: D 192 MET cc_start: 0.6201 (mtp) cc_final: 0.5475 (mpp) REVERT: D 193 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.4800 (mt) REVERT: D 308 CYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8037 (m) REVERT: D 538 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7342 (mmp80) REVERT: D 565 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8164 (ttt90) REVERT: D 604 LYS cc_start: 0.8092 (pttt) cc_final: 0.7866 (pptt) REVERT: D 786 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8261 (mppt) REVERT: D 829 LYS cc_start: 0.8365 (mmpt) cc_final: 0.7822 (tptp) REVERT: D 1142 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6971 (mtp180) outliers start: 74 outliers final: 52 residues processed: 578 average time/residue: 1.3696 time to fit residues: 928.7553 Evaluate side-chains 595 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 522 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 121 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 218 optimal weight: 0.9990 chunk 302 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 845 HIS B 180 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 845 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094372 restraints weight = 50144.594| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.10 r_work: 0.3152 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29361 Z= 0.123 Angle : 0.631 16.917 39824 Z= 0.302 Chirality : 0.042 0.234 4548 Planarity : 0.006 0.158 4992 Dihedral : 5.234 160.500 3909 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % Rotamer: Outliers : 2.22 % Allowed : 23.32 % Favored : 74.46 % 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 (0.14), residues: 3532 helix: 1.39 (0.13), residues: 1684 sheet: -0.27 (0.27), residues: 376 loop : 0.21 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 177 HIS 0.006 0.001 HIS C 291 PHE 0.032 0.001 PHE C 188 TYR 0.017 0.001 TYR D 553 ARG 0.014 0.001 ARG D 948 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 1416) hydrogen bonds : angle 4.42380 ( 3981) metal coordination : bond 0.00307 ( 16) metal coordination : angle 1.04536 ( 12) covalent geometry : bond 0.00302 (29344) covalent geometry : angle 0.63065 (39812) Misc. bond : bond 0.00516 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31113.54 seconds wall clock time: 533 minutes 59.92 seconds (32039.92 seconds total)