Starting phenix.real_space_refine on Tue Jun 24 17:48:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hyj_35086/06_2025/8hyj_35086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hyj_35086/06_2025/8hyj_35086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hyj_35086/06_2025/8hyj_35086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hyj_35086/06_2025/8hyj_35086.map" model { file = "/net/cci-nas-00/data/ceres_data/8hyj_35086/06_2025/8hyj_35086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hyj_35086/06_2025/8hyj_35086.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 83 5.49 5 Mg 1 5.21 5 S 161 5.16 5 C 17890 2.51 5 N 4986 2.21 5 O 5443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28568 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8794 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 42, 'TRANS': 1098} Chain breaks: 4 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 7912 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 40, 'TRANS': 1013} Chain breaks: 10 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 1, 'GLU:plan': 38, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 343 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2123 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 896 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1652 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 554 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1417 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 904 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 3, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 702 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "J" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 484 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 96} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 309 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 749 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "P" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 746 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17355 SG CYS C 90 60.680 84.146 143.944 1.00 95.55 S ATOM 17378 SG CYS C 93 57.920 83.536 141.364 1.00105.96 S ATOM 17419 SG CYS C 99 57.118 84.814 144.844 1.00 80.86 S ATOM 17441 SG CYS C 102 58.791 86.914 141.950 1.00 77.68 S ATOM 24296 SG CYS I 7 45.093 155.861 39.569 1.00 97.61 S ATOM 24312 SG CYS I 10 42.976 153.903 41.222 1.00 99.01 S ATOM 24439 SG CYS I 29 45.564 153.282 37.551 1.00117.62 S ATOM 24458 SG CYS I 32 42.257 154.176 37.378 1.00116.72 S ATOM 25006 SG CYS J 7 63.320 115.605 129.564 1.00 47.84 S ATOM 25030 SG CYS J 10 65.362 115.545 133.098 1.00 51.10 S ATOM 25284 SG CYS J 44 66.199 118.184 130.418 1.00 53.90 S ATOM 25290 SG CYS J 45 63.042 117.973 132.249 1.00 54.08 S ATOM 26226 SG CYS L 12 24.478 99.768 111.775 1.00 72.87 S ATOM 26244 SG CYS L 15 22.009 100.937 114.195 1.00 85.23 S ATOM 26337 SG CYS L 29 21.755 97.770 111.461 1.00 78.65 S ATOM 26353 SG CYS L 32 21.454 100.798 109.987 1.00 84.11 S Time building chain proxies: 16.21, per 1000 atoms: 0.57 Number of scatterers: 28568 At special positions: 0 Unit cell: (146.3, 173.8, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 161 16.00 P 83 15.00 Mg 1 11.99 O 5443 8.00 N 4986 7.00 C 17890 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=0, symmetry=0 Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 24 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 39 sheets defined 35.2% alpha, 15.2% beta 21 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 10.62 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.531A pdb=" N THR A 44 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 45 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.911A pdb=" N LEU A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.734A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 215 through 219 removed outlier: 4.059A pdb=" N LEU A 218 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 275 removed outlier: 4.040A pdb=" N THR A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.548A pdb=" N ALA A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.610A pdb=" N GLN A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.767A pdb=" N SER A 422 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 509 through 519 removed outlier: 4.320A pdb=" N TYR A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.597A pdb=" N ILE A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 4.213A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 616 removed outlier: 3.661A pdb=" N THR A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Proline residue: A 606 - end of helix removed outlier: 3.568A pdb=" N ALA A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.580A pdb=" N VAL A 646 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 648 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 675 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.718A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 750 through 784 Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 828 through 846 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 862 removed outlier: 3.654A pdb=" N SER A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 3.752A pdb=" N ARG A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 901 removed outlier: 3.651A pdb=" N ARG A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 901 " --> pdb=" O CYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 3.729A pdb=" N THR A 911 " --> pdb=" O SER A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.828A pdb=" N ASP A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.875A pdb=" N ARG A 981 " --> pdb=" O ASP A 978 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 982 " --> pdb=" O PHE A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 982' Processing helix chain 'A' and resid 1014 through 1033 removed outlier: 3.627A pdb=" N GLU A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A1029 " --> pdb=" O CYS A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 3.514A pdb=" N CYS A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1119 Processing helix chain 'A' and resid 1120 through 1140 removed outlier: 3.549A pdb=" N ALA A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 Processing helix chain 'A' and resid 1165 through 1176 Processing helix chain 'A' and resid 1180 through 1188 removed outlier: 3.907A pdb=" N GLU A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 4.018A pdb=" N CYS A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1213 removed outlier: 4.231A pdb=" N SER A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1225 removed outlier: 3.637A pdb=" N GLY A1224 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1225 " --> pdb=" O GLY A1222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1221 through 1225' Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.786A pdb=" N LEU B 26 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.271A pdb=" N CYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 39 " --> pdb=" O CYS B 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.922A pdb=" N TYR B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.699A pdb=" N ALA B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 304 through 321 removed outlier: 3.589A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.801A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.668A pdb=" N LEU B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 404 through 431 removed outlier: 3.525A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.088A pdb=" N TYR B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.768A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 586 through 599 Processing helix chain 'B' and resid 634 through 640 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.634A pdb=" N GLU B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 670' Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.660A pdb=" N GLU B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.593A pdb=" N LEU B 697 " --> pdb=" O SER B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.799A pdb=" N ASP B 710 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 949 through 954 removed outlier: 3.707A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 971 removed outlier: 4.577A pdb=" N LEU B 960 " --> pdb=" O THR B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1008 removed outlier: 3.539A pdb=" N GLN B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B1006 " --> pdb=" O GLU B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1048 removed outlier: 3.968A pdb=" N LYS B1047 " --> pdb=" O MET B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1087 Processing helix chain 'B' and resid 1089 through 1098 Processing helix chain 'B' and resid 1148 through 1162 removed outlier: 3.524A pdb=" N LYS B1152 " --> pdb=" O PRO B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.607A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.586A pdb=" N ARG C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 4.408A pdb=" N MET C 82 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.767A pdb=" N TRP C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.570A pdb=" N THR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 204' Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 211 through 216 removed outlier: 4.635A pdb=" N GLU C 214 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.828A pdb=" N TYR C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 278 through 294 removed outlier: 3.966A pdb=" N ASN C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.920A pdb=" N VAL D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 removed outlier: 4.279A pdb=" N ARG D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 4.048A pdb=" N VAL D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Proline residue: D 148 - end of helix Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 169 through 177 Processing helix chain 'D' and resid 178 through 181 removed outlier: 4.090A pdb=" N LYS D 181 " --> pdb=" O PRO D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 183 through 201 removed outlier: 6.073A pdb=" N GLN D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 22 through 42 removed outlier: 3.756A pdb=" N HIS E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 96 through 111 removed outlier: 3.696A pdb=" N ILE E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'F' and resid 66 through 82 Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.773A pdb=" N ILE F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.925A pdb=" N LEU G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.847A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.551A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.506A pdb=" N ALA K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 650 through 652 No H-bonds generated for 'chain 'W' and resid 650 through 652' Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.906A pdb=" N SER A 323 " --> pdb=" O ARG B1051 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 325 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B1049 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 341 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 353 removed outlier: 3.754A pdb=" N VAL A 400 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS A 401 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER A 374 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.618A pdb=" N VAL A 797 " --> pdb=" O ILE A 806 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 877 through 879 removed outlier: 3.868A pdb=" N ASN A1047 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1227 through 1228 removed outlier: 3.998A pdb=" N ILE F 114 " --> pdb=" O TRP F 126 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP F 126 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 76 removed outlier: 3.676A pdb=" N ALA B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 102 removed outlier: 5.332A pdb=" N ALA B 130 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 175 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 132 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AB4, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB5, first strand: chain 'B' and resid 398 through 401 removed outlier: 3.527A pdb=" N GLN B 220 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.844A pdb=" N PHE B 248 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 249 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 269 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 277 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 579 through 584 removed outlier: 5.565A pdb=" N TRP B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 576 " --> pdb=" O TRP B 580 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 582 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 660 through 663 removed outlier: 3.690A pdb=" N ARG B 629 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.911A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.911A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1014 through 1015 removed outlier: 7.063A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 789 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 859 through 861 removed outlier: 3.773A pdb=" N ILE B 861 " --> pdb=" O ILE B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 935 through 936 Processing sheet with id=AC5, first strand: chain 'B' and resid 1114 through 1115 removed outlier: 4.274A pdb=" N HIS B1106 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1145 " --> pdb=" O MET B1105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B1107 " --> pdb=" O VAL B1143 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B1143 " --> pdb=" O ILE B1107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 16 through 17 removed outlier: 3.850A pdb=" N GLU C 16 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 104 through 111 removed outlier: 3.595A pdb=" N VAL C 104 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 52 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY C 172 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AC9, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AD1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.726A pdb=" N GLN E 161 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.140A pdb=" N PHE G 76 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP G 9 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 74 " --> pdb=" O TRP G 9 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 13 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 70 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N ASP G 56 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N MET G 75 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR G 54 " --> pdb=" O MET G 75 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N SER G 77 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL G 52 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET G 79 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.140A pdb=" N PHE G 76 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP G 9 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 74 " --> pdb=" O TRP G 9 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 13 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 70 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 89 through 96 removed outlier: 6.729A pdb=" N PHE G 102 " --> pdb=" O HIS G 94 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL G 96 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL G 101 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR G 112 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET G 103 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN G 110 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE G 161 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN G 110 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 163 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER G 114 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY G 151 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER G 166 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL G 149 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY G 91 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL G 147 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE G 89 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 122 through 124 removed outlier: 3.887A pdb=" N ILE G 130 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 8 through 17 removed outlier: 5.667A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 115 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS H 96 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY H 95 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 139 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE H 8 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 14 through 19 Processing sheet with id=AD9, first strand: chain 'I' and resid 84 through 89 removed outlier: 3.788A pdb=" N TRP I 112 " --> pdb=" O PHE I 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.378A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 625 through 626 Processing sheet with id=AE3, first strand: chain 'W' and resid 638 through 639 985 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 14.36 Time building geometry restraints manager: 8.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4494 1.28 - 1.41: 7309 1.41 - 1.54: 16992 1.54 - 1.68: 221 1.68 - 1.81: 240 Bond restraints: 29256 Sorted by residual: bond pdb=" CA SER B 535 " pdb=" C SER B 535 " ideal model delta sigma weight residual 1.528 1.416 0.112 1.35e-02 5.49e+03 6.89e+01 bond pdb=" CA GLN B 955 " pdb=" C GLN B 955 " ideal model delta sigma weight residual 1.526 1.448 0.078 9.70e-03 1.06e+04 6.46e+01 bond pdb=" CA LYS B 211 " pdb=" C LYS B 211 " ideal model delta sigma weight residual 1.528 1.444 0.084 1.07e-02 8.73e+03 6.15e+01 bond pdb=" CA HIS C 177 " pdb=" C HIS C 177 " ideal model delta sigma weight residual 1.521 1.426 0.095 1.22e-02 6.72e+03 6.04e+01 bond pdb=" C LEU B 406 " pdb=" O LEU B 406 " ideal model delta sigma weight residual 1.236 1.141 0.096 1.25e-02 6.40e+03 5.88e+01 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 38643 3.83 - 7.65: 1116 7.65 - 11.48: 153 11.48 - 15.31: 30 15.31 - 19.14: 9 Bond angle restraints: 39951 Sorted by residual: angle pdb=" N VAL B 634 " pdb=" CA VAL B 634 " pdb=" C VAL B 634 " ideal model delta sigma weight residual 110.42 125.93 -15.51 9.40e-01 1.13e+00 2.72e+02 angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 111.36 126.20 -14.84 1.09e+00 8.42e-01 1.85e+02 angle pdb=" N SER B 730 " pdb=" CA SER B 730 " pdb=" C SER B 730 " ideal model delta sigma weight residual 111.07 125.56 -14.49 1.07e+00 8.73e-01 1.84e+02 angle pdb=" N ASP J 33 " pdb=" CA ASP J 33 " pdb=" C ASP J 33 " ideal model delta sigma weight residual 113.61 95.01 18.60 1.50e+00 4.44e-01 1.54e+02 angle pdb=" N GLY B 72 " pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 112.31 131.45 -19.14 1.59e+00 3.96e-01 1.45e+02 ... (remaining 39946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 16773 34.45 - 68.89: 669 68.89 - 103.34: 35 103.34 - 137.78: 1 137.78 - 172.23: 8 Dihedral angle restraints: 17486 sinusoidal: 7233 harmonic: 10253 Sorted by residual: dihedral pdb=" CA GLU B 77 " pdb=" C GLU B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" C VAL B 778 " pdb=" N VAL B 778 " pdb=" CA VAL B 778 " pdb=" CB VAL B 778 " ideal model delta harmonic sigma weight residual -122.00 -107.75 -14.25 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" C GLN B 974 " pdb=" N GLN B 974 " pdb=" CA GLN B 974 " pdb=" CB GLN B 974 " ideal model delta harmonic sigma weight residual -122.60 -108.96 -13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 17483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4038 0.134 - 0.269: 456 0.269 - 0.403: 115 0.403 - 0.537: 20 0.537 - 0.672: 7 Chirality restraints: 4636 Sorted by residual: chirality pdb=" CA ARG W 627 " pdb=" N ARG W 627 " pdb=" C ARG W 627 " pdb=" CB ARG W 627 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA LYS B 181 " pdb=" N LYS B 181 " pdb=" C LYS B 181 " pdb=" CB LYS B 181 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA GLU C 28 " pdb=" N GLU C 28 " pdb=" C GLU C 28 " pdb=" CB GLU C 28 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.71e+00 ... (remaining 4633 not shown) Planarity restraints: 4805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1030 " -0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C PRO A1030 " 0.091 2.00e-02 2.50e+03 pdb=" O PRO A1030 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL A1031 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 134 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 522 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 523 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 523 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 523 " 0.060 5.00e-02 4.00e+02 ... (remaining 4802 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 2306 2.70 - 3.25: 26972 3.25 - 3.80: 44375 3.80 - 4.35: 55494 4.35 - 4.90: 90323 Nonbonded interactions: 219470 Sorted by model distance: nonbonded pdb=" N ASP J 33 " pdb=" N ALA J 34 " model vdw 2.155 2.560 nonbonded pdb=" O SER A 707 " pdb=" OH TYR A 713 " model vdw 2.198 3.040 nonbonded pdb=" CZ PHE B 116 " pdb=" CB ALA B 121 " model vdw 2.200 3.760 nonbonded pdb=" NH2 ARG A1060 " pdb=" CG GLU E 210 " model vdw 2.200 3.520 nonbonded pdb=" O4 DT N 6 " pdb=" N6 DA T -6 " model vdw 2.211 3.120 ... (remaining 219465 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 80.940 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 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 : 0.015 0.112 29272 Z= 1.102 Angle : 1.524 40.263 39975 Z= 0.996 Chirality : 0.099 0.672 4636 Planarity : 0.007 0.114 4805 Dihedral : 17.343 172.228 10834 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.39 % Allowed : 9.01 % Favored : 88.60 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.12), residues: 3465 helix: -1.03 (0.14), residues: 1133 sheet: -1.53 (0.22), residues: 515 loop : -2.28 (0.12), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 119 HIS 0.016 0.002 HIS B 51 PHE 0.044 0.002 PHE C 24 TYR 0.033 0.002 TYR C 190 ARG 0.008 0.001 ARG B 629 Details of bonding type rmsd hydrogen bonds : bond 0.20977 ( 1011) hydrogen bonds : angle 7.73601 ( 2868) metal coordination : bond 0.01576 ( 16) metal coordination : angle 14.26044 ( 24) covalent geometry : bond 0.01500 (29256) covalent geometry : angle 1.48340 (39951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 388 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.7885 (pt) cc_final: 0.7497 (tp) REVERT: A 852 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6151 (m110) REVERT: A 1035 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 658 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.5816 (tp) REVERT: B 740 THR cc_start: 0.6161 (m) cc_final: 0.5838 (p) REVERT: B 902 LEU cc_start: 0.7248 (mp) cc_final: 0.6280 (tp) REVERT: B 1043 MET cc_start: 0.4568 (mtt) cc_final: 0.4266 (mtm) REVERT: B 1097 PHE cc_start: 0.7971 (t80) cc_final: 0.7594 (t80) REVERT: B 1146 TYR cc_start: 0.8627 (m-10) cc_final: 0.8364 (p90) REVERT: D 192 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8829 (pp30) REVERT: F 65 MET cc_start: 0.6230 (ttp) cc_final: 0.6005 (ttt) REVERT: F 74 LEU cc_start: 0.9063 (mt) cc_final: 0.8662 (tt) REVERT: F 98 LEU cc_start: 0.8704 (mt) cc_final: 0.8312 (mm) REVERT: F 102 MET cc_start: 0.9220 (tpt) cc_final: 0.8923 (tmm) REVERT: G 30 LEU cc_start: 0.9194 (mm) cc_final: 0.8943 (pp) REVERT: G 178 GLU cc_start: 0.5304 (mt-10) cc_final: 0.4687 (pm20) outliers start: 67 outliers final: 11 residues processed: 444 average time/residue: 0.4586 time to fit residues: 310.7010 Evaluate side-chains 209 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 40.0000 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 398 GLN A 461 GLN A 490 GLN A 543 GLN A 664 HIS A 947 GLN A1100 HIS ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 54 ASN B 65 GLN B 135 ASN B 204 GLN B 246 ASN B 397 ASN B 427 GLN B 441 HIS B 510 HIS B 513 HIS B 543 GLN B 577 ASN B 688 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN B 768 ASN B 770 GLN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 871 HIS B 918 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1038 GLN B1057 HIS ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN B1116 ASN C 94 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 202 ASN ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN E 37 GLN E 159 GLN ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 94 HIS H 137 GLN I 11 ASN I 12 ASN I 88 GLN J 16 ASN J 61 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN W 612 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.071251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.057134 restraints weight = 373359.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.058088 restraints weight = 264219.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.058687 restraints weight = 204896.652| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29272 Z= 0.192 Angle : 0.704 15.440 39975 Z= 0.363 Chirality : 0.043 0.191 4636 Planarity : 0.006 0.062 4805 Dihedral : 15.965 178.942 4721 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 0.25 % Allowed : 5.80 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3465 helix: -0.45 (0.15), residues: 1164 sheet: -1.35 (0.21), residues: 566 loop : -1.85 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 855 HIS 0.007 0.002 HIS B 120 PHE 0.020 0.002 PHE C 268 TYR 0.029 0.002 TYR A1169 ARG 0.006 0.001 ARG J 42 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 1011) hydrogen bonds : angle 5.26703 ( 2868) metal coordination : bond 0.01475 ( 16) metal coordination : angle 7.73618 ( 24) covalent geometry : bond 0.00390 (29256) covalent geometry : angle 0.67820 (39951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6250 (tt0) REVERT: A 724 PHE cc_start: 0.9234 (m-80) cc_final: 0.8884 (m-10) REVERT: B 495 GLN cc_start: 0.7825 (tt0) cc_final: 0.7253 (tm-30) REVERT: B 786 ASP cc_start: 0.7553 (t70) cc_final: 0.7164 (t0) REVERT: B 926 TYR cc_start: 0.8796 (t80) cc_final: 0.8561 (t80) REVERT: C 201 MET cc_start: 0.9058 (tmm) cc_final: 0.8799 (tmm) REVERT: C 251 MET cc_start: 0.8296 (mtt) cc_final: 0.7793 (mtt) REVERT: F 102 MET cc_start: 0.9267 (tpt) cc_final: 0.9051 (tmm) REVERT: G 138 ARG cc_start: 0.7573 (ptt-90) cc_final: 0.7279 (ptp90) REVERT: G 178 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6426 (pm20) REVERT: H 41 MET cc_start: 0.9363 (tmm) cc_final: 0.9094 (tmm) REVERT: H 121 MET cc_start: 0.8989 (ttm) cc_final: 0.8430 (ttm) REVERT: K 48 MET cc_start: 0.8149 (mmm) cc_final: 0.7565 (mmm) REVERT: K 67 LEU cc_start: 0.8088 (mp) cc_final: 0.7836 (mp) REVERT: W 627 ARG cc_start: 0.8061 (ptt180) cc_final: 0.7854 (mmm-85) outliers start: 7 outliers final: 0 residues processed: 243 average time/residue: 0.4142 time to fit residues: 162.3190 Evaluate side-chains 169 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 316 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 HIS A 86 HIS A 216 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 62 HIS B 543 GLN ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 280 GLN ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 HIS G 94 HIS ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 GLN H 137 GLN I 80 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.066077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.052481 restraints weight = 388055.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.053298 restraints weight = 278377.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.053873 restraints weight = 218125.503| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 29272 Z= 0.241 Angle : 0.756 13.074 39975 Z= 0.390 Chirality : 0.044 0.259 4636 Planarity : 0.006 0.082 4805 Dihedral : 16.055 173.550 4721 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 0.21 % Allowed : 6.55 % Favored : 93.23 % 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: -1.76 (0.13), residues: 3465 helix: -0.43 (0.15), residues: 1174 sheet: -1.22 (0.22), residues: 526 loop : -1.65 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1231 HIS 0.025 0.002 HIS W 653 PHE 0.029 0.002 PHE A 724 TYR 0.022 0.002 TYR A1169 ARG 0.012 0.001 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 1011) hydrogen bonds : angle 5.18290 ( 2868) metal coordination : bond 0.01514 ( 16) metal coordination : angle 7.64584 ( 24) covalent geometry : bond 0.00506 (29256) covalent geometry : angle 0.73251 (39951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.9090 (pmm) cc_final: 0.8841 (pmm) REVERT: A 470 MET cc_start: 0.8672 (mtm) cc_final: 0.8284 (mpp) REVERT: A 491 MET cc_start: 0.7661 (mmm) cc_final: 0.7315 (mmt) REVERT: A 724 PHE cc_start: 0.9311 (m-80) cc_final: 0.9039 (m-10) REVERT: B 786 ASP cc_start: 0.7708 (t70) cc_final: 0.7310 (t0) REVERT: B 1157 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8349 (mm-30) REVERT: C 201 MET cc_start: 0.8838 (tmm) cc_final: 0.8536 (tmm) REVERT: C 251 MET cc_start: 0.8355 (mtt) cc_final: 0.7664 (mtt) REVERT: D 93 MET cc_start: 0.4138 (mmp) cc_final: 0.3623 (mmm) REVERT: D 150 LYS cc_start: 0.9050 (pttp) cc_final: 0.8814 (mmtt) REVERT: F 102 MET cc_start: 0.9316 (tpt) cc_final: 0.9086 (tmm) REVERT: G 18 MET cc_start: 0.3141 (mmt) cc_final: 0.2781 (mmt) REVERT: G 24 MET cc_start: 0.6660 (tmm) cc_final: 0.5851 (tmm) REVERT: G 178 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6506 (pm20) REVERT: K 48 MET cc_start: 0.8505 (mmm) cc_final: 0.7839 (mmm) REVERT: W 638 VAL cc_start: 0.9046 (m) cc_final: 0.8400 (m) REVERT: W 647 PHE cc_start: 0.7577 (t80) cc_final: 0.7340 (t80) outliers start: 6 outliers final: 3 residues processed: 212 average time/residue: 0.4331 time to fit residues: 146.5851 Evaluate side-chains 154 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 321 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 324 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 350 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 450 ASN ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 229 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 110 HIS ** K 40 HIS ** 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 = 0.3906 r_free = 0.3906 target = 0.064144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.050859 restraints weight = 403844.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.051619 restraints weight = 288011.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.052169 restraints weight = 226448.688| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 29272 Z= 0.214 Angle : 0.687 11.121 39975 Z= 0.357 Chirality : 0.043 0.239 4636 Planarity : 0.005 0.049 4805 Dihedral : 16.144 172.420 4721 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % 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: -1.73 (0.13), residues: 3465 helix: -0.30 (0.15), residues: 1162 sheet: -1.27 (0.22), residues: 525 loop : -1.67 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1050 HIS 0.009 0.002 HIS W 653 PHE 0.025 0.002 PHE A 724 TYR 0.044 0.002 TYR B 442 ARG 0.011 0.001 ARG L 43 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 1011) hydrogen bonds : angle 5.22232 ( 2868) metal coordination : bond 0.01203 ( 16) metal coordination : angle 5.78324 ( 24) covalent geometry : bond 0.00451 (29256) covalent geometry : angle 0.67226 (39951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8711 (p0) cc_final: 0.8435 (t0) REVERT: A 405 MET cc_start: 0.9139 (pmm) cc_final: 0.8900 (pmm) REVERT: A 470 MET cc_start: 0.8617 (mtm) cc_final: 0.8361 (mtp) REVERT: A 491 MET cc_start: 0.8180 (mmm) cc_final: 0.7738 (mmt) REVERT: A 518 MET cc_start: 0.6523 (ptm) cc_final: 0.6040 (ppp) REVERT: A 724 PHE cc_start: 0.9307 (m-80) cc_final: 0.9023 (m-10) REVERT: B 713 ARG cc_start: 0.9307 (ptt90) cc_final: 0.9097 (ttp80) REVERT: B 786 ASP cc_start: 0.7735 (t70) cc_final: 0.7387 (t0) REVERT: B 1026 MET cc_start: 0.8911 (mmp) cc_final: 0.8310 (mmm) REVERT: C 251 MET cc_start: 0.8319 (mtt) cc_final: 0.7540 (mtt) REVERT: D 147 GLU cc_start: 0.8576 (pp20) cc_final: 0.8240 (pt0) REVERT: D 150 LYS cc_start: 0.9076 (pttp) cc_final: 0.8768 (ptpp) REVERT: G 18 MET cc_start: 0.3755 (mmt) cc_final: 0.2763 (mmt) REVERT: G 24 MET cc_start: 0.6411 (tmm) cc_final: 0.6171 (tmm) REVERT: G 178 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6781 (pm20) REVERT: H 39 MET cc_start: 0.5987 (tpt) cc_final: 0.5579 (mmm) REVERT: H 41 MET cc_start: 0.9339 (tmm) cc_final: 0.8521 (tmm) REVERT: H 121 MET cc_start: 0.9106 (ttm) cc_final: 0.8571 (tpp) REVERT: K 48 MET cc_start: 0.8511 (mmm) cc_final: 0.8004 (mmm) REVERT: W 647 PHE cc_start: 0.7225 (t80) cc_final: 0.6902 (t80) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.4216 time to fit residues: 128.9726 Evaluate side-chains 148 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 250 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 201 optimal weight: 30.0000 chunk 313 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 215 optimal weight: 30.0000 chunk 151 optimal weight: 0.0470 chunk 309 optimal weight: 20.0000 overall best weight: 6.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 HIS ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN K 51 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.063351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.050204 restraints weight = 405420.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.050949 restraints weight = 288327.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.051500 restraints weight = 226679.458| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29272 Z= 0.176 Angle : 0.635 13.567 39975 Z= 0.330 Chirality : 0.042 0.236 4636 Planarity : 0.004 0.057 4805 Dihedral : 16.185 174.200 4721 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.55 % 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: -1.50 (0.14), residues: 3465 helix: -0.01 (0.15), residues: 1147 sheet: -1.27 (0.22), residues: 518 loop : -1.55 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1050 HIS 0.010 0.001 HIS B 722 PHE 0.033 0.002 PHE H 24 TYR 0.018 0.002 TYR A1169 ARG 0.007 0.001 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 1011) hydrogen bonds : angle 5.13506 ( 2868) metal coordination : bond 0.01240 ( 16) metal coordination : angle 5.77549 ( 24) covalent geometry : bond 0.00374 (29256) covalent geometry : angle 0.61941 (39951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8678 (p0) cc_final: 0.8378 (t0) REVERT: A 405 MET cc_start: 0.9153 (pmm) cc_final: 0.8812 (pmm) REVERT: A 470 MET cc_start: 0.8662 (mtm) cc_final: 0.8384 (mtp) REVERT: A 491 MET cc_start: 0.8226 (mmm) cc_final: 0.7823 (mmt) REVERT: A 609 MET cc_start: 0.9016 (tpp) cc_final: 0.8572 (tpp) REVERT: A 724 PHE cc_start: 0.9346 (m-80) cc_final: 0.9031 (m-10) REVERT: B 223 MET cc_start: 0.7405 (ttt) cc_final: 0.7188 (ttt) REVERT: B 557 MET cc_start: 0.8246 (ppp) cc_final: 0.7946 (ppp) REVERT: B 713 ARG cc_start: 0.9304 (ptt90) cc_final: 0.9080 (ttp80) REVERT: B 786 ASP cc_start: 0.7726 (t70) cc_final: 0.7326 (t0) REVERT: B 917 MET cc_start: 0.9353 (mmp) cc_final: 0.9060 (mmp) REVERT: B 1026 MET cc_start: 0.8859 (mmp) cc_final: 0.8568 (mmm) REVERT: C 251 MET cc_start: 0.8310 (mtt) cc_final: 0.7666 (mtt) REVERT: D 93 MET cc_start: 0.3971 (mmp) cc_final: 0.2662 (mtt) REVERT: D 147 GLU cc_start: 0.8730 (pp20) cc_final: 0.8324 (pt0) REVERT: D 150 LYS cc_start: 0.9018 (pttp) cc_final: 0.8699 (ptpp) REVERT: G 18 MET cc_start: 0.4129 (mmt) cc_final: 0.3111 (mmt) REVERT: G 24 MET cc_start: 0.6547 (tmm) cc_final: 0.6264 (tmm) REVERT: G 178 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7000 (pm20) REVERT: H 41 MET cc_start: 0.9411 (tmm) cc_final: 0.8723 (tmm) REVERT: H 93 MET cc_start: 0.8110 (tpt) cc_final: 0.7878 (tpt) REVERT: H 121 MET cc_start: 0.8991 (ttm) cc_final: 0.8587 (tpp) REVERT: I 97 MET cc_start: 0.8899 (tpt) cc_final: 0.8699 (tpp) REVERT: K 48 MET cc_start: 0.8484 (mmm) cc_final: 0.7944 (mmm) REVERT: W 647 PHE cc_start: 0.6838 (t80) cc_final: 0.6403 (t80) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.4183 time to fit residues: 125.3000 Evaluate side-chains 148 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 210 optimal weight: 40.0000 chunk 291 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 307 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.062538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.049490 restraints weight = 409442.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.050243 restraints weight = 291999.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.050764 restraints weight = 228907.732| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29272 Z= 0.166 Angle : 0.619 12.475 39975 Z= 0.321 Chirality : 0.041 0.226 4636 Planarity : 0.004 0.050 4805 Dihedral : 16.306 173.442 4721 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: -1.47 (0.14), residues: 3465 helix: 0.08 (0.15), residues: 1161 sheet: -1.33 (0.22), residues: 505 loop : -1.57 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 855 HIS 0.020 0.001 HIS B 877 PHE 0.028 0.002 PHE H 24 TYR 0.022 0.002 TYR B1037 ARG 0.008 0.001 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 1011) hydrogen bonds : angle 5.06966 ( 2868) metal coordination : bond 0.01154 ( 16) metal coordination : angle 5.44397 ( 24) covalent geometry : bond 0.00354 (29256) covalent geometry : angle 0.60442 (39951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8627 (p0) cc_final: 0.8309 (t0) REVERT: A 405 MET cc_start: 0.9235 (pmm) cc_final: 0.8861 (pmm) REVERT: A 442 MET cc_start: 0.8944 (ptp) cc_final: 0.8544 (ptp) REVERT: A 470 MET cc_start: 0.8711 (mtm) cc_final: 0.8389 (mtp) REVERT: A 626 MET cc_start: 0.5526 (tpp) cc_final: 0.5243 (tpp) REVERT: A 631 MET cc_start: 0.9090 (mmm) cc_final: 0.8872 (tpt) REVERT: A 674 MET cc_start: 0.9088 (tpt) cc_final: 0.8860 (tpt) REVERT: A 724 PHE cc_start: 0.9328 (m-80) cc_final: 0.9033 (m-10) REVERT: B 223 MET cc_start: 0.7397 (ttt) cc_final: 0.7152 (ttt) REVERT: B 713 ARG cc_start: 0.9259 (ptt90) cc_final: 0.9051 (ttp80) REVERT: B 786 ASP cc_start: 0.7689 (t70) cc_final: 0.7262 (t0) REVERT: B 917 MET cc_start: 0.9375 (mmp) cc_final: 0.9027 (mmp) REVERT: B 1026 MET cc_start: 0.8798 (mmp) cc_final: 0.8493 (mmm) REVERT: C 251 MET cc_start: 0.8208 (mtt) cc_final: 0.7609 (mtt) REVERT: D 93 MET cc_start: 0.4208 (mmp) cc_final: 0.2427 (mtt) REVERT: D 147 GLU cc_start: 0.8750 (pp20) cc_final: 0.8438 (pt0) REVERT: G 18 MET cc_start: 0.4349 (mmt) cc_final: 0.3101 (mmt) REVERT: G 24 MET cc_start: 0.6597 (tmm) cc_final: 0.6052 (tmm) REVERT: G 178 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6680 (pm20) REVERT: H 93 MET cc_start: 0.8225 (tpt) cc_final: 0.7877 (tpt) REVERT: H 121 MET cc_start: 0.9032 (ttm) cc_final: 0.8585 (ttp) REVERT: I 97 MET cc_start: 0.8935 (tpt) cc_final: 0.8719 (tpp) REVERT: K 48 MET cc_start: 0.8491 (mmm) cc_final: 0.7958 (mmm) REVERT: W 647 PHE cc_start: 0.6511 (t80) cc_final: 0.6114 (t80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3870 time to fit residues: 113.5191 Evaluate side-chains 145 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 10.0000 chunk 333 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS E 143 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.061253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.048488 restraints weight = 419864.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.049219 restraints weight = 297647.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.049733 restraints weight = 233075.141| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.7880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29272 Z= 0.183 Angle : 0.657 10.775 39975 Z= 0.339 Chirality : 0.042 0.218 4636 Planarity : 0.005 0.054 4805 Dihedral : 16.390 174.811 4721 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -1.45 (0.14), residues: 3465 helix: 0.03 (0.15), residues: 1150 sheet: -1.30 (0.23), residues: 486 loop : -1.52 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1012 HIS 0.007 0.001 HIS B1106 PHE 0.023 0.002 PHE H 24 TYR 0.024 0.002 TYR I 44 ARG 0.010 0.001 ARG B1069 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 1011) hydrogen bonds : angle 5.23182 ( 2868) metal coordination : bond 0.01615 ( 16) metal coordination : angle 5.93046 ( 24) covalent geometry : bond 0.00388 (29256) covalent geometry : angle 0.64085 (39951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8594 (p0) cc_final: 0.8264 (t0) REVERT: A 405 MET cc_start: 0.9224 (pmm) cc_final: 0.8869 (pmm) REVERT: A 470 MET cc_start: 0.8823 (mtm) cc_final: 0.8487 (mtp) REVERT: A 518 MET cc_start: 0.7678 (ptm) cc_final: 0.6871 (ppp) REVERT: A 609 MET cc_start: 0.9004 (tpp) cc_final: 0.8642 (tpp) REVERT: A 674 MET cc_start: 0.9196 (tpt) cc_final: 0.8918 (tpp) REVERT: A 724 PHE cc_start: 0.9354 (m-80) cc_final: 0.9141 (m-10) REVERT: B 786 ASP cc_start: 0.7778 (t70) cc_final: 0.7357 (t0) REVERT: B 917 MET cc_start: 0.9323 (mmp) cc_final: 0.9030 (mmp) REVERT: B 1105 MET cc_start: 0.7555 (ptt) cc_final: 0.7321 (ppp) REVERT: C 251 MET cc_start: 0.8436 (mtt) cc_final: 0.7917 (mtt) REVERT: D 93 MET cc_start: 0.4916 (mmp) cc_final: 0.2459 (mtt) REVERT: D 147 GLU cc_start: 0.8664 (pp20) cc_final: 0.8246 (pt0) REVERT: D 150 LYS cc_start: 0.9074 (pttp) cc_final: 0.8759 (ptpp) REVERT: G 18 MET cc_start: 0.4838 (mmt) cc_final: 0.3350 (mmt) REVERT: G 178 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6723 (pm20) REVERT: H 41 MET cc_start: 0.9171 (tmm) cc_final: 0.8961 (tmm) REVERT: H 121 MET cc_start: 0.8975 (ttm) cc_final: 0.8199 (ttp) REVERT: I 97 MET cc_start: 0.8991 (tpt) cc_final: 0.8771 (tpp) REVERT: K 48 MET cc_start: 0.8597 (mmm) cc_final: 0.8027 (mmm) REVERT: W 647 PHE cc_start: 0.6338 (t80) cc_final: 0.5739 (t80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4026 time to fit residues: 118.6885 Evaluate side-chains 149 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 86 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 871 HIS B 877 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.061219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.048050 restraints weight = 407487.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.048794 restraints weight = 292602.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.049298 restraints weight = 230444.917| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.8137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29272 Z= 0.164 Angle : 0.629 10.203 39975 Z= 0.327 Chirality : 0.041 0.202 4636 Planarity : 0.004 0.054 4805 Dihedral : 16.424 174.130 4721 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -1.43 (0.14), residues: 3465 helix: 0.05 (0.15), residues: 1155 sheet: -1.45 (0.23), residues: 501 loop : -1.45 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 229 HIS 0.005 0.001 HIS B 711 PHE 0.032 0.002 PHE H 24 TYR 0.016 0.002 TYR B1037 ARG 0.013 0.001 ARG A 427 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1011) hydrogen bonds : angle 5.19024 ( 2868) metal coordination : bond 0.01092 ( 16) metal coordination : angle 5.10219 ( 24) covalent geometry : bond 0.00351 (29256) covalent geometry : angle 0.61682 (39951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.9210 (pmm) cc_final: 0.8812 (pmm) REVERT: A 518 MET cc_start: 0.7768 (ptm) cc_final: 0.6865 (ppp) REVERT: A 609 MET cc_start: 0.9038 (tpp) cc_final: 0.8628 (tpp) REVERT: A 674 MET cc_start: 0.9204 (tpt) cc_final: 0.8857 (tpp) REVERT: A 724 PHE cc_start: 0.9356 (m-80) cc_final: 0.9081 (m-10) REVERT: B 557 MET cc_start: 0.8416 (ppp) cc_final: 0.7897 (ppp) REVERT: B 786 ASP cc_start: 0.7767 (t70) cc_final: 0.7346 (t0) REVERT: B 917 MET cc_start: 0.9345 (mmp) cc_final: 0.9005 (mmp) REVERT: C 251 MET cc_start: 0.8502 (mtt) cc_final: 0.8036 (mtt) REVERT: D 93 MET cc_start: 0.4989 (mmp) cc_final: 0.1850 (mtt) REVERT: E 52 ASN cc_start: 0.9497 (m110) cc_final: 0.9203 (p0) REVERT: G 18 MET cc_start: 0.4745 (mmt) cc_final: 0.3383 (mmt) REVERT: G 178 GLU cc_start: 0.7742 (mt-10) cc_final: 0.6777 (pm20) REVERT: H 121 MET cc_start: 0.9000 (ttm) cc_final: 0.8528 (ttp) REVERT: I 97 MET cc_start: 0.9022 (tpt) cc_final: 0.8779 (tpp) REVERT: K 48 MET cc_start: 0.8517 (mmm) cc_final: 0.8058 (mmm) REVERT: W 647 PHE cc_start: 0.6429 (t80) cc_final: 0.5888 (t80) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.4037 time to fit residues: 118.3405 Evaluate side-chains 146 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 286 optimal weight: 50.0000 chunk 302 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 349 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1086 HIS B1104 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN E 154 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.060900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.048082 restraints weight = 413500.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.048822 restraints weight = 294366.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.049339 restraints weight = 230227.037| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.8437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29272 Z= 0.158 Angle : 0.632 9.464 39975 Z= 0.327 Chirality : 0.042 0.256 4636 Planarity : 0.004 0.048 4805 Dihedral : 16.478 174.019 4721 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -1.34 (0.14), residues: 3465 helix: 0.13 (0.15), residues: 1151 sheet: -1.41 (0.24), residues: 459 loop : -1.40 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 229 HIS 0.009 0.001 HIS B1106 PHE 0.023 0.002 PHE H 24 TYR 0.036 0.002 TYR G 115 ARG 0.007 0.001 ARG B 713 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1011) hydrogen bonds : angle 5.18355 ( 2868) metal coordination : bond 0.01036 ( 16) metal coordination : angle 5.14041 ( 24) covalent geometry : bond 0.00338 (29256) covalent geometry : angle 0.61910 (39951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.9219 (pmm) cc_final: 0.8839 (pmm) REVERT: A 609 MET cc_start: 0.9105 (tpp) cc_final: 0.8703 (tpp) REVERT: A 674 MET cc_start: 0.9190 (tpt) cc_final: 0.8817 (tpp) REVERT: A 724 PHE cc_start: 0.9374 (m-80) cc_final: 0.9107 (m-10) REVERT: B 786 ASP cc_start: 0.7739 (t70) cc_final: 0.7285 (t0) REVERT: B 917 MET cc_start: 0.9350 (mmp) cc_final: 0.9117 (mmp) REVERT: B 1032 MET cc_start: 0.8516 (mpp) cc_final: 0.8298 (mpp) REVERT: C 251 MET cc_start: 0.8426 (mtt) cc_final: 0.7931 (mtt) REVERT: D 93 MET cc_start: 0.4908 (mmp) cc_final: 0.1463 (mtt) REVERT: E 52 ASN cc_start: 0.9531 (m110) cc_final: 0.9239 (p0) REVERT: G 18 MET cc_start: 0.4691 (mmt) cc_final: 0.3364 (mmt) REVERT: G 24 MET cc_start: 0.7385 (tmm) cc_final: 0.6987 (tmm) REVERT: G 178 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6679 (pm20) REVERT: H 41 MET cc_start: 0.9094 (tmm) cc_final: 0.8864 (tmm) REVERT: H 121 MET cc_start: 0.8889 (ttm) cc_final: 0.8062 (ttp) REVERT: I 97 MET cc_start: 0.9104 (tpt) cc_final: 0.8798 (tpp) REVERT: K 48 MET cc_start: 0.8577 (mmm) cc_final: 0.8131 (mmm) REVERT: W 647 PHE cc_start: 0.6221 (t80) cc_final: 0.5650 (t80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3786 time to fit residues: 110.3439 Evaluate side-chains 147 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 130 optimal weight: 30.0000 chunk 289 optimal weight: 8.9990 chunk 98 optimal weight: 0.0030 chunk 135 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 299 optimal weight: 0.0070 chunk 161 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS K 65 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.062706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.049315 restraints weight = 397623.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.050037 restraints weight = 283870.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.050594 restraints weight = 224690.813| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.8237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29272 Z= 0.109 Angle : 0.595 10.418 39975 Z= 0.303 Chirality : 0.041 0.275 4636 Planarity : 0.004 0.054 4805 Dihedral : 16.312 173.966 4721 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.07 (0.14), residues: 3465 helix: 0.44 (0.15), residues: 1152 sheet: -1.26 (0.24), residues: 482 loop : -1.30 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 229 HIS 0.005 0.001 HIS E 154 PHE 0.018 0.001 PHE H 24 TYR 0.014 0.001 TYR K 87 ARG 0.005 0.001 ARG B 801 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 1011) hydrogen bonds : angle 4.81690 ( 2868) metal coordination : bond 0.00753 ( 16) metal coordination : angle 4.80683 ( 24) covalent geometry : bond 0.00236 (29256) covalent geometry : angle 0.58311 (39951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.9152 (pmm) cc_final: 0.8770 (pmm) REVERT: A 406 ASP cc_start: 0.9335 (m-30) cc_final: 0.9000 (m-30) REVERT: A 518 MET cc_start: 0.6872 (ptm) cc_final: 0.6300 (ppp) REVERT: A 609 MET cc_start: 0.9068 (tpp) cc_final: 0.8792 (tpp) REVERT: A 674 MET cc_start: 0.9201 (tpt) cc_final: 0.8911 (tpp) REVERT: A 724 PHE cc_start: 0.9385 (m-80) cc_final: 0.9089 (m-10) REVERT: B 557 MET cc_start: 0.8124 (ppp) cc_final: 0.7058 (ppp) REVERT: B 786 ASP cc_start: 0.7628 (t70) cc_final: 0.7183 (t0) REVERT: B 854 MET cc_start: 0.8987 (mmp) cc_final: 0.8706 (mmp) REVERT: B 917 MET cc_start: 0.9320 (mmp) cc_final: 0.9045 (mmp) REVERT: B 1105 MET cc_start: 0.7506 (ptt) cc_final: 0.7237 (ppp) REVERT: C 251 MET cc_start: 0.8207 (mtt) cc_final: 0.7703 (mtt) REVERT: D 93 MET cc_start: 0.4512 (mmp) cc_final: 0.1297 (mtt) REVERT: E 52 ASN cc_start: 0.9571 (m110) cc_final: 0.9296 (p0) REVERT: F 65 MET cc_start: 0.8333 (ttm) cc_final: 0.7746 (tpp) REVERT: G 18 MET cc_start: 0.4733 (mmt) cc_final: 0.3495 (mmt) REVERT: H 93 MET cc_start: 0.8054 (tpt) cc_final: 0.7841 (tpt) REVERT: H 121 MET cc_start: 0.8893 (ttm) cc_final: 0.7986 (ttp) REVERT: I 97 MET cc_start: 0.9185 (tpt) cc_final: 0.8903 (tpp) REVERT: K 48 MET cc_start: 0.8517 (mmm) cc_final: 0.8142 (mmm) REVERT: W 647 PHE cc_start: 0.6300 (t80) cc_final: 0.5868 (t80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3930 time to fit residues: 115.7965 Evaluate side-chains 147 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 55 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 253 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 83 optimal weight: 50.0000 chunk 338 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A 870 ASN ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.060746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.047881 restraints weight = 408964.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.048620 restraints weight = 288209.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.049139 restraints weight = 225681.023| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.8700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29272 Z= 0.174 Angle : 0.647 12.036 39975 Z= 0.333 Chirality : 0.042 0.249 4636 Planarity : 0.004 0.057 4805 Dihedral : 16.470 174.051 4721 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.17 (0.14), residues: 3465 helix: 0.28 (0.15), residues: 1153 sheet: -1.26 (0.24), residues: 471 loop : -1.32 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1070 HIS 0.012 0.001 HIS B 510 PHE 0.023 0.002 PHE H 24 TYR 0.038 0.002 TYR G 115 ARG 0.006 0.001 ARG B 713 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1011) hydrogen bonds : angle 5.07777 ( 2868) metal coordination : bond 0.01183 ( 16) metal coordination : angle 5.48504 ( 24) covalent geometry : bond 0.00372 (29256) covalent geometry : angle 0.63345 (39951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10429.03 seconds wall clock time: 181 minutes 25.02 seconds (10885.02 seconds total)