Starting phenix.real_space_refine on Sat Aug 8 14:21:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_35086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_35086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_35086.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_35086.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_35086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_35086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2026/8hyj_35086.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'ARG:plan': 6, 'HIS:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} 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: {'ASN:plan1': 7, 'GLU:plan': 38, 'ASP:plan': 21, 'TRP:plan': 1, 'TYR:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1} 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: {'GLU:plan': 8, 'ASP:plan': 10, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1} 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: {'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 3, 'GLU:plan': 7, '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: {'ASP:plan': 7, 'ARG:plan': 2, 'HIS:plan': 3, 'GLU:plan': 2} 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: {'ARG:plan': 4, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1} 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: {'ASP:plan': 4, 'GLN:plan1': 2} 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: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU: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: {'RNAv2': 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: 5.10, per 1000 atoms: 0.18 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 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: 2.99 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: 6.34 Time building geometry restraints manager: 3.06 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: 38642 3.83 - 7.65: 1116 7.65 - 11.48: 154 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: 16749 34.45 - 68.89: 658 68.89 - 103.34: 34 103.34 - 137.78: 1 137.78 - 172.23: 8 Dihedral angle restraints: 17450 sinusoidal: 7197 harmonic: 10253 Sorted by residual: dihedral pdb=" O5' G P 9 " pdb=" C5' G P 9 " pdb=" C4' G P 9 " pdb=" C3' G P 9 " ideal model delta sinusoidal sigma weight residual 180.00 120.87 59.13 3 6.40e+00 2.44e-02 5.21e+01 dihedral pdb=" O5' G P 8 " pdb=" C5' G P 8 " pdb=" C4' G P 8 " pdb=" C3' G P 8 " ideal model delta sinusoidal sigma weight residual -180.00 -139.93 -40.07 3 6.40e+00 2.44e-02 3.91e+01 dihedral pdb=" O5' U P 10 " pdb=" C5' U P 10 " pdb=" C4' U P 10 " pdb=" C3' U P 10 " ideal model delta sinusoidal sigma weight residual -180.00 -142.41 -37.59 3 6.40e+00 2.44e-02 3.61e+01 ... (remaining 17447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4027 0.134 - 0.269: 466 0.269 - 0.403: 115 0.403 - 0.537: 21 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.600 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 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= 1.112 Angle : 1.531 40.263 39975 Z= 1.009 Chirality : 0.100 0.672 4636 Planarity : 0.007 0.114 4805 Dihedral : 17.240 172.228 10798 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.46 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG B 629 TYR 0.033 0.002 TYR C 190 PHE 0.044 0.002 PHE C 24 TRP 0.037 0.003 TRP B 119 HIS 0.016 0.002 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.01504 / 1.11 (29256) covalent geometry : angle 1.49081 / 1.01 (39951) hydrogen bonds : bond 0.20977 / 13.94 ( 1011) hydrogen bonds : angle 7.73601 / 5.41 ( 2868) metal coordination : bond 0.01576 / 1.16 ( 16) metal coordination : angle 14.26044 / 10.13 ( 24) *********************** 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 : 0.837 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: 0.6152 (m110) REVERT: A 1035 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8321 (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: 0.7593 (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 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: 0.8925 (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: 0.1932 time to fit residues: 132.1763 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 HIS ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 364 GLN A 391 HIS A 398 GLN A 461 GLN A 483 HIS A 490 GLN A 543 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A1100 HIS ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 54 ASN B 57 ASN B 65 GLN B 135 ASN B 204 GLN B 246 ASN B 397 ASN B 414 HIS B 441 HIS B 510 HIS B 513 HIS B 577 ASN B 656 HIS B 688 HIS ** 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 768 ASN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1038 GLN B1052 ASN B1057 HIS B1104 GLN B1116 ASN C 94 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 197 ASN 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** H 67 ASN H 94 HIS H 137 GLN I 11 ASN I 12 ASN I 31 ASN I 88 GLN J 16 ASN J 61 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN L 47 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.072741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.058331 restraints weight = 361262.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.059207 restraints weight = 261260.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.059913 restraints weight = 206900.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.060405 restraints weight = 172891.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.060806 restraints weight = 150280.689| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29272 Z= 0.217 Angle : 0.771 17.598 39975 Z= 0.398 Chirality : 0.045 0.262 4636 Planarity : 0.006 0.083 4805 Dihedral : 15.669 176.415 4685 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 0.36 % Allowed : 5.41 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 3465 helix: -0.47 (0.15), residues: 1163 sheet: -1.39 (0.21), residues: 573 loop : -1.95 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 146 TYR 0.025 0.002 TYR B 442 PHE 0.026 0.002 PHE B 746 TRP 0.022 0.002 TRP B 461 HIS 0.017 0.002 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (29256) covalent geometry : angle 0.74223 / 0.40 (39951) hydrogen bonds : bond 0.05400 / 3.46 ( 1011) hydrogen bonds : angle 5.50130 / 3.80 ( 2868) metal coordination : bond 0.01541 / 1.12 ( 16) metal coordination : angle 8.47388 / 5.76 ( 24) *********************** 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 245 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 1.052 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: A 543 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6310 (tt0) REVERT: A 609 MET cc_start: 0.8038 (tpp) cc_final: 0.7754 (tpp) REVERT: A 724 PHE cc_start: 0.9295 (m-80) cc_final: 0.8966 (m-10) REVERT: B 495 GLN cc_start: 0.7790 (tt0) cc_final: 0.7239 (tm-30) REVERT: B 740 THR cc_start: 0.8928 (m) cc_final: 0.8497 (p) REVERT: B 786 ASP cc_start: 0.7540 (t70) cc_final: 0.7257 (t0) REVERT: B 917 MET cc_start: 0.9129 (mmp) cc_final: 0.8912 (mmm) REVERT: C 251 MET cc_start: 0.8155 (mtt) cc_final: 0.7572 (mtt) REVERT: F 102 MET cc_start: 0.9294 (tpt) cc_final: 0.9041 (tmm) REVERT: G 138 ARG cc_start: 0.7763 (ptt-90) cc_final: 0.7503 (ptp90) REVERT: G 178 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6624 (pm20) REVERT: H 41 MET cc_start: 0.9329 (tmm) cc_final: 0.9050 (tmm) REVERT: H 121 MET cc_start: 0.8854 (ttm) cc_final: 0.8149 (ttp) REVERT: K 48 MET cc_start: 0.8181 (mmm) cc_final: 0.7623 (mmm) REVERT: K 67 LEU cc_start: 0.7986 (mp) cc_final: 0.7594 (mp) outliers start: 10 outliers final: 1 residues processed: 245 average time/residue: 0.1661 time to fit residues: 65.7816 Evaluate side-chains 172 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 30.0000 chunk 289 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 317 optimal weight: 8.9990 chunk 342 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 255 optimal weight: 50.0000 chunk 287 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS A 86 HIS A 515 GLN A 546 GLN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN B 450 ASN B 711 HIS ** 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 749 GLN B 770 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS B1086 HIS B1104 GLN ** C 51 HIS ** 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.070516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.056531 restraints weight = 389680.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.057457 restraints weight = 276630.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.058102 restraints weight = 214239.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.058573 restraints weight = 177496.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.058868 restraints weight = 153952.598| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 29272 Z= 0.193 Angle : 0.672 13.745 39975 Z= 0.350 Chirality : 0.043 0.282 4636 Planarity : 0.005 0.083 4805 Dihedral : 15.613 175.254 4685 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 0.18 % Allowed : 3.99 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3465 helix: -0.25 (0.15), residues: 1180 sheet: -1.30 (0.21), residues: 555 loop : -1.63 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 419 TYR 0.033 0.001 TYR A 163 PHE 0.026 0.002 PHE E 175 TRP 0.016 0.002 TRP A 855 HIS 0.027 0.002 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (29256) covalent geometry : angle 0.65055 / 0.35 (39951) hydrogen bonds : bond 0.04473 / 2.87 ( 1011) hydrogen bonds : angle 5.15519 / 3.56 ( 2868) metal coordination : bond 0.01221 / 0.82 ( 16) metal coordination : angle 6.91552 / 4.82 ( 24) *********************** 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 216 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.926 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: 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 491 MET cc_start: 0.6934 (mmm) cc_final: 0.6702 (mmm) REVERT: A 724 PHE cc_start: 0.9164 (m-80) cc_final: 0.8780 (m-10) REVERT: A 755 MET cc_start: 0.3549 (ttt) cc_final: 0.3240 (ttt) REVERT: B 495 GLN cc_start: 0.7870 (tt0) cc_final: 0.7208 (tm-30) REVERT: B 785 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8921 (mp0) REVERT: B 786 ASP cc_start: 0.7535 (t70) cc_final: 0.7182 (t0) REVERT: C 201 MET cc_start: 0.8757 (tmm) cc_final: 0.8434 (tmm) REVERT: C 251 MET cc_start: 0.8237 (mtt) cc_final: 0.7607 (mtt) REVERT: F 102 MET cc_start: 0.9305 (tpt) cc_final: 0.9062 (tmm) REVERT: G 178 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6755 (pm20) REVERT: H 41 MET cc_start: 0.9406 (tmm) cc_final: 0.9174 (tmm) REVERT: H 121 MET cc_start: 0.8899 (ttm) cc_final: 0.8128 (ttp) REVERT: K 48 MET cc_start: 0.8243 (mmm) cc_final: 0.7708 (mmm) REVERT: K 67 LEU cc_start: 0.8208 (mp) cc_final: 0.7893 (mp) outliers start: 5 outliers final: 1 residues processed: 216 average time/residue: 0.1657 time to fit residues: 58.2343 Evaluate side-chains 166 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 92 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 246 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 144 optimal weight: 0.0970 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 HIS A 83 HIS A 216 ASN A 483 HIS A1233 GLN B 441 HIS ** 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 ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 HIS ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 12 ASN I 31 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 612 GLN W 653 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.069549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.055669 restraints weight = 388580.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.056573 restraints weight = 275686.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.057213 restraints weight = 214541.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.057568 restraints weight = 178305.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.057987 restraints weight = 157055.827| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29272 Z= 0.154 Angle : 0.619 15.503 39975 Z= 0.318 Chirality : 0.042 0.291 4636 Planarity : 0.004 0.052 4805 Dihedral : 15.617 179.346 4685 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3465 helix: 0.03 (0.15), residues: 1177 sheet: -1.31 (0.22), residues: 545 loop : -1.46 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 354 TYR 0.017 0.001 TYR B 442 PHE 0.029 0.002 PHE B 283 TRP 0.017 0.002 TRP A 855 HIS 0.009 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (29256) covalent geometry : angle 0.59673 / 0.32 (39951) hydrogen bonds : bond 0.03830 / 2.46 ( 1011) hydrogen bonds : angle 4.88778 / 3.39 ( 2868) metal coordination : bond 0.01028 / 0.74 ( 16) metal coordination : angle 6.69172 / 4.64 ( 24) *********************** 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 212 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.805 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: A 491 MET cc_start: 0.7174 (mmm) cc_final: 0.6640 (mmt) REVERT: A 631 MET cc_start: 0.9139 (tpt) cc_final: 0.8722 (tpp) REVERT: A 724 PHE cc_start: 0.9232 (m-80) cc_final: 0.8987 (m-10) REVERT: B 495 GLN cc_start: 0.7997 (tt0) cc_final: 0.7203 (tm-30) REVERT: B 786 ASP cc_start: 0.7629 (t70) cc_final: 0.7297 (t0) REVERT: B 854 MET cc_start: 0.9263 (mmm) cc_final: 0.8770 (mmm) REVERT: B 917 MET cc_start: 0.9310 (mmp) cc_final: 0.8952 (mmm) REVERT: B 926 TYR cc_start: 0.8668 (t80) cc_final: 0.8458 (t80) REVERT: C 201 MET cc_start: 0.8590 (tmm) cc_final: 0.8202 (tmm) REVERT: C 251 MET cc_start: 0.8077 (mtt) cc_final: 0.7444 (mtt) REVERT: D 150 LYS cc_start: 0.9044 (pttp) cc_final: 0.8830 (mmmt) REVERT: F 65 MET cc_start: 0.6697 (ttt) cc_final: 0.6096 (tmm) REVERT: F 102 MET cc_start: 0.9311 (tpt) cc_final: 0.9086 (tmm) REVERT: G 178 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7043 (pm20) REVERT: H 41 MET cc_start: 0.9260 (tmm) cc_final: 0.9036 (tmm) REVERT: H 121 MET cc_start: 0.8963 (ttm) cc_final: 0.8219 (tpp) REVERT: K 48 MET cc_start: 0.8289 (mmm) cc_final: 0.7775 (mmm) REVERT: K 67 LEU cc_start: 0.8180 (mp) cc_final: 0.7890 (mp) REVERT: W 638 VAL cc_start: 0.9340 (m) cc_final: 0.8892 (m) REVERT: W 647 PHE cc_start: 0.7372 (t80) cc_final: 0.7160 (t80) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1682 time to fit residues: 57.3165 Evaluate side-chains 163 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 68 optimal weight: 20.0000 chunk 294 optimal weight: 0.5980 chunk 128 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 321 optimal weight: 40.0000 chunk 210 optimal weight: 30.0000 chunk 256 optimal weight: 50.0000 chunk 263 optimal weight: 0.9990 chunk 348 optimal weight: 50.0000 overall best weight: 8.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 GLN B 62 HIS ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS H 137 GLN I 12 ASN I 80 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.066889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.053199 restraints weight = 387802.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.053984 restraints weight = 278693.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.054569 restraints weight = 220252.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.055001 restraints weight = 185303.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.055251 restraints weight = 161817.974| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 29272 Z= 0.230 Angle : 0.721 15.822 39975 Z= 0.371 Chirality : 0.044 0.274 4636 Planarity : 0.005 0.090 4805 Dihedral : 15.732 174.905 4685 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3465 helix: -0.17 (0.15), residues: 1173 sheet: -1.35 (0.21), residues: 563 loop : -1.52 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 185 TYR 0.023 0.002 TYR A1169 PHE 0.021 0.002 PHE B 951 TRP 0.022 0.002 TRP A1050 HIS 0.017 0.002 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (29256) covalent geometry : angle 0.70210 / 0.37 (39951) hydrogen bonds : bond 0.04814 / 3.07 ( 1011) hydrogen bonds : angle 5.12617 / 3.55 ( 2868) metal coordination : bond 0.01871 / 1.44 ( 16) metal coordination : angle 6.72384 / 4.58 ( 24) *********************** 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 198 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.887 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 470 MET cc_start: 0.8440 (mtp) cc_final: 0.8220 (mpp) REVERT: A 484 THR cc_start: 0.8402 (p) cc_final: 0.7838 (p) REVERT: A 491 MET cc_start: 0.7422 (mmm) cc_final: 0.6985 (mmt) REVERT: A 721 MET cc_start: 0.3487 (tmm) cc_final: 0.2959 (tmm) REVERT: A 724 PHE cc_start: 0.9313 (m-80) cc_final: 0.9033 (m-80) REVERT: A 754 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8732 (mm-30) REVERT: B 786 ASP cc_start: 0.7955 (t70) cc_final: 0.7694 (t0) REVERT: B 854 MET cc_start: 0.9422 (mmm) cc_final: 0.9211 (mmm) REVERT: B 917 MET cc_start: 0.9415 (mmp) cc_final: 0.9085 (mmp) REVERT: B 1026 MET cc_start: 0.8638 (mmp) cc_final: 0.8301 (mmm) REVERT: C 201 MET cc_start: 0.8413 (tmm) cc_final: 0.8096 (tmm) REVERT: C 251 MET cc_start: 0.8279 (mtt) cc_final: 0.7594 (mtt) REVERT: D 150 LYS cc_start: 0.9041 (pttp) cc_final: 0.8767 (mmmt) REVERT: D 159 MET cc_start: -0.6608 (tpt) cc_final: -0.6855 (tpt) REVERT: G 24 MET cc_start: 0.6467 (tmm) cc_final: 0.5644 (tmm) REVERT: G 178 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6703 (pm20) REVERT: K 48 MET cc_start: 0.8452 (mmm) cc_final: 0.7753 (mmm) REVERT: W 647 PHE cc_start: 0.7367 (t80) cc_final: 0.7056 (t80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1722 time to fit residues: 55.0010 Evaluate side-chains 155 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 1 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 250 optimal weight: 0.0070 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 209 optimal weight: 8.9990 chunk 188 optimal weight: 0.3980 chunk 340 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 321 optimal weight: 8.9990 overall best weight: 4.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 86 HIS A 216 ASN B 718 GLN B 724 GLN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN H 137 GLN I 110 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.066852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.053208 restraints weight = 396281.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.054062 restraints weight = 282476.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.054648 restraints weight = 220918.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.055057 restraints weight = 183515.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.055310 restraints weight = 160674.273| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29272 Z= 0.148 Angle : 0.617 12.111 39975 Z= 0.316 Chirality : 0.043 0.293 4636 Planarity : 0.004 0.068 4805 Dihedral : 15.679 173.981 4685 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3465 helix: 0.12 (0.15), residues: 1163 sheet: -1.18 (0.22), residues: 509 loop : -1.43 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 104 TYR 0.020 0.001 TYR A1169 PHE 0.023 0.002 PHE B 371 TRP 0.014 0.001 TRP A1050 HIS 0.009 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (29256) covalent geometry : angle 0.60106 / 0.32 (39951) hydrogen bonds : bond 0.03727 / 2.39 ( 1011) hydrogen bonds : angle 4.88003 / 3.39 ( 2868) metal coordination : bond 0.01101 / 0.75 ( 16) metal coordination : angle 5.66311 / 3.83 ( 24) *********************** 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 187 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.086 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: A 133 ASP cc_start: 0.8784 (p0) cc_final: 0.8512 (t70) REVERT: A 405 MET cc_start: 0.9144 (pmm) cc_final: 0.8923 (pmm) REVERT: A 470 MET cc_start: 0.8283 (mtp) cc_final: 0.7971 (mpp) REVERT: A 491 MET cc_start: 0.7583 (mmm) cc_final: 0.7218 (mmt) REVERT: A 724 PHE cc_start: 0.9250 (m-80) cc_final: 0.9007 (m-10) REVERT: A 754 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8648 (mm-30) REVERT: A 755 MET cc_start: 0.6004 (ttt) cc_final: 0.5770 (ttt) REVERT: B 786 ASP cc_start: 0.7796 (t70) cc_final: 0.7468 (t0) REVERT: B 926 TYR cc_start: 0.8768 (t80) cc_final: 0.8528 (t80) REVERT: B 1026 MET cc_start: 0.8640 (mmp) cc_final: 0.8389 (mmm) REVERT: C 251 MET cc_start: 0.8094 (mtt) cc_final: 0.7511 (mtt) REVERT: D 93 MET cc_start: 0.4094 (mmp) cc_final: 0.2862 (mtt) REVERT: F 65 MET cc_start: 0.7020 (ttt) cc_final: 0.4852 (tmm) REVERT: G 178 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6972 (pm20) REVERT: K 48 MET cc_start: 0.8283 (mmm) cc_final: 0.7753 (mmm) REVERT: K 67 LEU cc_start: 0.8275 (mp) cc_final: 0.8074 (mp) REVERT: W 647 PHE cc_start: 0.7222 (t80) cc_final: 0.6963 (t80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1666 time to fit residues: 50.8135 Evaluate side-chains 152 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 313 optimal weight: 0.3980 chunk 217 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 208 optimal weight: 0.0030 chunk 141 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 302 optimal weight: 30.0000 chunk 312 optimal weight: 40.0000 chunk 33 optimal weight: 7.9990 chunk 245 optimal weight: 20.0000 overall best weight: 4.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.066404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.052829 restraints weight = 397579.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.053619 restraints weight = 284472.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.054192 restraints weight = 222544.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.054598 restraints weight = 185693.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.054853 restraints weight = 162604.922| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29272 Z= 0.148 Angle : 0.608 11.991 39975 Z= 0.312 Chirality : 0.042 0.283 4636 Planarity : 0.004 0.062 4805 Dihedral : 15.643 173.063 4685 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3465 helix: 0.25 (0.15), residues: 1161 sheet: -1.23 (0.22), residues: 521 loop : -1.37 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 77 TYR 0.018 0.001 TYR A1169 PHE 0.016 0.001 PHE B 371 TRP 0.011 0.001 TRP A1050 HIS 0.013 0.001 HIS W 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (29256) covalent geometry : angle 0.59308 / 0.31 (39951) hydrogen bonds : bond 0.03710 / 2.37 ( 1011) hydrogen bonds : angle 4.83153 / 3.36 ( 2868) metal coordination : bond 0.00987 / 0.66 ( 16) metal coordination : angle 5.53197 / 3.68 ( 24) *********************** 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 183 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.864 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: A 133 ASP cc_start: 0.8810 (p0) cc_final: 0.8520 (t70) REVERT: A 405 MET cc_start: 0.9182 (pmm) cc_final: 0.8868 (pmm) REVERT: A 470 MET cc_start: 0.8298 (mtp) cc_final: 0.8055 (mpp) REVERT: A 491 MET cc_start: 0.7702 (mmm) cc_final: 0.7122 (mmt) REVERT: A 631 MET cc_start: 0.9171 (tpt) cc_final: 0.8865 (tpp) REVERT: A 724 PHE cc_start: 0.9253 (m-80) cc_final: 0.9020 (m-10) REVERT: A 754 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8671 (mm-30) REVERT: B 786 ASP cc_start: 0.7753 (t70) cc_final: 0.7441 (t0) REVERT: B 917 MET cc_start: 0.9269 (mmp) cc_final: 0.9014 (mmp) REVERT: B 1026 MET cc_start: 0.8726 (mmp) cc_final: 0.8472 (mmm) REVERT: C 251 MET cc_start: 0.8098 (mtt) cc_final: 0.7561 (mtt) REVERT: D 93 MET cc_start: 0.4138 (mmp) cc_final: 0.2748 (mtt) REVERT: G 178 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6891 (pm20) REVERT: K 48 MET cc_start: 0.8363 (mmm) cc_final: 0.7889 (mmm) REVERT: W 647 PHE cc_start: 0.7212 (t80) cc_final: 0.6912 (t80) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1546 time to fit residues: 46.9883 Evaluate side-chains 151 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 260 optimal weight: 9.9990 chunk 338 optimal weight: 9.9990 chunk 311 optimal weight: 8.9990 chunk 249 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 413 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN A 781 ASN A1127 GLN B 124 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 40 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 = 0.3900 r_free = 0.3900 target = 0.063819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.050668 restraints weight = 413094.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.051451 restraints weight = 293442.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.052000 restraints weight = 230098.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.052318 restraints weight = 192000.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.052624 restraints weight = 169991.825| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 29272 Z= 0.229 Angle : 0.739 10.991 39975 Z= 0.378 Chirality : 0.045 0.553 4636 Planarity : 0.005 0.056 4805 Dihedral : 15.897 172.615 4685 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.75 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3465 helix: -0.10 (0.15), residues: 1162 sheet: -1.21 (0.23), residues: 481 loop : -1.59 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 33 TYR 0.039 0.002 TYR B 442 PHE 0.027 0.002 PHE B 746 TRP 0.024 0.002 TRP A1050 HIS 0.013 0.002 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (29256) covalent geometry : angle 0.72525 / 0.38 (39951) hydrogen bonds : bond 0.04891 / 3.13 ( 1011) hydrogen bonds : angle 5.19816 / 3.61 ( 2868) metal coordination : bond 0.01410 / 0.99 ( 16) metal coordination : angle 5.78625 / 3.92 ( 24) *********************** 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 171 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.974 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 133 ASP cc_start: 0.8688 (p0) cc_final: 0.8395 (t0) REVERT: A 405 MET cc_start: 0.9195 (pmm) cc_final: 0.8874 (pmm) REVERT: A 406 ASP cc_start: 0.9255 (m-30) cc_final: 0.8988 (m-30) REVERT: A 491 MET cc_start: 0.7956 (mmm) cc_final: 0.7513 (mmt) REVERT: A 631 MET cc_start: 0.9233 (tpt) cc_final: 0.8921 (tpp) REVERT: A 724 PHE cc_start: 0.9304 (m-80) cc_final: 0.9043 (m-10) REVERT: A 754 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8778 (mm-30) REVERT: A 755 MET cc_start: 0.6653 (ttt) cc_final: 0.6263 (ttt) REVERT: B 786 ASP cc_start: 0.7942 (t70) cc_final: 0.7618 (t0) REVERT: B 854 MET cc_start: 0.9494 (mmm) cc_final: 0.9105 (mmm) REVERT: B 917 MET cc_start: 0.9313 (mmp) cc_final: 0.9064 (mmp) REVERT: B 1026 MET cc_start: 0.8816 (mmp) cc_final: 0.8591 (mmm) REVERT: C 201 MET cc_start: 0.8646 (tmm) cc_final: 0.8439 (tmm) REVERT: C 251 MET cc_start: 0.8284 (mtt) cc_final: 0.7696 (mtt) REVERT: D 93 MET cc_start: 0.4125 (mmp) cc_final: 0.2688 (mtt) REVERT: F 65 MET cc_start: 0.7628 (ttt) cc_final: 0.6897 (tmm) REVERT: G 178 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7175 (pm20) REVERT: H 93 MET cc_start: 0.7889 (tpt) cc_final: 0.7675 (tpp) REVERT: K 48 MET cc_start: 0.8561 (mmm) cc_final: 0.7887 (mmm) REVERT: W 647 PHE cc_start: 0.7026 (t80) cc_final: 0.6563 (t80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1620 time to fit residues: 45.7156 Evaluate side-chains 140 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 170 optimal weight: 0.3980 chunk 224 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 353 optimal weight: 40.0000 chunk 36 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 439 ASN A 781 ASN A 852 ASN ** B 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN E 52 ASN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.064342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.050995 restraints weight = 401465.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.051785 restraints weight = 284635.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.052311 restraints weight = 222789.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.052707 restraints weight = 187482.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.052946 restraints weight = 164428.422| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29272 Z= 0.140 Angle : 0.630 13.581 39975 Z= 0.320 Chirality : 0.043 0.298 4636 Planarity : 0.004 0.057 4805 Dihedral : 15.850 171.101 4685 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 0.04 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3465 helix: 0.13 (0.15), residues: 1169 sheet: -1.39 (0.23), residues: 490 loop : -1.44 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1134 TYR 0.018 0.001 TYR A1169 PHE 0.016 0.001 PHE A 47 TRP 0.015 0.001 TRP B1012 HIS 0.004 0.001 HIS E 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (29256) covalent geometry : angle 0.61401 / 0.32 (39951) hydrogen bonds : bond 0.03639 / 2.33 ( 1011) hydrogen bonds : angle 4.97511 / 3.46 ( 2868) metal coordination : bond 0.01597 / 0.91 ( 16) metal coordination : angle 5.79595 / 4.24 ( 24) *********************** 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 173 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.051 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: 0.8426 (t0) REVERT: A 405 MET cc_start: 0.9228 (pmm) cc_final: 0.8922 (pmm) REVERT: A 442 MET cc_start: 0.7498 (ptt) cc_final: 0.7142 (ptp) REVERT: A 470 MET cc_start: 0.8611 (mtm) cc_final: 0.8193 (mpp) REVERT: A 491 MET cc_start: 0.7994 (mmm) cc_final: 0.7597 (mmt) REVERT: A 631 MET cc_start: 0.9264 (tpt) cc_final: 0.8977 (tpp) REVERT: A 724 PHE cc_start: 0.9281 (m-80) cc_final: 0.9034 (m-10) REVERT: A 754 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8859 (mm-30) REVERT: A 755 MET cc_start: 0.6364 (ttt) cc_final: 0.6037 (ttt) REVERT: A 783 MET cc_start: 0.8913 (tpp) cc_final: 0.7962 (ptt) REVERT: B 786 ASP cc_start: 0.7872 (t70) cc_final: 0.7550 (t0) REVERT: B 917 MET cc_start: 0.9318 (mmp) cc_final: 0.9053 (mmp) REVERT: B 1026 MET cc_start: 0.8807 (mmp) cc_final: 0.8589 (mmm) REVERT: C 251 MET cc_start: 0.8208 (mtt) cc_final: 0.7655 (mtt) REVERT: D 93 MET cc_start: 0.4137 (mmp) cc_final: 0.2713 (mtt) REVERT: F 65 MET cc_start: 0.7326 (ttt) cc_final: 0.6682 (tmm) REVERT: G 18 MET cc_start: 0.3385 (mmm) cc_final: 0.3168 (mtp) REVERT: G 178 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7186 (pm20) REVERT: K 48 MET cc_start: 0.8394 (mmm) cc_final: 0.7874 (mmm) REVERT: W 647 PHE cc_start: 0.7164 (t80) cc_final: 0.6796 (t80) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1594 time to fit residues: 46.0144 Evaluate side-chains 143 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 105 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 273 optimal weight: 0.0670 chunk 227 optimal weight: 5.9990 overall best weight: 6.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.063172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.050075 restraints weight = 406138.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.050834 restraints weight = 288809.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.051349 restraints weight = 226367.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.051737 restraints weight = 190278.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.051948 restraints weight = 167339.097| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 29272 Z= 0.192 Angle : 0.680 11.131 39975 Z= 0.349 Chirality : 0.043 0.275 4636 Planarity : 0.005 0.046 4805 Dihedral : 15.937 171.471 4685 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3465 helix: 0.07 (0.15), residues: 1153 sheet: -1.40 (0.23), residues: 490 loop : -1.44 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1134 TYR 0.020 0.002 TYR G 123 PHE 0.021 0.002 PHE A 47 TRP 0.021 0.002 TRP B 514 HIS 0.006 0.001 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (29256) covalent geometry : angle 0.66471 / 0.35 (39951) hydrogen bonds : bond 0.04408 / 2.83 ( 1011) hydrogen bonds : angle 5.14202 / 3.57 ( 2868) metal coordination : bond 0.01492 / 1.10 ( 16) metal coordination : angle 5.87111 / 4.02 ( 24) ********************** 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 170 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.069 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: 0.8657 (p0) cc_final: 0.8385 (t0) REVERT: A 405 MET cc_start: 0.9219 (pmm) cc_final: 0.8884 (pmm) REVERT: A 470 MET cc_start: 0.8682 (mtm) cc_final: 0.8244 (mpp) REVERT: A 491 MET cc_start: 0.8196 (mmm) cc_final: 0.7723 (mmt) REVERT: A 631 MET cc_start: 0.9258 (tpt) cc_final: 0.9006 (tpp) REVERT: A 721 MET cc_start: -0.0460 (tpt) cc_final: -0.1054 (tpt) REVERT: A 724 PHE cc_start: 0.9289 (m-80) cc_final: 0.8966 (m-10) REVERT: A 755 MET cc_start: 0.5683 (ttt) cc_final: 0.5320 (ttt) REVERT: A 783 MET cc_start: 0.8902 (tpp) cc_final: 0.8063 (ptt) REVERT: B 786 ASP cc_start: 0.7944 (t70) cc_final: 0.7613 (t0) REVERT: B 917 MET cc_start: 0.9311 (mmp) cc_final: 0.9070 (mmp) REVERT: C 251 MET cc_start: 0.8290 (mtt) cc_final: 0.7690 (mtt) REVERT: D 93 MET cc_start: 0.4250 (mmp) cc_final: 0.2093 (mtt) REVERT: F 65 MET cc_start: 0.7554 (ttt) cc_final: 0.6968 (tmm) REVERT: G 18 MET cc_start: 0.3606 (mtt) cc_final: 0.3115 (mtp) REVERT: G 24 MET cc_start: 0.6651 (tmm) cc_final: 0.6288 (tmm) REVERT: G 178 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7231 (pm20) REVERT: K 48 MET cc_start: 0.8533 (mmm) cc_final: 0.8020 (mmm) REVERT: W 647 PHE cc_start: 0.7116 (t80) cc_final: 0.6680 (t80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1465 time to fit residues: 41.9786 Evaluate side-chains 141 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 264 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 339 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 307 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN B 135 ASN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.062494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.049510 restraints weight = 415140.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.050263 restraints weight = 294773.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.050805 restraints weight = 230453.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.051120 restraints weight = 192506.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.051434 restraints weight = 170004.780| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 29272 Z= 0.192 Angle : 0.684 11.147 39975 Z= 0.353 Chirality : 0.044 0.292 4636 Planarity : 0.005 0.048 4805 Dihedral : 16.063 171.784 4685 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.70 % Favored : 93.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3465 helix: 0.00 (0.15), residues: 1160 sheet: -1.46 (0.22), residues: 509 loop : -1.51 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1134 TYR 0.021 0.002 TYR B1037 PHE 0.026 0.002 PHE A 724 TRP 0.016 0.002 TRP B1012 HIS 0.006 0.001 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (29256) covalent geometry : angle 0.67151 / 0.35 (39951) hydrogen bonds : bond 0.04104 / 2.62 ( 1011) hydrogen bonds : angle 5.18862 / 3.60 ( 2868) metal coordination : bond 0.01259 / 0.90 ( 16) metal coordination : angle 5.40007 / 3.78 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.72 seconds wall clock time: 88 minutes 13.55 seconds (5293.55 seconds total)