Starting phenix.real_space_refine on Fri Mar 6 00:06:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f75_31485/03_2026/7f75_31485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f75_31485/03_2026/7f75_31485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f75_31485/03_2026/7f75_31485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f75_31485/03_2026/7f75_31485.map" model { file = "/net/cci-nas-00/data/ceres_data/7f75_31485/03_2026/7f75_31485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f75_31485/03_2026/7f75_31485.cif" } resolution = 4.2 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= 0.006 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 2 6.06 5 P 121 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 16516 2.51 5 N 4697 2.21 5 O 5488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26887 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1540 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'ARG:plan': 4, 'TYR:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1538 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 8041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8041 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 188} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1080} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 939 Unresolved non-hydrogen angles: 1163 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 15, 'ARG:plan': 46, 'GLU:plan': 24, 'PHE:plan': 11, 'ASP:plan': 20, 'ASN:plan1': 8, 'HIS:plan': 4, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 598 Chain: "D" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1142, 7891 Classifications: {'peptide': 1142} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 1090} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1128 Unresolved non-hydrogen angles: 1406 Unresolved non-hydrogen dihedrals: 928 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'TYR:plan': 8, 'TRP:plan': 2, 'GLU:plan': 40, 'HIS:plan': 10, 'ARG:plan': 38, 'ASP:plan': 15, 'PHE:plan': 7, 'GLN:plan1': 17, 'ASN:plan1': 14} Unresolved non-hydrogen planarities: 638 Chain: "E" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 405 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2047 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 9, 'TYR:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "H" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 542 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1077 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 120} Chain: "I" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1225 Classifications: {'DNA': 59} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 58} Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1285 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 763 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11575 SG CYS D 60 113.745 84.384 50.519 1.00 86.06 S ATOM 11682 SG CYS D 75 117.734 85.878 50.564 1.00 85.04 S ATOM 16813 SG CYS D 818 81.683 91.755 106.987 1.00 16.08 S ATOM 17262 SG CYS D 892 80.681 91.784 103.478 1.00 9.76 S ATOM 17305 SG CYS D 899 81.475 88.710 105.117 1.00 7.66 S ATOM 17321 SG CYS D 902 77.754 89.714 106.610 1.00 8.60 S Time building chain proxies: 6.11, per 1000 atoms: 0.23 Number of scatterers: 26887 At special positions: 0 Unit cell: (150.305, 156.84, 139.849, 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 2 29.99 S 62 16.00 P 121 15.00 Mg 1 11.99 O 5488 8.00 N 4697 7.00 C 16516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 13 " distance=2.40 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: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 60 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 902 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 892 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 899 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 818 " Number of angles added : 6 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6326 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 39 sheets defined 39.9% alpha, 8.9% beta 37 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.893A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.942A pdb=" N ILE B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.790A pdb=" N ILE B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.905A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 77 through 85 removed outlier: 4.197A pdb=" N LYS C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.878A pdb=" N ASP C 222 " --> pdb=" O ASN C 219 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS C 223 " --> pdb=" O THR C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 223' Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.951A pdb=" N ALA C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.501A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.535A pdb=" N ASN C 283 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.759A pdb=" N ARG C 407 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 436 removed outlier: 4.357A pdb=" N ARG C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.804A pdb=" N TYR C 572 " --> pdb=" O GLU C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 removed outlier: 4.091A pdb=" N VAL C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 628 through 632 removed outlier: 3.504A pdb=" N ASN C 631 " --> pdb=" O PHE C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.626A pdb=" N MET C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 968 through 983 Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'C' and resid 1004 through 1009 Processing helix chain 'C' and resid 1043 through 1048 removed outlier: 4.106A pdb=" N LYS C1047 " --> pdb=" O MET C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1086 removed outlier: 3.677A pdb=" N TYR C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1097 Processing helix chain 'C' and resid 1105 through 1116 removed outlier: 3.900A pdb=" N VAL C1114 " --> pdb=" O TYR C1110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C1115 " --> pdb=" O GLU C1111 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1139 removed outlier: 3.809A pdb=" N GLY C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.631A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG D 91 " --> pdb=" O ARG D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.956A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 4.071A pdb=" N ARG D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.889A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.544A pdb=" N ILE D 227 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 3.542A pdb=" N ARG D 239 " --> pdb=" O PRO D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 273 removed outlier: 4.020A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 Processing helix chain 'D' and resid 298 through 301 removed outlier: 4.258A pdb=" N ARG D 301 " --> pdb=" O ASN D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.512A pdb=" N LEU D 320 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 366 through 378 Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 396 through 405 removed outlier: 4.022A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.559A pdb=" N GLN D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.701A pdb=" N GLY D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 562 through 568 Processing helix chain 'D' and resid 604 through 608 removed outlier: 4.473A pdb=" N ALA D 607 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN D 608 " --> pdb=" O VAL D 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 604 through 608' Processing helix chain 'D' and resid 616 through 632 Processing helix chain 'D' and resid 635 through 655 removed outlier: 3.782A pdb=" N LYS D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 689 removed outlier: 4.246A pdb=" N GLN D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 671 " --> pdb=" O ASP D 667 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 718 removed outlier: 4.434A pdb=" N ILE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 737 through 743 removed outlier: 4.172A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 808 removed outlier: 4.293A pdb=" N HIS D 781 " --> pdb=" O PHE D 777 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 843 Processing helix chain 'D' and resid 870 through 875 Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.634A pdb=" N THR D 891 " --> pdb=" O SER D 888 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 892 " --> pdb=" O ALA D 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 888 through 892' Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 919 through 929 removed outlier: 3.540A pdb=" N GLU D 929 " --> pdb=" O GLN D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 932 No H-bonds generated for 'chain 'D' and resid 930 through 932' Processing helix chain 'D' and resid 953 through 962 Processing helix chain 'D' and resid 1039 through 1059 removed outlier: 3.756A pdb=" N GLN D1052 " --> pdb=" O LEU D1048 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS D1053 " --> pdb=" O HIS D1049 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D1055 " --> pdb=" O VAL D1051 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET D1057 " --> pdb=" O LYS D1053 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1073 removed outlier: 3.995A pdb=" N GLU D1068 " --> pdb=" O ASP D1064 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL D1069 " --> pdb=" O LYS D1065 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N MET D1070 " --> pdb=" O HIS D1066 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1093 through 1102 Processing helix chain 'D' and resid 1103 through 1108 removed outlier: 4.209A pdb=" N LEU D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1129 removed outlier: 3.521A pdb=" N SER D1127 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D1128 " --> pdb=" O THR D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1138 Processing helix chain 'D' and resid 1141 through 1153 Processing helix chain 'D' and resid 1162 through 1168 Processing helix chain 'E' and resid 6 through 14 removed outlier: 4.089A pdb=" N ASN E 11 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS E 12 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 removed outlier: 4.682A pdb=" N THR E 21 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 116 through 130 Processing helix chain 'F' and resid 133 through 153 removed outlier: 4.277A pdb=" N GLU F 140 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG F 152 " --> pdb=" O SER F 148 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 186 through 205 removed outlier: 4.056A pdb=" N TRP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TRP F 193 " --> pdb=" O TYR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 234 removed outlier: 3.717A pdb=" N THR F 218 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 4.005A pdb=" N ASP F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.988A pdb=" N ASP F 280 " --> pdb=" O HIS F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 313 through 323 removed outlier: 4.105A pdb=" N VAL F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'F' and resid 342 through 359 removed outlier: 4.073A pdb=" N ILE F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.660A pdb=" N SER F 363 " --> pdb=" O HIS F 359 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 364 " --> pdb=" O PRO F 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 359 through 364' Processing helix chain 'F' and resid 365 through 370 removed outlier: 5.643A pdb=" N ASP F 368 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 370 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 52 through 61 removed outlier: 3.534A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER H 61 " --> pdb=" O TYR H 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 52 through 57 removed outlier: 4.008A pdb=" N ILE G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 68 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.631A pdb=" N LEU G 114 " --> pdb=" O ARG G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 removed outlier: 4.016A pdb=" N PHE G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN G 122 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G 123 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 125 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 250 Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.848A pdb=" N GLU I 255 " --> pdb=" O THR I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 268 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 281 through 287 Processing helix chain 'I' and resid 292 through 306 Processing helix chain 'L' and resid 7 through 14 Processing helix chain 'L' and resid 15 through 28 removed outlier: 3.643A pdb=" N ILE L 19 " --> pdb=" O ALA L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 44 Processing helix chain 'L' and resid 51 through 65 Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 85 through 92 removed outlier: 3.777A pdb=" N GLU L 89 " --> pdb=" O ASP L 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.565A pdb=" N LYS A 8 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 181 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.702A pdb=" N ALA A 52 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 143 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 102 removed outlier: 3.791A pdb=" N PHE A 136 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 108 removed outlier: 6.582A pdb=" N GLY A 105 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR A 129 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 107 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.644A pdb=" N THR A 149 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 168 " --> pdb=" O THR A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.628A pdb=" N GLU B 181 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 142 removed outlier: 6.246A pdb=" N ARG B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 56 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.724A pdb=" N THR B 149 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 168 " --> pdb=" O THR B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 15 through 16 removed outlier: 6.030A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.973A pdb=" N ARG C 97 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 92 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 137 removed outlier: 6.816A pdb=" N SER C 136 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER C 530 " --> pdb=" O CYS C 515 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 144 through 148 removed outlier: 3.600A pdb=" N LEU C 170 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 171 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 190 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.513A pdb=" N ILE C 347 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 544 through 545 Processing sheet with id=AC1, first strand: chain 'C' and resid 547 through 549 Processing sheet with id=AC2, first strand: chain 'C' and resid 674 through 675 Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 685 removed outlier: 3.541A pdb=" N ILE C 681 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP C 691 " --> pdb=" O GLU C 683 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL C 685 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 690 " --> pdb=" O TYR C 710 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 710 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL C 692 " --> pdb=" O ASP C 708 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 708 " --> pdb=" O VAL C 692 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 749 removed outlier: 3.635A pdb=" N GLU C 752 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 758 through 763 removed outlier: 4.612A pdb=" N SER C1031 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 774 through 775 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 799 removed outlier: 3.603A pdb=" N GLU C 793 " --> pdb=" O ILE C 913 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 909 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C 907 " --> pdb=" O ALA C 799 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 908 " --> pdb=" O PHE C 893 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 889 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 914 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE C 887 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 808 through 809 Processing sheet with id=AC9, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.562A pdb=" N HIS C1049 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.562A pdb=" N HIS C1049 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1140 through 1143 Processing sheet with id=AD3, first strand: chain 'C' and resid 1145 through 1146 removed outlier: 3.935A pdb=" N GLU C1150 " --> pdb=" O SER C1146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 94 through 101 removed outlier: 10.690A pdb=" N LEU D 97 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ALA D 99 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL D 230 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.913A pdb=" N VAL D 135 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D 169 " --> pdb=" O VAL D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 241 through 243 removed outlier: 6.830A pdb=" N PHE D 249 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 536 through 539 removed outlier: 3.511A pdb=" N THR D 560 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 539 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 558 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 905 through 906 removed outlier: 3.659A pdb=" N SER D 911 " --> pdb=" O ASN D 906 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 977 through 980 removed outlier: 3.501A pdb=" N VAL D 992 " --> pdb=" O VAL D 979 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 21 through 26 removed outlier: 6.873A pdb=" N LYS H 4 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE H 47 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE H 6 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 27 through 31 Processing sheet with id=AE3, first strand: chain 'L' and resid 68 through 69 removed outlier: 3.877A pdb=" N GLY L 77 " --> pdb=" O LEU L 69 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6282 1.33 - 1.45: 5740 1.45 - 1.57: 15163 1.57 - 1.69: 241 1.69 - 1.82: 107 Bond restraints: 27533 Sorted by residual: bond pdb=" C ASP E 3 " pdb=" N PRO E 4 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.20e-03 1.49e+04 3.07e+01 bond pdb=" N PRO G 120 " pdb=" CD PRO G 120 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" C3' DA J 9 " pdb=" O3' DA J 9 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.80e+00 bond pdb=" C GLY C 72 " pdb=" N GLU C 73 " ideal model delta sigma weight residual 1.331 1.286 0.045 2.07e-02 2.33e+03 4.75e+00 bond pdb=" C TYR C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.63e+00 ... (remaining 27528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 36725 2.39 - 4.78: 1094 4.78 - 7.18: 125 7.18 - 9.57: 27 9.57 - 11.96: 10 Bond angle restraints: 37981 Sorted by residual: angle pdb=" C GLY C1147 " pdb=" N ASP C1148 " pdb=" CA ASP C1148 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.83e+01 angle pdb=" CA LEU C 319 " pdb=" C LEU C 319 " pdb=" N PRO C 320 " ideal model delta sigma weight residual 118.45 113.36 5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" C LEU C 319 " pdb=" N PRO C 320 " pdb=" CA PRO C 320 " ideal model delta sigma weight residual 119.84 126.35 -6.51 1.25e+00 6.40e-01 2.71e+01 angle pdb=" N ILE C 30 " pdb=" CA ILE C 30 " pdb=" C ILE C 30 " ideal model delta sigma weight residual 111.91 107.33 4.58 8.90e-01 1.26e+00 2.64e+01 angle pdb=" C LYS C 101 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " ideal model delta sigma weight residual 122.61 130.30 -7.69 1.56e+00 4.11e-01 2.43e+01 ... (remaining 37976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 15539 35.82 - 71.65: 814 71.65 - 107.47: 29 107.47 - 143.29: 2 143.29 - 179.11: 4 Dihedral angle restraints: 16388 sinusoidal: 6599 harmonic: 9789 Sorted by residual: dihedral pdb=" CB CYS G 10 " pdb=" SG CYS G 10 " pdb=" SG CYS G 13 " pdb=" CB CYS G 13 " ideal model delta sinusoidal sigma weight residual 93.00 34.85 58.15 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N ARG A 30 " pdb=" CA ARG A 30 " ideal model delta harmonic sigma weight residual 180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ALA D 613 " pdb=" C ALA D 613 " pdb=" N PRO D 614 " pdb=" CA PRO D 614 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 16385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3326 0.058 - 0.116: 937 0.116 - 0.174: 209 0.174 - 0.232: 35 0.232 - 0.291: 5 Chirality restraints: 4512 Sorted by residual: chirality pdb=" CB VAL H 14 " pdb=" CA VAL H 14 " pdb=" CG1 VAL H 14 " pdb=" CG2 VAL H 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CG LEU D 331 " pdb=" CB LEU D 331 " pdb=" CD1 LEU D 331 " pdb=" CD2 LEU D 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR D 857 " pdb=" CA THR D 857 " pdb=" OG1 THR D 857 " pdb=" CG2 THR D 857 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4509 not shown) Planarity restraints: 4572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 234 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO D 235 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 276 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO D 277 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 277 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 277 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 953 " 0.048 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO D 954 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 954 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 954 " 0.040 5.00e-02 4.00e+02 ... (remaining 4569 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 120 2.48 - 3.09: 16997 3.09 - 3.69: 40962 3.69 - 4.30: 53670 4.30 - 4.90: 85403 Nonbonded interactions: 197152 Sorted by model distance: nonbonded pdb=" OP2 DG K 17 " pdb=" N2 DG K 17 " model vdw 1.879 3.120 nonbonded pdb=" OD2 ASP D 451 " pdb="MG MG D1501 " model vdw 2.122 2.170 nonbonded pdb=" C2' DA K 21 " pdb=" OP1 DA K 22 " model vdw 2.221 3.440 nonbonded pdb=" OG1 THR C 247 " pdb=" OE1 GLU C 249 " model vdw 2.239 3.040 nonbonded pdb=" O LEU C 41 " pdb=" OH TYR C 69 " model vdw 2.244 3.040 ... (remaining 197147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 15 or (resid 16 through 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 40 or (resid 41 through \ 42 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE or name CZ )) or resid 43 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 67 or (resid 68 and (na \ me N or name CA or name C or name O or name CB )) or resid 69 through 97 or (res \ id 98 and (name N or name CA or name C or name O or name CB )) or resid 99 or (r \ esid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 o \ r (resid 102 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 03 through 131 or (resid 132 and (name N or name CA or name C or name O or name \ CB )) or resid 133 through 162 or (resid 163 and (name N or name CA or name C or \ name O or name CB )) or resid 164 through 200 or (resid 201 and (name N or name \ CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 and \ (name N or name CA or name C or name O or name CB )) or resid 208 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB or name CG )) \ or (resid 213 through 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 225)) selection = (chain 'B' and (resid 6 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or (resid 11 and (name N or name CA or name C or name O \ or name CB or name OG1)) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 16 or (resid 17 throug \ h 19 and (name N or name CA or name C or name O or name CB )) or resid 20 throug \ h 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or re \ sid 24 through 29 or (resid 30 and (name N or name CA or name C or name O or nam \ e CB )) or resid 31 through 33 or (resid 34 and (name N or name CA or name C or \ name O or name CB or name OG1)) or resid 35 through 47 or (resid 48 and (name N \ or name CA or name C or name O or name CB )) or resid 49 through 75 or (resid 76 \ through 77 and (name N or name CA or name C or name O or name CB or name OG1)) \ or resid 78 or (resid 79 and (name N or name CA or name C or name O or name CB o \ r name CG1)) or resid 80 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 107 through 121 or (resid 122 an \ d (name N or name CA or name C or name O or name CB )) or resid 123 or (resid 12 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 125 through \ 128 or (resid 129 and (name N or name CA or name C or name O or name CB or name \ OG1)) or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 140 or (resid 141 and (name N or name CA or name C or name O o \ r name CB or name OG1)) or resid 142 through 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or resid 149 through 165 or (resid 166 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 16 \ 7 through 170 or (resid 171 and (name N or name CA or name C or name O or name C \ B or name OG1)) or resid 172 through 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 183 or (resid 184 and (name \ N or name CA or name C or name O or name CB )) or resid 185 through 190 or (res \ id 191 and (name N or name CA or name C or name O or name CB )) or resid 192 thr \ ough 225)) } 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.730 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.495 27540 Z= 0.359 Angle : 1.034 39.480 37989 Z= 0.558 Chirality : 0.058 0.291 4512 Planarity : 0.007 0.076 4572 Dihedral : 19.489 179.115 10059 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.98 % Favored : 90.85 % Rotamer: Outliers : 2.25 % Allowed : 11.45 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -4.47 (0.11), residues: 3376 helix: -2.80 (0.11), residues: 1222 sheet: -2.53 (0.25), residues: 318 loop : -3.25 (0.12), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 928 TYR 0.022 0.003 TYR C 946 PHE 0.036 0.003 PHE C 420 TRP 0.032 0.003 TRP D 105 HIS 0.009 0.002 HIS C 862 Details of bonding type rmsd covalent geometry : bond 0.00659 (27533) covalent geometry : angle 0.98946 (37981) SS BOND : bond 0.37372 ( 1) SS BOND : angle 13.66925 ( 2) hydrogen bonds : bond 0.16282 ( 1000) hydrogen bonds : angle 6.96219 ( 2760) metal coordination : bond 0.31271 ( 6) metal coordination : angle 22.70496 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 537 time to evaluate : 0.899 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: A 64 GLU cc_start: 0.7429 (pt0) cc_final: 0.6806 (pp20) REVERT: A 72 VAL cc_start: 0.8987 (m) cc_final: 0.8609 (p) REVERT: B 187 GLN cc_start: 0.7578 (pm20) cc_final: 0.7206 (pt0) REVERT: B 190 ASN cc_start: 0.7968 (t0) cc_final: 0.7645 (t0) REVERT: C 89 SER cc_start: 0.9323 (m) cc_final: 0.8972 (p) REVERT: C 131 GLU cc_start: 0.7151 (tt0) cc_final: 0.6893 (tt0) REVERT: C 459 LYS cc_start: 0.7720 (mmtp) cc_final: 0.7504 (mmmt) REVERT: C 966 MET cc_start: 0.8348 (mtm) cc_final: 0.7983 (ptp) REVERT: C 1001 TRP cc_start: 0.8587 (m100) cc_final: 0.8171 (m100) REVERT: C 1074 ARG cc_start: 0.7565 (mpt-90) cc_final: 0.7133 (ttt90) REVERT: C 1081 TRP cc_start: 0.8504 (m-10) cc_final: 0.8274 (m-10) REVERT: D 8 GLU cc_start: 0.6562 (tm-30) cc_final: 0.6094 (tm-30) REVERT: D 18 ASP cc_start: 0.6860 (m-30) cc_final: 0.6487 (t70) REVERT: D 116 LEU cc_start: 0.7915 (pp) cc_final: 0.7452 (mt) REVERT: D 210 LEU cc_start: 0.8851 (tp) cc_final: 0.8598 (tp) REVERT: D 329 GLN cc_start: 0.6676 (mt0) cc_final: 0.5669 (tm-30) REVERT: D 455 MET cc_start: 0.8658 (ttm) cc_final: 0.8377 (ttm) REVERT: D 521 GLU cc_start: 0.7710 (pm20) cc_final: 0.6867 (tm-30) REVERT: D 1154 LYS cc_start: 0.8647 (tttt) cc_final: 0.8235 (ttmm) REVERT: F 293 HIS cc_start: 0.4762 (OUTLIER) cc_final: 0.4365 (t70) REVERT: F 312 ASP cc_start: 0.6697 (m-30) cc_final: 0.5825 (p0) REVERT: H 50 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (p) REVERT: H 56 GLU cc_start: 0.8084 (tp30) cc_final: 0.7767 (tp30) REVERT: G 37 LEU cc_start: 0.7094 (mt) cc_final: 0.5927 (mt) REVERT: G 45 ILE cc_start: 0.7545 (mt) cc_final: 0.7197 (mt) REVERT: G 51 ASP cc_start: 0.6956 (m-30) cc_final: 0.6610 (t0) REVERT: G 68 ASN cc_start: 0.4210 (m-40) cc_final: 0.3064 (p0) REVERT: G 102 GLN cc_start: 0.7370 (tp40) cc_final: 0.7049 (tt0) REVERT: I 266 LEU cc_start: 0.4693 (mt) cc_final: 0.4363 (pp) REVERT: L 11 LEU cc_start: 0.5294 (mt) cc_final: 0.5080 (pt) REVERT: L 23 LEU cc_start: 0.5940 (mt) cc_final: 0.5216 (mt) outliers start: 51 outliers final: 29 residues processed: 581 average time/residue: 0.1713 time to fit residues: 155.1066 Evaluate side-chains 388 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 357 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 280 HIS C 390 ASN C 403 HIS C 646 GLN ** C 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 HIS ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 499 ASN D 781 HIS D1052 GLN D1164 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.163090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134300 restraints weight = 52305.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133118 restraints weight = 77173.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133829 restraints weight = 71043.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134146 restraints weight = 54203.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134370 restraints weight = 47641.385| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27540 Z= 0.145 Angle : 0.653 8.466 37989 Z= 0.349 Chirality : 0.043 0.186 4512 Planarity : 0.005 0.074 4572 Dihedral : 19.508 179.395 4957 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.61 % Favored : 92.36 % Rotamer: Outliers : 0.75 % Allowed : 6.10 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -3.23 (0.13), residues: 3376 helix: -1.28 (0.14), residues: 1247 sheet: -2.20 (0.27), residues: 295 loop : -2.86 (0.12), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 434 TYR 0.017 0.002 TYR D 698 PHE 0.031 0.001 PHE D 216 TRP 0.026 0.002 TRP G 19 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00316 (27533) covalent geometry : angle 0.65018 (37981) SS BOND : bond 0.00000 ( 1) SS BOND : angle 1.00282 ( 2) hydrogen bonds : bond 0.04402 ( 1000) hydrogen bonds : angle 5.08979 ( 2760) metal coordination : bond 0.00448 ( 6) metal coordination : angle 4.75998 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 470 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7946 (t) cc_final: 0.7440 (p) REVERT: A 55 SER cc_start: 0.9526 (m) cc_final: 0.9267 (p) REVERT: A 64 GLU cc_start: 0.7323 (pt0) cc_final: 0.6535 (pp20) REVERT: A 143 GLN cc_start: 0.8017 (mp10) cc_final: 0.7802 (mp10) REVERT: B 187 GLN cc_start: 0.7860 (pm20) cc_final: 0.7571 (pt0) REVERT: C 131 GLU cc_start: 0.7371 (tt0) cc_final: 0.7044 (tt0) REVERT: C 401 ILE cc_start: 0.8906 (pt) cc_final: 0.8515 (mp) REVERT: C 564 LEU cc_start: 0.9306 (tp) cc_final: 0.8968 (tp) REVERT: C 639 MET cc_start: 0.7761 (mtp) cc_final: 0.7349 (mtp) REVERT: C 1001 TRP cc_start: 0.8602 (m100) cc_final: 0.8065 (m100) REVERT: C 1074 ARG cc_start: 0.7564 (mpt-90) cc_final: 0.7032 (ttt90) REVERT: C 1078 MET cc_start: 0.7968 (mtt) cc_final: 0.7658 (mtt) REVERT: C 1134 GLU cc_start: 0.7510 (tt0) cc_final: 0.7290 (tt0) REVERT: D 116 LEU cc_start: 0.8301 (pp) cc_final: 0.7595 (mt) REVERT: D 284 GLU cc_start: 0.8591 (tt0) cc_final: 0.8319 (tt0) REVERT: D 329 GLN cc_start: 0.6292 (mt0) cc_final: 0.5276 (tm-30) REVERT: D 455 MET cc_start: 0.8639 (ttm) cc_final: 0.8161 (ttm) REVERT: D 521 GLU cc_start: 0.7856 (pm20) cc_final: 0.7187 (tm-30) REVERT: D 532 HIS cc_start: 0.8013 (t-90) cc_final: 0.7605 (t70) REVERT: D 785 LYS cc_start: 0.7828 (tttt) cc_final: 0.7561 (mttp) REVERT: D 1154 LYS cc_start: 0.8575 (tttt) cc_final: 0.8250 (ttmm) REVERT: H 36 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8068 (mtpt) REVERT: G 37 LEU cc_start: 0.7170 (mt) cc_final: 0.6416 (mt) REVERT: G 45 ILE cc_start: 0.7615 (mt) cc_final: 0.7377 (mt) REVERT: G 68 ASN cc_start: 0.3969 (m-40) cc_final: 0.2940 (p0) REVERT: G 102 GLN cc_start: 0.7400 (tp40) cc_final: 0.6957 (tt0) REVERT: I 271 ILE cc_start: 0.1050 (OUTLIER) cc_final: 0.0291 (tp) REVERT: I 274 VAL cc_start: 0.5252 (m) cc_final: 0.4866 (m) REVERT: L 23 LEU cc_start: 0.6019 (mt) cc_final: 0.5434 (mt) outliers start: 17 outliers final: 16 residues processed: 486 average time/residue: 0.1625 time to fit residues: 126.6117 Evaluate side-chains 374 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 357 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 116 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 82 optimal weight: 0.0000 chunk 302 optimal weight: 3.9990 chunk 314 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 284 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 499 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136964 restraints weight = 52280.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135479 restraints weight = 80391.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135947 restraints weight = 77031.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136270 restraints weight = 60586.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136336 restraints weight = 53203.031| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27540 Z= 0.135 Angle : 0.610 15.412 37989 Z= 0.323 Chirality : 0.042 0.182 4512 Planarity : 0.005 0.062 4572 Dihedral : 19.314 179.468 4957 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.82 % Favored : 92.15 % Rotamer: Outliers : 0.88 % Allowed : 5.04 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.58 (0.14), residues: 3376 helix: -0.50 (0.15), residues: 1240 sheet: -1.94 (0.27), residues: 299 loop : -2.64 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 112 TYR 0.015 0.001 TYR D 134 PHE 0.022 0.001 PHE D 216 TRP 0.010 0.001 TRP C 39 HIS 0.006 0.001 HIS C 862 Details of bonding type rmsd covalent geometry : bond 0.00297 (27533) covalent geometry : angle 0.60234 (37981) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.87084 ( 2) hydrogen bonds : bond 0.03971 ( 1000) hydrogen bonds : angle 4.68416 ( 2760) metal coordination : bond 0.01643 ( 6) metal coordination : angle 7.46271 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 440 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9550 (m) cc_final: 0.9272 (p) REVERT: A 64 GLU cc_start: 0.7426 (pt0) cc_final: 0.6616 (pp20) REVERT: A 119 GLU cc_start: 0.7266 (tm-30) cc_final: 0.7029 (tm-30) REVERT: C 131 GLU cc_start: 0.7309 (tt0) cc_final: 0.6976 (tt0) REVERT: C 401 ILE cc_start: 0.8887 (pt) cc_final: 0.8595 (mp) REVERT: C 564 LEU cc_start: 0.9337 (tp) cc_final: 0.8993 (tp) REVERT: C 662 MET cc_start: 0.7466 (ppp) cc_final: 0.7226 (ppp) REVERT: C 740 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8501 (tt0) REVERT: C 1001 TRP cc_start: 0.8551 (m100) cc_final: 0.7901 (m100) REVERT: C 1074 ARG cc_start: 0.7463 (mpt-90) cc_final: 0.6931 (ttt90) REVERT: C 1078 MET cc_start: 0.7882 (mtt) cc_final: 0.7641 (mtt) REVERT: D 116 LEU cc_start: 0.8163 (pp) cc_final: 0.7445 (mt) REVERT: D 329 GLN cc_start: 0.6887 (mt0) cc_final: 0.5796 (tm-30) REVERT: D 455 MET cc_start: 0.8489 (ttm) cc_final: 0.8157 (ttm) REVERT: D 521 GLU cc_start: 0.7827 (pm20) cc_final: 0.7307 (tm-30) REVERT: D 532 HIS cc_start: 0.7961 (t-90) cc_final: 0.7563 (t70) REVERT: D 785 LYS cc_start: 0.7890 (tttt) cc_final: 0.7500 (mtmm) REVERT: D 1154 LYS cc_start: 0.8654 (tttt) cc_final: 0.8349 (ttmm) REVERT: F 270 ILE cc_start: 0.8181 (mt) cc_final: 0.7958 (mm) REVERT: F 352 LYS cc_start: 0.7838 (tppp) cc_final: 0.7463 (tppt) REVERT: G 37 LEU cc_start: 0.7118 (mt) cc_final: 0.6507 (mt) REVERT: G 45 ILE cc_start: 0.7525 (mt) cc_final: 0.7277 (mt) REVERT: G 68 ASN cc_start: 0.3926 (m-40) cc_final: 0.2949 (p0) REVERT: G 122 GLN cc_start: 0.5721 (tm-30) cc_final: 0.4689 (mp10) REVERT: L 11 LEU cc_start: 0.5423 (mt) cc_final: 0.4935 (pt) REVERT: L 69 LEU cc_start: 0.7048 (mm) cc_final: 0.6799 (mm) outliers start: 20 outliers final: 20 residues processed: 457 average time/residue: 0.1592 time to fit residues: 118.2943 Evaluate side-chains 370 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 350 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 322 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 344 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136495 restraints weight = 52231.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134786 restraints weight = 83178.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135123 restraints weight = 77317.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135973 restraints weight = 62598.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135930 restraints weight = 53615.837| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27540 Z= 0.128 Angle : 0.597 11.520 37989 Z= 0.313 Chirality : 0.042 0.177 4512 Planarity : 0.004 0.059 4572 Dihedral : 19.192 179.409 4957 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.12 % Rotamer: Outliers : 0.88 % Allowed : 3.27 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.21 (0.14), residues: 3376 helix: -0.11 (0.15), residues: 1240 sheet: -1.71 (0.28), residues: 297 loop : -2.50 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 166 TYR 0.020 0.001 TYR L 59 PHE 0.024 0.001 PHE D 216 TRP 0.015 0.001 TRP L 81 HIS 0.003 0.001 HIS D 458 Details of bonding type rmsd covalent geometry : bond 0.00284 (27533) covalent geometry : angle 0.59293 (37981) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.65728 ( 2) hydrogen bonds : bond 0.03757 ( 1000) hydrogen bonds : angle 4.48080 ( 2760) metal coordination : bond 0.00711 ( 6) metal coordination : angle 5.47134 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 434 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9537 (m) cc_final: 0.9276 (p) REVERT: A 64 GLU cc_start: 0.7319 (pt0) cc_final: 0.6570 (pp20) REVERT: A 193 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8178 (ttpp) REVERT: C 131 GLU cc_start: 0.7271 (tt0) cc_final: 0.7041 (tt0) REVERT: C 644 GLN cc_start: 0.8661 (tt0) cc_final: 0.8106 (tt0) REVERT: C 740 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8588 (tt0) REVERT: C 1001 TRP cc_start: 0.8511 (m100) cc_final: 0.7752 (m100) REVERT: C 1074 ARG cc_start: 0.7519 (mpt-90) cc_final: 0.6895 (ttt90) REVERT: D 116 LEU cc_start: 0.8220 (pp) cc_final: 0.7477 (mt) REVERT: D 284 GLU cc_start: 0.8668 (tt0) cc_final: 0.8356 (tt0) REVERT: D 329 GLN cc_start: 0.6985 (mt0) cc_final: 0.5753 (tm-30) REVERT: D 455 MET cc_start: 0.8484 (ttm) cc_final: 0.8137 (ttm) REVERT: D 521 GLU cc_start: 0.7836 (pm20) cc_final: 0.7296 (tm-30) REVERT: D 766 SER cc_start: 0.8531 (t) cc_final: 0.7954 (m) REVERT: D 785 LYS cc_start: 0.7842 (tttt) cc_final: 0.7489 (mtmm) REVERT: D 1154 LYS cc_start: 0.8648 (tttt) cc_final: 0.8378 (ttmm) REVERT: E 26 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8548 (tpp-160) REVERT: F 270 ILE cc_start: 0.8157 (mt) cc_final: 0.7857 (mm) REVERT: G 37 LEU cc_start: 0.7202 (mt) cc_final: 0.6742 (mt) REVERT: G 45 ILE cc_start: 0.7365 (mt) cc_final: 0.6948 (mt) REVERT: G 68 ASN cc_start: 0.3890 (m-40) cc_final: 0.2876 (p0) REVERT: G 122 GLN cc_start: 0.5746 (tm-30) cc_final: 0.4549 (mp10) REVERT: I 297 GLU cc_start: 0.4761 (mt-10) cc_final: 0.4027 (tp30) REVERT: L 11 LEU cc_start: 0.5266 (mt) cc_final: 0.4819 (pt) outliers start: 20 outliers final: 20 residues processed: 453 average time/residue: 0.1572 time to fit residues: 116.5720 Evaluate side-chains 368 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 348 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 179 optimal weight: 5.9990 chunk 215 optimal weight: 0.0970 chunk 119 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 246 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 ASN C 403 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 532 HIS D 809 GLN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.165177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139130 restraints weight = 51983.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136991 restraints weight = 82642.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137817 restraints weight = 78930.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138127 restraints weight = 60983.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138250 restraints weight = 52595.693| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27540 Z= 0.112 Angle : 0.563 11.440 37989 Z= 0.297 Chirality : 0.041 0.181 4512 Planarity : 0.004 0.066 4572 Dihedral : 19.111 179.453 4957 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.02 % Favored : 92.95 % Rotamer: Outliers : 0.88 % Allowed : 2.56 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.89 (0.14), residues: 3376 helix: 0.17 (0.15), residues: 1235 sheet: -1.43 (0.29), residues: 298 loop : -2.33 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 181 TYR 0.017 0.001 TYR F 189 PHE 0.023 0.001 PHE D 216 TRP 0.012 0.001 TRP G 19 HIS 0.003 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00243 (27533) covalent geometry : angle 0.56085 (37981) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.71066 ( 2) hydrogen bonds : bond 0.03467 ( 1000) hydrogen bonds : angle 4.27303 ( 2760) metal coordination : bond 0.00335 ( 6) metal coordination : angle 3.72864 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 423 time to evaluate : 0.716 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: A 55 SER cc_start: 0.9511 (m) cc_final: 0.9234 (p) REVERT: A 64 GLU cc_start: 0.7292 (pt0) cc_final: 0.6552 (pp20) REVERT: A 222 ASN cc_start: 0.8490 (m-40) cc_final: 0.8143 (t0) REVERT: C 131 GLU cc_start: 0.7335 (tt0) cc_final: 0.7063 (tt0) REVERT: C 644 GLN cc_start: 0.8700 (tt0) cc_final: 0.8191 (tt0) REVERT: C 740 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8541 (tt0) REVERT: C 966 MET cc_start: 0.8272 (ptp) cc_final: 0.8032 (ptp) REVERT: C 1001 TRP cc_start: 0.8476 (m100) cc_final: 0.7664 (m100) REVERT: C 1074 ARG cc_start: 0.7466 (mpt-90) cc_final: 0.6922 (ttt90) REVERT: D 284 GLU cc_start: 0.8567 (tt0) cc_final: 0.8270 (tt0) REVERT: D 329 GLN cc_start: 0.6948 (mt0) cc_final: 0.5754 (tm-30) REVERT: D 455 MET cc_start: 0.8422 (ttm) cc_final: 0.8053 (ttm) REVERT: D 521 GLU cc_start: 0.7774 (pm20) cc_final: 0.7288 (tm-30) REVERT: D 532 HIS cc_start: 0.7971 (t-90) cc_final: 0.7730 (t70) REVERT: D 785 LYS cc_start: 0.7742 (tttt) cc_final: 0.7359 (mtmm) REVERT: D 1154 LYS cc_start: 0.8574 (tttt) cc_final: 0.8369 (ttmm) REVERT: E 26 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8582 (tpt170) REVERT: F 246 MET cc_start: 0.7447 (mmt) cc_final: 0.7223 (mmt) REVERT: F 270 ILE cc_start: 0.8148 (mt) cc_final: 0.7883 (mm) REVERT: G 37 LEU cc_start: 0.7154 (mt) cc_final: 0.6827 (mt) REVERT: G 45 ILE cc_start: 0.7227 (mt) cc_final: 0.6866 (mt) REVERT: G 68 ASN cc_start: 0.4202 (m-40) cc_final: 0.3212 (p0) REVERT: G 112 ARG cc_start: 0.6990 (mtt90) cc_final: 0.6340 (mtt-85) REVERT: G 122 GLN cc_start: 0.5776 (tm-30) cc_final: 0.4535 (mp10) REVERT: I 274 VAL cc_start: 0.5577 (m) cc_final: 0.5284 (m) REVERT: I 297 GLU cc_start: 0.4745 (mt-10) cc_final: 0.4025 (tp30) REVERT: L 11 LEU cc_start: 0.5173 (mt) cc_final: 0.4806 (pt) outliers start: 20 outliers final: 20 residues processed: 442 average time/residue: 0.1558 time to fit residues: 112.2242 Evaluate side-chains 353 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 333 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 275 optimal weight: 2.9990 chunk 271 optimal weight: 0.0470 chunk 253 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 304 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 287 optimal weight: 7.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136230 restraints weight = 52268.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134963 restraints weight = 87075.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135519 restraints weight = 83903.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135824 restraints weight = 59358.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135915 restraints weight = 54479.357| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27540 Z= 0.141 Angle : 0.597 12.039 37989 Z= 0.315 Chirality : 0.042 0.180 4512 Planarity : 0.004 0.059 4572 Dihedral : 19.107 179.755 4957 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.15 % Favored : 91.82 % Rotamer: Outliers : 0.88 % Allowed : 2.65 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.81 (0.14), residues: 3376 helix: 0.23 (0.15), residues: 1240 sheet: -1.46 (0.29), residues: 306 loop : -2.27 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 311 TYR 0.021 0.002 TYR D 776 PHE 0.020 0.001 PHE D 216 TRP 0.015 0.001 TRP G 19 HIS 0.004 0.001 HIS D 458 Details of bonding type rmsd covalent geometry : bond 0.00316 (27533) covalent geometry : angle 0.59483 (37981) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.35120 ( 2) hydrogen bonds : bond 0.03808 ( 1000) hydrogen bonds : angle 4.34466 ( 2760) metal coordination : bond 0.00555 ( 6) metal coordination : angle 3.94390 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 406 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6627 (mm-30) REVERT: A 55 SER cc_start: 0.9523 (m) cc_final: 0.9226 (p) REVERT: A 64 GLU cc_start: 0.7574 (pt0) cc_final: 0.6692 (pp20) REVERT: A 222 ASN cc_start: 0.8556 (m-40) cc_final: 0.8025 (t0) REVERT: C 131 GLU cc_start: 0.7426 (tt0) cc_final: 0.7163 (tt0) REVERT: C 644 GLN cc_start: 0.8782 (tt0) cc_final: 0.8435 (tt0) REVERT: C 740 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8729 (tt0) REVERT: C 1001 TRP cc_start: 0.8479 (m100) cc_final: 0.7660 (m100) REVERT: C 1074 ARG cc_start: 0.7557 (mpt-90) cc_final: 0.6969 (ttt90) REVERT: C 1078 MET cc_start: 0.7918 (mtt) cc_final: 0.7496 (mtt) REVERT: D 116 LEU cc_start: 0.7906 (pp) cc_final: 0.7266 (mt) REVERT: D 255 ASN cc_start: 0.8666 (m-40) cc_final: 0.8451 (m-40) REVERT: D 284 GLU cc_start: 0.8556 (tt0) cc_final: 0.8327 (tt0) REVERT: D 329 GLN cc_start: 0.7003 (mt0) cc_final: 0.5902 (tm-30) REVERT: D 455 MET cc_start: 0.8445 (ttm) cc_final: 0.8043 (ttm) REVERT: D 662 ASP cc_start: 0.8536 (t0) cc_final: 0.8259 (t0) REVERT: D 785 LYS cc_start: 0.7740 (tttt) cc_final: 0.7538 (mttp) REVERT: D 1154 LYS cc_start: 0.8630 (tttt) cc_final: 0.8359 (ttmm) REVERT: F 270 ILE cc_start: 0.8289 (mt) cc_final: 0.8005 (mm) REVERT: G 37 LEU cc_start: 0.7202 (mt) cc_final: 0.6875 (mt) REVERT: G 45 ILE cc_start: 0.7196 (mt) cc_final: 0.6842 (mt) REVERT: G 68 ASN cc_start: 0.4184 (m-40) cc_final: 0.3203 (p0) REVERT: G 79 LEU cc_start: 0.7238 (tp) cc_final: 0.7004 (tp) REVERT: L 11 LEU cc_start: 0.5219 (mt) cc_final: 0.4731 (pt) REVERT: L 87 LEU cc_start: 0.4410 (mm) cc_final: 0.4172 (pt) outliers start: 20 outliers final: 20 residues processed: 424 average time/residue: 0.1512 time to fit residues: 105.0722 Evaluate side-chains 350 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 330 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 206 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 532 HIS ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.162147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135354 restraints weight = 51516.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134022 restraints weight = 90613.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134620 restraints weight = 83945.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134835 restraints weight = 61669.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134956 restraints weight = 56956.039| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27540 Z= 0.137 Angle : 0.595 10.679 37989 Z= 0.313 Chirality : 0.042 0.179 4512 Planarity : 0.004 0.059 4572 Dihedral : 19.064 179.190 4957 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.41 % Favored : 92.57 % Rotamer: Outliers : 0.88 % Allowed : 2.34 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.72 (0.14), residues: 3376 helix: 0.29 (0.15), residues: 1248 sheet: -1.27 (0.30), residues: 289 loop : -2.23 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 326 TYR 0.017 0.001 TYR C 76 PHE 0.015 0.001 PHE C 420 TRP 0.018 0.001 TRP G 19 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00307 (27533) covalent geometry : angle 0.59284 (37981) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.40689 ( 2) hydrogen bonds : bond 0.03752 ( 1000) hydrogen bonds : angle 4.25468 ( 2760) metal coordination : bond 0.00596 ( 6) metal coordination : angle 4.27075 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 409 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6866 (mm-30) REVERT: A 55 SER cc_start: 0.9530 (m) cc_final: 0.9252 (p) REVERT: A 64 GLU cc_start: 0.7423 (pt0) cc_final: 0.6504 (pp20) REVERT: A 119 GLU cc_start: 0.7285 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 212 LEU cc_start: 0.8668 (tp) cc_final: 0.8466 (tt) REVERT: A 222 ASN cc_start: 0.8511 (m-40) cc_final: 0.8012 (t0) REVERT: C 131 GLU cc_start: 0.7322 (tt0) cc_final: 0.7080 (tt0) REVERT: C 479 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 644 GLN cc_start: 0.8731 (tt0) cc_final: 0.8353 (tt0) REVERT: C 740 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8736 (tt0) REVERT: C 912 TYR cc_start: 0.8654 (m-10) cc_final: 0.7981 (m-10) REVERT: C 1074 ARG cc_start: 0.7561 (mpt-90) cc_final: 0.6988 (ttt90) REVERT: C 1152 ILE cc_start: 0.7555 (mm) cc_final: 0.7352 (mm) REVERT: D 105 TRP cc_start: 0.8177 (m100) cc_final: 0.7968 (m-10) REVERT: D 116 LEU cc_start: 0.8166 (pp) cc_final: 0.7508 (mt) REVERT: D 255 ASN cc_start: 0.8748 (m-40) cc_final: 0.8497 (m-40) REVERT: D 455 MET cc_start: 0.8566 (ttm) cc_final: 0.8159 (ttm) REVERT: D 662 ASP cc_start: 0.8514 (t0) cc_final: 0.8245 (t0) REVERT: D 1154 LYS cc_start: 0.8670 (tttt) cc_final: 0.8382 (ttmm) REVERT: F 270 ILE cc_start: 0.8358 (mt) cc_final: 0.8064 (mm) REVERT: H 36 LYS cc_start: 0.8924 (tppt) cc_final: 0.8242 (tptt) REVERT: G 21 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6643 (pp20) REVERT: G 45 ILE cc_start: 0.7217 (mt) cc_final: 0.6908 (mt) REVERT: G 68 ASN cc_start: 0.4230 (m-40) cc_final: 0.3241 (p0) REVERT: G 79 LEU cc_start: 0.7279 (tp) cc_final: 0.7023 (tp) REVERT: G 122 GLN cc_start: 0.6074 (tm-30) cc_final: 0.4680 (mp10) REVERT: L 87 LEU cc_start: 0.4153 (mm) cc_final: 0.3857 (pt) outliers start: 20 outliers final: 20 residues processed: 427 average time/residue: 0.1516 time to fit residues: 107.2107 Evaluate side-chains 349 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 329 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 chunk 37 optimal weight: 0.0870 chunk 166 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 309 optimal weight: 0.4980 chunk 220 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 478 ASN D 532 HIS D 781 HIS F 359 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139314 restraints weight = 51808.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137455 restraints weight = 85704.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137961 restraints weight = 80833.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138370 restraints weight = 63316.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138495 restraints weight = 54807.703| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27540 Z= 0.109 Angle : 0.570 13.669 37989 Z= 0.296 Chirality : 0.041 0.312 4512 Planarity : 0.004 0.100 4572 Dihedral : 18.959 179.938 4957 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.34 % Rotamer: Outliers : 0.93 % Allowed : 1.15 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.15), residues: 3376 helix: 0.47 (0.16), residues: 1249 sheet: -1.13 (0.30), residues: 299 loop : -2.11 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 31 TYR 0.024 0.001 TYR D 776 PHE 0.019 0.001 PHE L 24 TRP 0.018 0.001 TRP G 19 HIS 0.003 0.000 HIS D 781 Details of bonding type rmsd covalent geometry : bond 0.00234 (27533) covalent geometry : angle 0.56895 (37981) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.61203 ( 2) hydrogen bonds : bond 0.03291 ( 1000) hydrogen bonds : angle 4.06235 ( 2760) metal coordination : bond 0.00263 ( 6) metal coordination : angle 2.89163 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 426 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9495 (m) cc_final: 0.9261 (p) REVERT: A 64 GLU cc_start: 0.7306 (pt0) cc_final: 0.6438 (pp20) REVERT: A 119 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7057 (tm-30) REVERT: A 222 ASN cc_start: 0.8655 (m-40) cc_final: 0.7950 (t0) REVERT: B 174 SER cc_start: 0.8049 (m) cc_final: 0.7716 (p) REVERT: C 131 GLU cc_start: 0.7336 (tt0) cc_final: 0.7088 (mt-10) REVERT: C 333 PRO cc_start: 0.7791 (Cg_exo) cc_final: 0.7520 (Cg_endo) REVERT: C 644 GLN cc_start: 0.8688 (tt0) cc_final: 0.8354 (tt0) REVERT: C 740 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8642 (tt0) REVERT: C 912 TYR cc_start: 0.8731 (m-10) cc_final: 0.8044 (m-10) REVERT: C 1074 ARG cc_start: 0.7520 (mpt-90) cc_final: 0.7019 (ttt90) REVERT: C 1078 MET cc_start: 0.7864 (mtt) cc_final: 0.7493 (mtt) REVERT: D 116 LEU cc_start: 0.7919 (pp) cc_final: 0.7161 (mt) REVERT: D 268 LEU cc_start: 0.9186 (tp) cc_final: 0.8935 (tt) REVERT: D 284 GLU cc_start: 0.8429 (tt0) cc_final: 0.8184 (tt0) REVERT: D 455 MET cc_start: 0.8509 (ttm) cc_final: 0.8198 (ttm) REVERT: D 662 ASP cc_start: 0.8423 (t0) cc_final: 0.8122 (t0) REVERT: D 1154 LYS cc_start: 0.8619 (tttt) cc_final: 0.8346 (ttmm) REVERT: F 270 ILE cc_start: 0.8187 (mt) cc_final: 0.7895 (mm) REVERT: H 36 LYS cc_start: 0.8833 (tppt) cc_final: 0.8184 (tptt) REVERT: G 45 ILE cc_start: 0.7156 (mt) cc_final: 0.6811 (mt) REVERT: G 68 ASN cc_start: 0.4622 (m-40) cc_final: 0.3656 (p0) REVERT: I 250 GLU cc_start: 0.4599 (mt-10) cc_final: 0.3397 (pm20) REVERT: L 87 LEU cc_start: 0.4076 (mm) cc_final: 0.3828 (pt) outliers start: 21 outliers final: 20 residues processed: 445 average time/residue: 0.1459 time to fit residues: 108.9374 Evaluate side-chains 341 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 274 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 220 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 532 HIS D 781 HIS F 359 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138406 restraints weight = 51953.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136313 restraints weight = 83196.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137173 restraints weight = 80861.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137468 restraints weight = 58429.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137646 restraints weight = 51599.686| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27540 Z= 0.115 Angle : 0.580 13.398 37989 Z= 0.300 Chirality : 0.041 0.299 4512 Planarity : 0.004 0.060 4572 Dihedral : 18.900 179.882 4957 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.88 % Allowed : 0.97 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.43 (0.15), residues: 3376 helix: 0.52 (0.16), residues: 1251 sheet: -1.32 (0.29), residues: 317 loop : -2.03 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 31 TYR 0.013 0.001 TYR F 105 PHE 0.021 0.001 PHE B 20 TRP 0.021 0.001 TRP G 19 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00255 (27533) covalent geometry : angle 0.57857 (37981) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.53533 ( 2) hydrogen bonds : bond 0.03454 ( 1000) hydrogen bonds : angle 4.02352 ( 2760) metal coordination : bond 0.00356 ( 6) metal coordination : angle 3.34077 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 402 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: A 55 SER cc_start: 0.9517 (m) cc_final: 0.9258 (p) REVERT: A 64 GLU cc_start: 0.7465 (pt0) cc_final: 0.6622 (pp20) REVERT: A 119 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7101 (tm-30) REVERT: C 131 GLU cc_start: 0.7380 (tt0) cc_final: 0.7117 (mt-10) REVERT: C 644 GLN cc_start: 0.8740 (tt0) cc_final: 0.8388 (tt0) REVERT: C 740 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8653 (tt0) REVERT: C 912 TYR cc_start: 0.8702 (m-10) cc_final: 0.7985 (m-10) REVERT: C 973 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8383 (tt0) REVERT: C 1074 ARG cc_start: 0.7546 (mpt-90) cc_final: 0.6821 (ttt90) REVERT: C 1078 MET cc_start: 0.7948 (mtt) cc_final: 0.7596 (mtt) REVERT: D 116 LEU cc_start: 0.8056 (pp) cc_final: 0.7236 (mt) REVERT: D 268 LEU cc_start: 0.9167 (tp) cc_final: 0.8791 (tt) REVERT: D 284 GLU cc_start: 0.8454 (tt0) cc_final: 0.8218 (tt0) REVERT: D 455 MET cc_start: 0.8455 (ttm) cc_final: 0.8127 (ttm) REVERT: D 662 ASP cc_start: 0.8412 (t0) cc_final: 0.8136 (t0) REVERT: D 1154 LYS cc_start: 0.8632 (tttt) cc_final: 0.8332 (ttmm) REVERT: F 270 ILE cc_start: 0.8283 (mt) cc_final: 0.7952 (mm) REVERT: H 36 LYS cc_start: 0.8844 (tppt) cc_final: 0.8203 (tptt) REVERT: G 1 MET cc_start: 0.5695 (mpp) cc_final: 0.5444 (mpp) REVERT: G 68 ASN cc_start: 0.4773 (m-40) cc_final: 0.4070 (p0) REVERT: I 250 GLU cc_start: 0.4545 (mt-10) cc_final: 0.3390 (pm20) REVERT: L 87 LEU cc_start: 0.4129 (mm) cc_final: 0.3845 (pt) outliers start: 20 outliers final: 20 residues processed: 421 average time/residue: 0.1461 time to fit residues: 102.7304 Evaluate side-chains 341 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 194 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 chunk 312 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 274 optimal weight: 20.0000 chunk 49 optimal weight: 0.0970 chunk 259 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 22 optimal weight: 0.0060 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.163077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136330 restraints weight = 51861.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134253 restraints weight = 87654.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135070 restraints weight = 80487.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135402 restraints weight = 61765.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135589 restraints weight = 53122.851| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27540 Z= 0.126 Angle : 0.591 12.907 37989 Z= 0.306 Chirality : 0.042 0.345 4512 Planarity : 0.004 0.059 4572 Dihedral : 18.872 179.625 4957 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.32 % Favored : 92.65 % Rotamer: Outliers : 0.88 % Allowed : 0.62 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.43 (0.15), residues: 3376 helix: 0.50 (0.16), residues: 1249 sheet: -1.23 (0.30), residues: 296 loop : -2.03 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 31 TYR 0.019 0.001 TYR L 59 PHE 0.019 0.001 PHE B 20 TRP 0.023 0.001 TRP G 19 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00283 (27533) covalent geometry : angle 0.58908 (37981) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.56549 ( 2) hydrogen bonds : bond 0.03572 ( 1000) hydrogen bonds : angle 4.09706 ( 2760) metal coordination : bond 0.00518 ( 6) metal coordination : angle 3.80691 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 392 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9515 (m) cc_final: 0.9241 (p) REVERT: A 64 GLU cc_start: 0.7499 (pt0) cc_final: 0.6609 (pp20) REVERT: A 119 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 131 GLU cc_start: 0.7371 (tt0) cc_final: 0.7116 (tt0) REVERT: C 333 PRO cc_start: 0.7862 (Cg_exo) cc_final: 0.7632 (Cg_endo) REVERT: C 479 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7162 (mt-10) REVERT: C 644 GLN cc_start: 0.8787 (tt0) cc_final: 0.8409 (tt0) REVERT: C 912 TYR cc_start: 0.8691 (m-10) cc_final: 0.8028 (m-10) REVERT: C 1074 ARG cc_start: 0.7581 (mpt-90) cc_final: 0.6854 (ttt90) REVERT: C 1078 MET cc_start: 0.8038 (mtt) cc_final: 0.7631 (mtt) REVERT: D 116 LEU cc_start: 0.7885 (pp) cc_final: 0.7114 (mt) REVERT: D 125 LEU cc_start: 0.8271 (mt) cc_final: 0.8006 (mt) REVERT: D 268 LEU cc_start: 0.9227 (tp) cc_final: 0.8825 (tt) REVERT: D 284 GLU cc_start: 0.8410 (tt0) cc_final: 0.8178 (tt0) REVERT: D 455 MET cc_start: 0.8497 (ttm) cc_final: 0.8165 (ttm) REVERT: D 662 ASP cc_start: 0.8426 (t0) cc_final: 0.8176 (t0) REVERT: D 710 ASP cc_start: 0.7548 (p0) cc_final: 0.7055 (t70) REVERT: D 1154 LYS cc_start: 0.8644 (tttt) cc_final: 0.8336 (ttmm) REVERT: F 270 ILE cc_start: 0.8337 (mt) cc_final: 0.8011 (mm) REVERT: H 36 LYS cc_start: 0.8834 (tppt) cc_final: 0.8198 (tptt) REVERT: G 1 MET cc_start: 0.5836 (mpp) cc_final: 0.5632 (mpp) REVERT: G 68 ASN cc_start: 0.4839 (m-40) cc_final: 0.4308 (p0) REVERT: L 87 LEU cc_start: 0.4345 (mm) cc_final: 0.4024 (pt) outliers start: 20 outliers final: 20 residues processed: 410 average time/residue: 0.1464 time to fit residues: 100.8470 Evaluate side-chains 340 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 320 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 142 optimal weight: 0.9990 chunk 51 optimal weight: 0.0060 chunk 162 optimal weight: 10.0000 chunk 204 optimal weight: 0.0170 chunk 83 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 chunk 271 optimal weight: 0.0670 chunk 18 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 222 ASN B 220 HIS D 478 ASN D 532 HIS ** G 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139156 restraints weight = 51583.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137575 restraints weight = 83126.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138125 restraints weight = 78573.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138557 restraints weight = 59311.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138640 restraints weight = 51617.198| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27540 Z= 0.107 Angle : 0.570 13.045 37989 Z= 0.294 Chirality : 0.041 0.277 4512 Planarity : 0.004 0.060 4572 Dihedral : 18.811 179.724 4957 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.93 % Allowed : 0.49 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.29 (0.15), residues: 3376 helix: 0.59 (0.16), residues: 1254 sheet: -0.94 (0.32), residues: 276 loop : -1.96 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1106 TYR 0.021 0.001 TYR C1090 PHE 0.018 0.001 PHE D 107 TRP 0.021 0.001 TRP G 19 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00231 (27533) covalent geometry : angle 0.56923 (37981) SS BOND : bond 0.00114 ( 1) SS BOND : angle 0.69918 ( 2) hydrogen bonds : bond 0.03234 ( 1000) hydrogen bonds : angle 3.98045 ( 2760) metal coordination : bond 0.00255 ( 6) metal coordination : angle 2.57658 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.10 seconds wall clock time: 62 minutes 27.70 seconds (3747.70 seconds total)