Starting phenix.real_space_refine on Sun Sep 13 23:07:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f75_31485/09_2026/7f75_31485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f75_31485/09_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_31485/09_2026/7f75_31485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f75_31485/09_2026/7f75_31485.map" model { file = "/net/cci-nas-00/data/ceres_data/7f75_31485/09_2026/7f75_31485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f75_31485/09_2026/7f75_31485.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7f75_31485/09_2026/7f75_31485.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f75_31485/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.66, per 1000 atoms: 0.21 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 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: 2.93 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: 2.89 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 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.08e+01 bond pdb=" C3' DA J 12 " pdb=" O3' DA J 12 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" C3' DA K 26 " pdb=" C2' DA K 26 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 ... (remaining 27528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 36644 2.39 - 4.78: 1173 4.78 - 7.18: 127 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=" O4' DC K 14 " pdb=" C4' DC K 14 " pdb=" C3' DC K 14 " ideal model delta sigma weight residual 106.00 102.91 3.09 6.00e-01 2.78e+00 2.66e+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 ... (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: 3269 0.058 - 0.116: 985 0.116 - 0.174: 216 0.174 - 0.232: 37 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: 0.510 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.520 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.495 27540 Z= 0.431 Angle : 1.053 39.480 37989 Z= 0.623 Chirality : 0.059 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/Z covalent geometry : bond 0.00679 / 0.39 (27533) covalent geometry : angle 1.00930 / 0.62 (37981) SS BOND : bond 0.37372 / 19.67 ( 1) SS BOND : angle 13.66925 / 7.52 ( 2) hydrogen bonds : bond 0.16282 / 11.54 ( 1000) hydrogen bonds : angle 6.96219 / 4.78 ( 2760) metal coordination : bond 0.31271 / 16.51 ( 6) metal coordination : angle 22.70496 / 11.87 ( 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 : 0.737 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: 0.5826 (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: 0.7766 (tp30) REVERT: G 37 LEU cc_start: 0.7094 (mt) cc_final: 0.5928 (mt) REVERT: G 45 ILE cc_start: 0.7545 (mt) cc_final: 0.7199 (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: 0.3065 (p0) REVERT: G 102 GLN cc_start: 0.7370 (tp40) cc_final: 0.7048 (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: 0.1701 time to fit residues: 155.2853 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 : 0.948 ------------------------------------------------------------------------------- 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... A 220 HIS 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 ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN D 349 HIS ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 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** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137213 restraints weight = 52964.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.135902 restraints weight = 86936.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136628 restraints weight = 81595.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136798 restraints weight = 59411.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136967 restraints weight = 54238.697| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27540 Z= 0.155 Angle : 0.705 12.338 37989 Z= 0.378 Chirality : 0.047 0.359 4512 Planarity : 0.006 0.083 4572 Dihedral : 19.651 179.832 4957 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 0.71 % Allowed : 5.70 % Favored : 93.59 % 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: -3.37 (0.13), residues: 3376 helix: -1.43 (0.14), residues: 1235 sheet: -2.33 (0.26), residues: 307 loop : -2.89 (0.12), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 434 TYR 0.017 0.002 TYR I 263 PHE 0.030 0.002 PHE D 216 TRP 0.028 0.002 TRP G 19 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (27533) covalent geometry : angle 0.70081 / 0.38 (37981) SS BOND : bond 0.00736 / 0.39 ( 1) SS BOND : angle 0.93354 / 0.50 ( 2) hydrogen bonds : bond 0.04958 / 3.34 ( 1000) hydrogen bonds : angle 5.39290 / 3.71 ( 2760) metal coordination : bond 0.01217 / 0.80 ( 6) metal coordination : angle 5.84793 / 2.81 ( 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 475 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 459 time to evaluate : 0.605 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: 0.7349 (pt0) cc_final: 0.6609 (pp20) REVERT: B 187 GLN cc_start: 0.7834 (pm20) cc_final: 0.7536 (pt0) REVERT: C 131 GLU cc_start: 0.7345 (tt0) cc_final: 0.7017 (tt0) REVERT: C 193 THR cc_start: 0.6465 (t) cc_final: 0.6259 (m) REVERT: C 382 ILE cc_start: 0.8001 (pt) cc_final: 0.7761 (pt) REVERT: C 564 LEU cc_start: 0.9310 (tp) cc_final: 0.8946 (tp) REVERT: C 639 MET cc_start: 0.7547 (mtp) cc_final: 0.7143 (mtp) REVERT: C 654 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8193 (mt-10) REVERT: C 740 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8536 (tt0) REVERT: C 1001 TRP cc_start: 0.8592 (m100) cc_final: 0.8070 (m100) REVERT: C 1074 ARG cc_start: 0.7579 (mpt-90) cc_final: 0.7055 (ttt90) REVERT: C 1078 MET cc_start: 0.7936 (mtt) cc_final: 0.7645 (mtt) REVERT: C 1083 LEU cc_start: 0.9333 (tp) cc_final: 0.9094 (tp) REVERT: D 116 LEU cc_start: 0.8281 (pp) cc_final: 0.7661 (mt) REVERT: D 329 GLN cc_start: 0.6402 (mt0) cc_final: 0.5177 (tm-30) REVERT: D 455 MET cc_start: 0.8521 (ttm) cc_final: 0.8029 (ttm) REVERT: D 517 LYS cc_start: 0.8523 (mttp) cc_final: 0.8275 (mtpp) REVERT: D 521 GLU cc_start: 0.7750 (pm20) cc_final: 0.6856 (tm-30) REVERT: D 532 HIS cc_start: 0.8044 (t-90) cc_final: 0.7627 (t70) REVERT: D 785 LYS cc_start: 0.7847 (tttt) cc_final: 0.7502 (mtmm) REVERT: D 1154 LYS cc_start: 0.8535 (tttt) cc_final: 0.8171 (ttmm) REVERT: F 352 LYS cc_start: 0.7875 (tptt) cc_final: 0.7632 (tptp) REVERT: H 36 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8078 (mtpt) REVERT: G 37 LEU cc_start: 0.7039 (mt) cc_final: 0.6220 (mt) REVERT: G 45 ILE cc_start: 0.7608 (mt) cc_final: 0.7367 (mt) REVERT: G 51 ASP cc_start: 0.6707 (m-30) cc_final: 0.6397 (t0) REVERT: G 68 ASN cc_start: 0.3988 (m-40) cc_final: 0.2961 (p0) REVERT: G 102 GLN cc_start: 0.7402 (tp40) cc_final: 0.7066 (tt0) REVERT: L 23 LEU cc_start: 0.5778 (mt) cc_final: 0.5190 (mt) REVERT: L 69 LEU cc_start: 0.6947 (mm) cc_final: 0.6739 (mm) outliers start: 16 outliers final: 16 residues processed: 474 average time/residue: 0.1588 time to fit residues: 121.0129 Evaluate side-chains 372 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 356 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 0.8980 chunk 245 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 chunk 284 optimal weight: 4.9990 chunk 247 optimal weight: 0.0470 chunk 321 optimal weight: 6.9990 overall best weight: 2.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 HIS ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 HIS D 478 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS ** F 231 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 = 0.3986 r_free = 0.3986 target = 0.162357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137096 restraints weight = 53072.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135769 restraints weight = 90233.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136227 restraints weight = 84757.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136315 restraints weight = 65930.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136436 restraints weight = 60548.144| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27540 Z= 0.157 Angle : 0.669 12.731 37989 Z= 0.356 Chirality : 0.046 0.340 4512 Planarity : 0.005 0.069 4572 Dihedral : 19.513 177.910 4957 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.50 % Rotamer: Outliers : 0.80 % Allowed : 4.69 % Favored : 94.52 % 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: -2.85 (0.13), residues: 3376 helix: -0.78 (0.15), residues: 1234 sheet: -2.18 (0.26), residues: 315 loop : -2.74 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 313 TYR 0.017 0.002 TYR C 76 PHE 0.027 0.001 PHE D 216 TRP 0.011 0.001 TRP L 81 HIS 0.010 0.001 HIS C 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (27533) covalent geometry : angle 0.65881 / 0.36 (37981) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 0.98994 / 0.53 ( 2) hydrogen bonds : bond 0.04505 / 3.04 ( 1000) hydrogen bonds : angle 5.05731 / 3.49 ( 2760) metal coordination : bond 0.01270 / 0.80 ( 6) metal coordination : angle 9.04586 / 4.54 ( 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 451 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 433 time to evaluate : 0.969 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: 0.9511 (m) cc_final: 0.9167 (p) REVERT: A 64 GLU cc_start: 0.7375 (pt0) cc_final: 0.6629 (pp20) REVERT: B 187 GLN cc_start: 0.7905 (pm20) cc_final: 0.7636 (pt0) REVERT: C 131 GLU cc_start: 0.7326 (tt0) cc_final: 0.7017 (tt0) REVERT: C 401 ILE cc_start: 0.8906 (pt) cc_final: 0.8518 (mp) REVERT: C 564 LEU cc_start: 0.9360 (tp) cc_final: 0.8973 (tp) REVERT: C 639 MET cc_start: 0.7613 (mtp) cc_final: 0.7381 (mtp) REVERT: C 654 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8230 (mt-10) REVERT: C 740 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8524 (tt0) REVERT: C 1001 TRP cc_start: 0.8608 (m100) cc_final: 0.8104 (m100) REVERT: C 1074 ARG cc_start: 0.7514 (mpt-90) cc_final: 0.6977 (ttt90) REVERT: D 116 LEU cc_start: 0.8199 (pp) cc_final: 0.7468 (mt) REVERT: D 320 LEU cc_start: 0.8280 (tp) cc_final: 0.8062 (tp) REVERT: D 329 GLN cc_start: 0.6888 (mt0) cc_final: 0.5821 (tm-30) REVERT: D 521 GLU cc_start: 0.7856 (pm20) cc_final: 0.7202 (tm-30) REVERT: D 532 HIS cc_start: 0.8010 (t-90) cc_final: 0.7576 (t70) REVERT: D 785 LYS cc_start: 0.7835 (tttt) cc_final: 0.7456 (mtmm) REVERT: D 1154 LYS cc_start: 0.8524 (tttt) cc_final: 0.8200 (ttmm) REVERT: F 166 GLU cc_start: 0.7836 (tp30) cc_final: 0.7587 (tp30) REVERT: H 36 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8152 (mtpt) REVERT: G 37 LEU cc_start: 0.7106 (mt) cc_final: 0.6402 (mt) REVERT: G 45 ILE cc_start: 0.7496 (mt) cc_final: 0.7133 (mt) REVERT: G 68 ASN cc_start: 0.3807 (m-40) cc_final: 0.2779 (p0) REVERT: L 87 LEU cc_start: 0.5451 (mm) cc_final: 0.5131 (mm) outliers start: 18 outliers final: 18 residues processed: 449 average time/residue: 0.1499 time to fit residues: 110.2803 Evaluate side-chains 354 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 336 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 2.9990 chunk 171 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 322 optimal weight: 0.0770 chunk 55 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 344 optimal weight: 8.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 HIS C 403 HIS D 263 ASN D 478 ASN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136871 restraints weight = 52144.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135191 restraints weight = 88149.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135912 restraints weight = 80918.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136222 restraints weight = 61296.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136349 restraints weight = 52766.022| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2476 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= 0.123 Angle : 0.621 10.940 37989 Z= 0.330 Chirality : 0.044 0.342 4512 Planarity : 0.004 0.065 4572 Dihedral : 19.397 178.383 4957 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.61 % Favored : 92.36 % Rotamer: Outliers : 0.84 % Allowed : 3.09 % Favored : 96.07 % 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: -2.46 (0.14), residues: 3376 helix: -0.39 (0.15), residues: 1231 sheet: -1.76 (0.29), residues: 290 loop : -2.59 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 311 TYR 0.021 0.001 TYR L 59 PHE 0.029 0.001 PHE D 216 TRP 0.011 0.001 TRP G 19 HIS 0.008 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (27533) covalent geometry : angle 0.61836 / 0.33 (37981) SS BOND : bond 0.00199 / 0.10 ( 1) SS BOND : angle 0.63208 / 0.34 ( 2) hydrogen bonds : bond 0.04030 / 2.67 ( 1000) hydrogen bonds : angle 4.78289 / 3.31 ( 2760) metal coordination : bond 0.00547 / 0.35 ( 6) metal coordination : angle 4.97710 / 2.17 ( 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 435 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 416 time to evaluate : 0.709 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: 0.7670 (t) cc_final: 0.7328 (p) REVERT: A 55 SER cc_start: 0.9521 (m) cc_final: 0.9229 (p) REVERT: A 64 GLU cc_start: 0.7298 (pt0) cc_final: 0.6557 (pp20) REVERT: B 144 ARG cc_start: 0.7774 (tpt170) cc_final: 0.7286 (ttm170) REVERT: C 131 GLU cc_start: 0.7307 (tt0) cc_final: 0.6972 (tt0) REVERT: C 401 ILE cc_start: 0.8803 (pt) cc_final: 0.8483 (mp) REVERT: C 564 LEU cc_start: 0.9363 (tp) cc_final: 0.8952 (tp) REVERT: C 740 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8556 (tt0) REVERT: C 1001 TRP cc_start: 0.8567 (m100) cc_final: 0.7900 (m100) REVERT: C 1074 ARG cc_start: 0.7528 (mpt-90) cc_final: 0.7053 (ttt90) REVERT: D 116 LEU cc_start: 0.8138 (pp) cc_final: 0.7361 (mt) REVERT: D 284 GLU cc_start: 0.8665 (tt0) cc_final: 0.8462 (tt0) REVERT: D 329 GLN cc_start: 0.6803 (mt0) cc_final: 0.5763 (tm-30) REVERT: D 521 GLU cc_start: 0.7731 (pm20) cc_final: 0.7188 (tm-30) REVERT: D 532 HIS cc_start: 0.7984 (t-90) cc_final: 0.7587 (t70) REVERT: D 785 LYS cc_start: 0.7777 (tttt) cc_final: 0.7470 (mtmm) REVERT: D 821 ASP cc_start: 0.6840 (m-30) cc_final: 0.6409 (m-30) REVERT: D 1154 LYS cc_start: 0.8635 (tttt) cc_final: 0.8366 (ttmm) REVERT: G 37 LEU cc_start: 0.7184 (mt) cc_final: 0.6518 (mt) REVERT: G 45 ILE cc_start: 0.7512 (mt) cc_final: 0.7307 (mt) REVERT: G 68 ASN cc_start: 0.3914 (m-40) cc_final: 0.2918 (p0) outliers start: 19 outliers final: 18 residues processed: 434 average time/residue: 0.1540 time to fit residues: 109.5849 Evaluate side-chains 365 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 347 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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: 3.9990 chunk 119 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 317 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 287 ASN C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** 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 23 HIS G 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135056 restraints weight = 51942.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133757 restraints weight = 85211.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134378 restraints weight = 79707.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134656 restraints weight = 59646.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134711 restraints weight = 54743.197| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27540 Z= 0.147 Angle : 0.634 11.390 37989 Z= 0.338 Chirality : 0.045 0.365 4512 Planarity : 0.004 0.059 4572 Dihedral : 19.329 177.971 4957 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.35 % Favored : 91.62 % Rotamer: Outliers : 0.93 % Allowed : 3.32 % Favored : 95.76 % 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: -2.23 (0.14), residues: 3376 helix: -0.18 (0.15), residues: 1240 sheet: -1.61 (0.29), residues: 297 loop : -2.48 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 264 TYR 0.015 0.001 TYR C 76 PHE 0.025 0.002 PHE D 216 TRP 0.011 0.001 TRP G 19 HIS 0.007 0.001 HIS F 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (27533) covalent geometry : angle 0.63101 / 0.34 (37981) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.75580 / 0.40 ( 2) hydrogen bonds : bond 0.04177 / 2.79 ( 1000) hydrogen bonds : angle 4.69110 / 3.25 ( 2760) metal coordination : bond 0.00570 / 0.36 ( 6) metal coordination : angle 4.94809 / 2.13 ( 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 435 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 414 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9526 (m) cc_final: 0.9231 (p) REVERT: A 64 GLU cc_start: 0.7479 (pt0) cc_final: 0.6599 (pp20) REVERT: C 131 GLU cc_start: 0.7269 (tt0) cc_final: 0.7031 (tt0) REVERT: C 382 ILE cc_start: 0.8109 (pt) cc_final: 0.7902 (pt) REVERT: C 401 ILE cc_start: 0.8794 (pt) cc_final: 0.8537 (mp) REVERT: C 644 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: C 740 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8650 (tt0) REVERT: C 1001 TRP cc_start: 0.8547 (m100) cc_final: 0.7765 (m100) REVERT: C 1074 ARG cc_start: 0.7589 (mpt-90) cc_final: 0.6994 (ttt90) REVERT: D 116 LEU cc_start: 0.8316 (pp) cc_final: 0.7353 (mt) REVERT: D 329 GLN cc_start: 0.6932 (mt0) cc_final: 0.5793 (tm-30) REVERT: D 455 MET cc_start: 0.8554 (ttm) cc_final: 0.8231 (ttm) REVERT: D 521 GLU cc_start: 0.7830 (pm20) cc_final: 0.7333 (tm-30) REVERT: D 532 HIS cc_start: 0.7924 (t-90) cc_final: 0.7548 (t70) REVERT: D 766 SER cc_start: 0.8552 (t) cc_final: 0.7971 (m) REVERT: D 785 LYS cc_start: 0.7881 (tttt) cc_final: 0.7530 (mtmm) REVERT: D 1154 LYS cc_start: 0.8676 (tttt) cc_final: 0.8366 (ttmm) REVERT: E 26 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8523 (tpp-160) REVERT: F 311 THR cc_start: 0.6066 (m) cc_final: 0.5835 (p) REVERT: G 37 LEU cc_start: 0.7247 (mt) cc_final: 0.6701 (mt) REVERT: G 45 ILE cc_start: 0.7611 (mt) cc_final: 0.7192 (mt) REVERT: G 68 ASN cc_start: 0.4179 (m-40) cc_final: 0.3663 (p0) REVERT: L 11 LEU cc_start: 0.5302 (mt) cc_final: 0.4882 (pt) REVERT: L 22 GLU cc_start: 0.3881 (mm-30) cc_final: 0.3598 (mm-30) REVERT: L 23 LEU cc_start: 0.6245 (mm) cc_final: 0.6027 (mm) REVERT: L 73 ASP cc_start: 0.7043 (p0) cc_final: 0.6832 (p0) outliers start: 21 outliers final: 20 residues processed: 432 average time/residue: 0.1570 time to fit residues: 110.6406 Evaluate side-chains 356 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 335 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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: 10.0000 chunk 271 optimal weight: 6.9990 chunk 253 optimal weight: 40.0000 chunk 127 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 304 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 169 optimal weight: 0.0010 chunk 190 optimal weight: 3.9990 chunk 287 optimal weight: 0.0870 overall best weight: 3.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.160428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134161 restraints weight = 52157.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132171 restraints weight = 88904.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132801 restraints weight = 85482.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133016 restraints weight = 63134.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133127 restraints weight = 55778.627| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27540 Z= 0.167 Angle : 0.653 12.064 37989 Z= 0.347 Chirality : 0.045 0.351 4512 Planarity : 0.005 0.057 4572 Dihedral : 19.305 178.777 4957 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.59 % Favored : 91.38 % Rotamer: Outliers : 0.84 % Allowed : 4.16 % Favored : 95.00 % 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: -2.12 (0.14), residues: 3376 helix: -0.01 (0.15), residues: 1234 sheet: -1.56 (0.29), residues: 300 loop : -2.48 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 803 TYR 0.017 0.002 TYR H 7 PHE 0.022 0.002 PHE D 216 TRP 0.014 0.001 TRP L 81 HIS 0.007 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (27533) covalent geometry : angle 0.65052 / 0.35 (37981) SS BOND : bond 0.00200 / 0.11 ( 1) SS BOND : angle 0.79804 / 0.42 ( 2) hydrogen bonds : bond 0.04329 / 2.90 ( 1000) hydrogen bonds : angle 4.64440 / 3.23 ( 2760) metal coordination : bond 0.00698 / 0.42 ( 6) metal coordination : angle 4.98252 / 2.27 ( 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 425 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 406 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9535 (m) cc_final: 0.9238 (p) REVERT: A 64 GLU cc_start: 0.7374 (pt0) cc_final: 0.6575 (pp20) REVERT: A 119 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7084 (tm-30) REVERT: C 131 GLU cc_start: 0.7410 (tt0) cc_final: 0.7042 (tt0) REVERT: C 401 ILE cc_start: 0.8772 (pt) cc_final: 0.8508 (mp) REVERT: C 740 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8730 (tt0) REVERT: C 1001 TRP cc_start: 0.8520 (m100) cc_final: 0.7744 (m100) REVERT: C 1074 ARG cc_start: 0.7576 (mpt-90) cc_final: 0.6939 (ttt90) REVERT: D 35 ASN cc_start: 0.7040 (t0) cc_final: 0.6819 (p0) REVERT: D 116 LEU cc_start: 0.8393 (pp) cc_final: 0.7508 (mt) REVERT: D 284 GLU cc_start: 0.8561 (tt0) cc_final: 0.8279 (tt0) REVERT: D 329 GLN cc_start: 0.6989 (mt0) cc_final: 0.5875 (tm-30) REVERT: D 455 MET cc_start: 0.8486 (ttm) cc_final: 0.8137 (ttm) REVERT: D 521 GLU cc_start: 0.7879 (pm20) cc_final: 0.7396 (tm-30) REVERT: D 662 ASP cc_start: 0.8547 (t0) cc_final: 0.8254 (t0) REVERT: D 766 SER cc_start: 0.8617 (t) cc_final: 0.8027 (m) REVERT: D 785 LYS cc_start: 0.7908 (tttt) cc_final: 0.7593 (mtmm) REVERT: D 1154 LYS cc_start: 0.8677 (tttt) cc_final: 0.8326 (ttmm) REVERT: E 26 ARG cc_start: 0.8815 (tpp80) cc_final: 0.8532 (tpp-160) REVERT: F 246 MET cc_start: 0.7593 (mmt) cc_final: 0.7375 (mmt) REVERT: G 37 LEU cc_start: 0.7502 (mt) cc_final: 0.6928 (mt) REVERT: G 45 ILE cc_start: 0.7521 (mt) cc_final: 0.7174 (mt) REVERT: G 68 ASN cc_start: 0.4559 (m-40) cc_final: 0.3972 (p0) REVERT: L 11 LEU cc_start: 0.5160 (mt) cc_final: 0.4770 (pt) outliers start: 19 outliers final: 19 residues processed: 423 average time/residue: 0.1522 time to fit residues: 106.6934 Evaluate side-chains 348 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 329 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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: 0.0030 chunk 103 optimal weight: 0.0770 chunk 153 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 overall best weight: 2.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN D 255 ASN D 330 ASN D 478 ASN D 532 HIS ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135446 restraints weight = 52377.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133424 restraints weight = 96828.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134044 restraints weight = 92235.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134480 restraints weight = 69548.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134709 restraints weight = 58443.077| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27540 Z= 0.142 Angle : 0.631 11.873 37989 Z= 0.334 Chirality : 0.044 0.348 4512 Planarity : 0.004 0.057 4572 Dihedral : 19.255 178.796 4957 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.23 % Favored : 91.74 % Rotamer: Outliers : 0.88 % Allowed : 1.86 % Favored : 97.26 % 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: -1.98 (0.14), residues: 3376 helix: 0.10 (0.15), residues: 1239 sheet: -1.35 (0.31), residues: 281 loop : -2.42 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 264 TYR 0.021 0.001 TYR C 76 PHE 0.024 0.001 PHE D 216 TRP 0.030 0.001 TRP D 105 HIS 0.007 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (27533) covalent geometry : angle 0.62871 / 0.33 (37981) SS BOND : bond 0.00101 / 0.05 ( 1) SS BOND : angle 0.69565 / 0.37 ( 2) hydrogen bonds : bond 0.04122 / 2.72 ( 1000) hydrogen bonds : angle 4.52177 / 3.15 ( 2760) metal coordination : bond 0.00578 / 0.35 ( 6) metal coordination : angle 4.67637 / 2.20 ( 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 430 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 410 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9519 (m) cc_final: 0.9240 (p) REVERT: A 64 GLU cc_start: 0.7397 (pt0) cc_final: 0.6507 (pp20) REVERT: C 131 GLU cc_start: 0.7458 (tt0) cc_final: 0.7096 (tt0) REVERT: C 1001 TRP cc_start: 0.8515 (m100) cc_final: 0.7711 (m100) REVERT: C 1074 ARG cc_start: 0.7573 (mpt-90) cc_final: 0.7009 (ttt90) REVERT: C 1078 MET cc_start: 0.7963 (mtt) cc_final: 0.7483 (mtt) REVERT: D 116 LEU cc_start: 0.8238 (pp) cc_final: 0.7289 (mt) REVERT: D 284 GLU cc_start: 0.8477 (tt0) cc_final: 0.8202 (tt0) REVERT: D 329 GLN cc_start: 0.7074 (mt0) cc_final: 0.5958 (tm-30) REVERT: D 455 MET cc_start: 0.8443 (ttm) cc_final: 0.8129 (ttm) REVERT: D 662 ASP cc_start: 0.8458 (t0) cc_final: 0.8191 (t0) REVERT: D 785 LYS cc_start: 0.7815 (tttt) cc_final: 0.7500 (mtmm) REVERT: D 1154 LYS cc_start: 0.8698 (tttt) cc_final: 0.8365 (ttmm) REVERT: E 26 ARG cc_start: 0.8795 (tpp80) cc_final: 0.8499 (tpp-160) REVERT: F 246 MET cc_start: 0.7556 (mmt) cc_final: 0.7313 (mmt) REVERT: G 21 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6675 (pp20) REVERT: G 37 LEU cc_start: 0.7503 (mt) cc_final: 0.7078 (mt) REVERT: G 45 ILE cc_start: 0.7316 (mt) cc_final: 0.7005 (mt) REVERT: G 68 ASN cc_start: 0.4297 (m-40) cc_final: 0.4021 (p0) outliers start: 20 outliers final: 20 residues processed: 427 average time/residue: 0.1541 time to fit residues: 109.0687 Evaluate side-chains 346 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 326 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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: 7.9990 chunk 300 optimal weight: 5.9990 chunk 164 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 HIS C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 324 GLN D 330 ASN ** D 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130333 restraints weight = 52338.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128818 restraints weight = 93142.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129540 restraints weight = 90408.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129281 restraints weight = 65866.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129580 restraints weight = 61553.101| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 27540 Z= 0.251 Angle : 0.772 11.642 37989 Z= 0.408 Chirality : 0.048 0.330 4512 Planarity : 0.006 0.067 4572 Dihedral : 19.366 178.534 4957 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.49 % Favored : 89.48 % Rotamer: Outliers : 0.88 % Allowed : 2.74 % Favored : 96.37 % 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: -2.32 (0.14), residues: 3376 helix: -0.19 (0.15), residues: 1240 sheet: -1.69 (0.29), residues: 287 loop : -2.59 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 697 TYR 0.017 0.002 TYR C 368 PHE 0.039 0.002 PHE D 648 TRP 0.018 0.002 TRP L 81 HIS 0.007 0.002 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (27533) covalent geometry : angle 0.76810 / 0.41 (37981) SS BOND : bond 0.00375 / 0.20 ( 1) SS BOND : angle 0.63039 / 0.34 ( 2) hydrogen bonds : bond 0.05266 / 3.60 ( 1000) hydrogen bonds : angle 4.94469 / 3.46 ( 2760) metal coordination : bond 0.01269 / 0.73 ( 6) metal coordination : angle 6.41427 / 3.08 ( 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 388 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 368 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9561 (m) cc_final: 0.9293 (p) REVERT: C 131 GLU cc_start: 0.7357 (tt0) cc_final: 0.7065 (tt0) REVERT: C 1001 TRP cc_start: 0.8549 (m100) cc_final: 0.7723 (m100) REVERT: C 1074 ARG cc_start: 0.7610 (mpt-90) cc_final: 0.6978 (ttt90) REVERT: C 1078 MET cc_start: 0.8120 (mtt) cc_final: 0.7672 (mtt) REVERT: C 1081 TRP cc_start: 0.8659 (m-10) cc_final: 0.8438 (m-10) REVERT: D 116 LEU cc_start: 0.8216 (pp) cc_final: 0.7462 (mt) REVERT: D 129 ILE cc_start: 0.8547 (mm) cc_final: 0.8336 (mm) REVERT: D 329 GLN cc_start: 0.7194 (mt0) cc_final: 0.6668 (tt0) REVERT: D 455 MET cc_start: 0.8466 (ttm) cc_final: 0.8122 (ttm) REVERT: D 766 SER cc_start: 0.8498 (t) cc_final: 0.7981 (m) REVERT: D 794 THR cc_start: 0.8804 (p) cc_final: 0.8437 (t) REVERT: D 1154 LYS cc_start: 0.8771 (tttt) cc_final: 0.8374 (ttmm) REVERT: E 26 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8654 (tpp-160) REVERT: E 62 GLU cc_start: 0.8111 (tp30) cc_final: 0.7826 (tp30) REVERT: G 45 ILE cc_start: 0.7275 (mt) cc_final: 0.6935 (mt) REVERT: G 68 ASN cc_start: 0.4372 (m-40) cc_final: 0.3992 (p0) outliers start: 20 outliers final: 19 residues processed: 386 average time/residue: 0.1570 time to fit residues: 101.4463 Evaluate side-chains 317 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 298 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 4.9990 chunk 94 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 274 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN D 255 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 458 HIS D 532 HIS D 809 GLN F 205 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131777 restraints weight = 52297.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130640 restraints weight = 77569.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131059 restraints weight = 76622.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131309 restraints weight = 56209.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131369 restraints weight = 51582.087| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27540 Z= 0.149 Angle : 0.663 13.231 37989 Z= 0.348 Chirality : 0.045 0.329 4512 Planarity : 0.005 0.091 4572 Dihedral : 19.309 179.995 4957 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.50 % Favored : 91.47 % Rotamer: Outliers : 0.84 % Allowed : 1.11 % Favored : 98.05 % 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: -2.08 (0.14), residues: 3376 helix: 0.01 (0.15), residues: 1239 sheet: -1.44 (0.31), residues: 283 loop : -2.46 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 284 TYR 0.017 0.002 TYR C 563 PHE 0.024 0.002 PHE C 420 TRP 0.014 0.001 TRP G 19 HIS 0.010 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (27533) covalent geometry : angle 0.65997 / 0.35 (37981) SS BOND : bond 0.00153 / 0.08 ( 1) SS BOND : angle 0.58781 / 0.31 ( 2) hydrogen bonds : bond 0.04397 / 2.93 ( 1000) hydrogen bonds : angle 4.65221 / 3.26 ( 2760) metal coordination : bond 0.00594 / 0.37 ( 6) metal coordination : angle 5.47579 / 2.63 ( 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 402 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 383 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9544 (m) cc_final: 0.9292 (p) REVERT: B 80 LEU cc_start: 0.8163 (mp) cc_final: 0.7961 (mp) REVERT: C 131 GLU cc_start: 0.7363 (tt0) cc_final: 0.6980 (tt0) REVERT: C 459 LYS cc_start: 0.8723 (mmmt) cc_final: 0.7957 (mmtp) REVERT: C 564 LEU cc_start: 0.9203 (tp) cc_final: 0.8970 (tp) REVERT: C 1001 TRP cc_start: 0.8477 (m100) cc_final: 0.7676 (m100) REVERT: C 1074 ARG cc_start: 0.7528 (mpt-90) cc_final: 0.7007 (ttt90) REVERT: C 1078 MET cc_start: 0.8021 (mtt) cc_final: 0.7529 (mtt) REVERT: C 1081 TRP cc_start: 0.8753 (m-10) cc_final: 0.8532 (m-10) REVERT: D 110 ILE cc_start: 0.7110 (mm) cc_final: 0.6719 (mm) REVERT: D 116 LEU cc_start: 0.8164 (pp) cc_final: 0.7318 (mt) REVERT: D 284 GLU cc_start: 0.8356 (tt0) cc_final: 0.8153 (tt0) REVERT: D 329 GLN cc_start: 0.7608 (mt0) cc_final: 0.6128 (tm-30) REVERT: D 455 MET cc_start: 0.8593 (ttm) cc_final: 0.8241 (ttm) REVERT: D 785 LYS cc_start: 0.7817 (tttt) cc_final: 0.7431 (mtmm) REVERT: D 794 THR cc_start: 0.8772 (p) cc_final: 0.8402 (t) REVERT: D 1154 LYS cc_start: 0.8670 (tttt) cc_final: 0.8283 (ttmm) REVERT: E 26 ARG cc_start: 0.8855 (tpp80) cc_final: 0.8602 (tpp-160) REVERT: E 62 GLU cc_start: 0.7981 (tp30) cc_final: 0.7768 (tp30) REVERT: G 37 LEU cc_start: 0.7593 (mt) cc_final: 0.7255 (mt) REVERT: G 45 ILE cc_start: 0.7196 (mt) cc_final: 0.6867 (mt) REVERT: G 68 ASN cc_start: 0.4385 (m-40) cc_final: 0.4094 (p0) REVERT: G 122 GLN cc_start: 0.5907 (tm-30) cc_final: 0.4614 (mp10) outliers start: 19 outliers final: 19 residues processed: 400 average time/residue: 0.1478 time to fit residues: 98.5216 Evaluate side-chains 326 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 307 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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: 0.0030 chunk 312 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 274 optimal weight: 20.0000 chunk 49 optimal weight: 0.0020 chunk 259 optimal weight: 3.9990 chunk 336 optimal weight: 50.0000 chunk 22 optimal weight: 1.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 330 ASN D 478 ASN D 532 HIS ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132864 restraints weight = 52161.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131472 restraints weight = 84959.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132002 restraints weight = 82415.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132019 restraints weight = 59222.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132151 restraints weight = 55676.727| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27540 Z= 0.151 Angle : 0.658 12.824 37989 Z= 0.345 Chirality : 0.045 0.318 4512 Planarity : 0.005 0.079 4572 Dihedral : 19.276 179.876 4957 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.21 % Favored : 90.76 % Rotamer: Outliers : 0.88 % Allowed : 0.57 % Favored : 98.54 % 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: -1.99 (0.14), residues: 3376 helix: 0.11 (0.15), residues: 1234 sheet: -1.44 (0.31), residues: 277 loop : -2.41 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.016 0.002 TYR C 76 PHE 0.023 0.002 PHE D 648 TRP 0.015 0.001 TRP G 19 HIS 0.007 0.001 HIS C 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (27533) covalent geometry : angle 0.65535 / 0.34 (37981) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.60892 / 0.32 ( 2) hydrogen bonds : bond 0.04266 / 2.84 ( 1000) hydrogen bonds : angle 4.57316 / 3.20 ( 2760) metal coordination : bond 0.00663 / 0.39 ( 6) metal coordination : angle 5.13777 / 2.47 ( 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 389 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 369 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9543 (m) cc_final: 0.9275 (p) REVERT: A 64 GLU cc_start: 0.7693 (pt0) cc_final: 0.6575 (pp20) REVERT: B 80 LEU cc_start: 0.8161 (mp) cc_final: 0.7951 (mp) REVERT: C 131 GLU cc_start: 0.7316 (tt0) cc_final: 0.6982 (tt0) REVERT: C 459 LYS cc_start: 0.8723 (mmmt) cc_final: 0.7952 (mmtp) REVERT: C 1001 TRP cc_start: 0.8495 (m100) cc_final: 0.7734 (m100) REVERT: C 1074 ARG cc_start: 0.7560 (mpt-90) cc_final: 0.6891 (ttt90) REVERT: D 110 ILE cc_start: 0.7013 (mm) cc_final: 0.6615 (mm) REVERT: D 116 LEU cc_start: 0.8130 (pp) cc_final: 0.7248 (mt) REVERT: D 284 GLU cc_start: 0.8436 (tt0) cc_final: 0.8233 (tt0) REVERT: D 455 MET cc_start: 0.8604 (ttm) cc_final: 0.8254 (ttm) REVERT: D 794 THR cc_start: 0.8745 (p) cc_final: 0.8393 (t) REVERT: D 1154 LYS cc_start: 0.8697 (tttt) cc_final: 0.8305 (ttmm) REVERT: E 26 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8580 (tpp-160) REVERT: G 20 LEU cc_start: 0.6680 (mp) cc_final: 0.6418 (mp) REVERT: G 37 LEU cc_start: 0.7534 (mt) cc_final: 0.7113 (mt) REVERT: G 45 ILE cc_start: 0.7193 (mt) cc_final: 0.6877 (mt) REVERT: G 68 ASN cc_start: 0.4587 (m-40) cc_final: 0.4373 (p0) outliers start: 20 outliers final: 20 residues processed: 387 average time/residue: 0.1409 time to fit residues: 91.5162 Evaluate side-chains 328 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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: 0.8980 chunk 51 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 213 optimal weight: 0.2980 chunk 274 optimal weight: 20.0000 chunk 271 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 646 GLN D 255 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 532 HIS ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.160360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133332 restraints weight = 51723.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131547 restraints weight = 90795.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132217 restraints weight = 83500.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132544 restraints weight = 65704.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132843 restraints weight = 55235.230| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27540 Z= 0.130 Angle : 0.646 15.668 37989 Z= 0.336 Chirality : 0.044 0.313 4512 Planarity : 0.004 0.071 4572 Dihedral : 19.230 179.361 4957 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.03 % Rotamer: Outliers : 0.84 % Allowed : 0.49 % Favored : 98.67 % 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: -1.87 (0.14), residues: 3376 helix: 0.20 (0.15), residues: 1234 sheet: -1.42 (0.30), residues: 287 loop : -2.33 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 37 TYR 0.022 0.002 TYR G 105 PHE 0.023 0.001 PHE D 216 TRP 0.025 0.002 TRP C1081 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (27533) covalent geometry : angle 0.64375 / 0.34 (37981) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.31815 / 0.18 ( 2) hydrogen bonds : bond 0.03977 / 2.62 ( 1000) hydrogen bonds : angle 4.44132 / 3.10 ( 2760) metal coordination : bond 0.00454 / 0.28 ( 6) metal coordination : angle 4.63038 / 2.25 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.20 seconds wall clock time: 62 minutes 14.32 seconds (3734.32 seconds total)