Starting phenix.real_space_refine on Mon Aug 10 01:39:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4d_17406/08_2026/8p4d_17406.map" } resolution = 3.6 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 92 5.49 5 S 239 5.16 5 C 25147 2.51 5 N 7071 2.21 5 O 7705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40255 Number of models: 1 Model: "" Number of chains: 19 Chain: "N" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "T" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 11166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11166 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1340} Chain breaks: 5 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 9052 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 4 Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2115 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 15, 'TRANS': 247} Chain breaks: 1 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "P" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 410 Classifications: {'RNAv2': 19} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3749 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 17, 'TRANS': 451} Chain breaks: 5 Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35713 SG CYS Y 16 24.501 129.220 123.698 1.00 81.24 S ATOM 35735 SG CYS Y 19 25.462 127.466 127.532 1.00 84.47 S ATOM 35847 SG CYS Y 33 21.762 127.610 126.887 1.00 73.71 S Time building chain proxies: 9.67, per 1000 atoms: 0.24 Number of scatterers: 40255 At special positions: 0 Unit cell: (158.55, 168, 193.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 239 16.00 P 92 15.00 O 7705 8.00 N 7071 7.00 C 25147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 114 " distance=1.97 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 Atom "ATOM 185 O5' DA N 24 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9024 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 56 sheets defined 34.1% alpha, 18.7% beta 39 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 7.12 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.605A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.009A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.616A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.859A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.856A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.284A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.534A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 696 through 722 removed outlier: 3.687A pdb=" N GLN A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.732A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.539A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.520A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 932 removed outlier: 3.735A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.664A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.501A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.691A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.539A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.630A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.104A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1295 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.560A pdb=" N VAL A1385 " --> pdb=" O GLU A1381 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.850A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1436 through 1446 Processing helix chain 'A' and resid 1454 through 1460 removed outlier: 3.749A pdb=" N MET A1459 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.526A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.465A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.426A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 281 through 287 removed outlier: 3.534A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.713A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.526A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.659A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.944A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.582A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 583 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.827A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.842A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 711' Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.643A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.835A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.529A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.621A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.645A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.664A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.868A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.589A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.890A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.253A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.964A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.534A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.511A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.840A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.794A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.546A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.716A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.444A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.641A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.760A pdb=" N LEU D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.791A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 262 removed outlier: 3.860A pdb=" N GLU M 252 " --> pdb=" O PRO M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 281 No H-bonds generated for 'chain 'M' and resid 279 through 281' Processing helix chain 'M' and resid 282 through 287 removed outlier: 3.595A pdb=" N LEU M 286 " --> pdb=" O LYS M 282 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS M 287 " --> pdb=" O LEU M 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 282 through 287' Processing helix chain 'M' and resid 371 through 375 Processing helix chain 'M' and resid 376 through 388 Processing helix chain 'M' and resid 388 through 398 removed outlier: 3.670A pdb=" N ARG M 392 " --> pdb=" O ILE M 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR M 398 " --> pdb=" O GLU M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.589A pdb=" N GLU M 406 " --> pdb=" O LYS M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 424 removed outlier: 3.861A pdb=" N ARG M 422 " --> pdb=" O ILE M 418 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS M 423 " --> pdb=" O CYS M 419 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU M 424 " --> pdb=" O THR M 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 418 through 424' Processing helix chain 'M' and resid 504 through 508 Processing helix chain 'M' and resid 538 through 551 Processing helix chain 'M' and resid 554 through 564 removed outlier: 3.829A pdb=" N GLU M 560 " --> pdb=" O GLU M 556 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE M 561 " --> pdb=" O MET M 557 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 3.643A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.653A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 249 removed outlier: 3.563A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.718A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 573 through 575 No H-bonds generated for 'chain 'Z' and resid 573 through 575' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.560A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.690A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.669A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 369 removed outlier: 3.710A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 459 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.770A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.209A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.209A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.610A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 3.618A pdb=" N LEU A1257 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB8, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.933A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP B 127 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC3, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.558A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.547A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.588A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR L 17 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC9, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.153A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD2, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.790A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD4, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD5, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.465A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 44 through 55 removed outlier: 5.165A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.421A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.518A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE1, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE2, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE3, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.056A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE7, first strand: chain 'G' and resid 83 through 92 removed outlier: 6.612A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE G 147 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE9, first strand: chain 'M' and resid 242 through 243 removed outlier: 7.269A pdb=" N LEU M 341 " --> pdb=" O ILE M 364 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE M 364 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP M 343 " --> pdb=" O TYR M 362 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 272 through 275 removed outlier: 10.068A pdb=" N GLN M 272 " --> pdb=" O ASP M 454 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE M 456 " --> pdb=" O GLN M 272 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N ASP M 455 " --> pdb=" O PRO M 444 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 494 through 501 removed outlier: 7.284A pdb=" N VAL M 491 " --> pdb=" O PRO M 497 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY M 487 " --> pdb=" O ILE M 501 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE M 514 " --> pdb=" O GLN M 529 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN M 529 " --> pdb=" O ILE M 514 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLU M 516 " --> pdb=" O MET M 527 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF4, first strand: chain 'Y' and resid 83 through 90 removed outlier: 7.116A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 352 through 355 removed outlier: 3.995A pdb=" N PHE Z 358 " --> pdb=" O ASP Z 355 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'Z' and resid 477 through 479 removed outlier: 5.843A pdb=" N ILE Z 492 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE Z 503 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG Z 494 " --> pdb=" O ILE Z 501 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.064A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id=AG1, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.382A pdb=" N HIS Z 625 " --> pdb=" O ILE Z 614 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE Z 614 " --> pdb=" O HIS Z 625 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.954A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 1479 hydrogen bonds defined for protein. 4101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 14.56 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7727 1.33 - 1.45: 10049 1.45 - 1.57: 22871 1.57 - 1.70: 183 1.70 - 1.82: 379 Bond restraints: 41209 Sorted by residual: bond pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 1.522 1.447 0.075 1.16e-02 7.43e+03 4.17e+01 bond pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 1.530 1.459 0.071 1.17e-02 7.31e+03 3.66e+01 bond pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " ideal model delta sigma weight residual 1.458 1.401 0.057 1.20e-02 6.94e+03 2.28e+01 bond pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.29e-02 6.01e+03 2.08e+01 bond pdb=" CA ILE Z 448 " pdb=" C ILE Z 448 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.30e-02 5.92e+03 1.92e+01 ... (remaining 41204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 55540 3.36 - 6.73: 447 6.73 - 10.09: 45 10.09 - 13.45: 7 13.45 - 16.82: 2 Bond angle restraints: 56041 Sorted by residual: angle pdb=" N THR Z 449 " pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 111.28 94.46 16.82 1.35e+00 5.49e-01 1.55e+02 angle pdb=" C LYS M 449 " pdb=" N PRO M 450 " pdb=" CA PRO M 450 " ideal model delta sigma weight residual 120.21 131.07 -10.86 9.60e-01 1.09e+00 1.28e+02 angle pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 109.21 94.20 15.01 1.36e+00 5.41e-01 1.22e+02 angle pdb=" N GLY Z 423 " pdb=" CA GLY Z 423 " pdb=" C GLY Z 423 " ideal model delta sigma weight residual 114.69 126.96 -12.27 1.19e+00 7.06e-01 1.06e+02 angle pdb=" N LYS Z 447 " pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 109.15 96.49 12.66 1.44e+00 4.82e-01 7.73e+01 ... (remaining 56036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 24201 35.00 - 70.01: 733 70.01 - 105.01: 43 105.01 - 140.01: 0 140.01 - 175.02: 4 Dihedral angle restraints: 24981 sinusoidal: 11033 harmonic: 13948 Sorted by residual: dihedral pdb=" C4' C P 30 " pdb=" C3' C P 30 " pdb=" C2' C P 30 " pdb=" C1' C P 30 " ideal model delta sinusoidal sigma weight residual 36.34 -37.52 73.86 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.34 -36.86 73.21 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' G P 36 " pdb=" C3' G P 36 " pdb=" C2' G P 36 " pdb=" C1' G P 36 " ideal model delta sinusoidal sigma weight residual 36.34 -27.44 63.78 1 3.10e+00 1.04e-01 5.58e+02 ... (remaining 24978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 6106 0.125 - 0.249: 140 0.249 - 0.374: 15 0.374 - 0.499: 2 0.499 - 0.624: 3 Chirality restraints: 6266 Sorted by residual: chirality pdb=" CA TYR M 362 " pdb=" N TYR M 362 " pdb=" C TYR M 362 " pdb=" CB TYR M 362 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" CA ASN M 324 " pdb=" N ASN M 324 " pdb=" C ASN M 324 " pdb=" CB ASN M 324 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" CA TRP M 293 " pdb=" N TRP M 293 " pdb=" C TRP M 293 " pdb=" CB TRP M 293 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.08e+00 ... (remaining 6263 not shown) Planarity restraints: 6931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 120 " -0.090 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO G 121 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE Z 450 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ILE Z 450 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE Z 450 " 0.023 2.00e-02 2.50e+03 pdb=" N MET Z 451 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 81 " 0.043 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO H 82 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 82 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 82 " 0.036 5.00e-02 4.00e+02 ... (remaining 6928 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 29 1.26 - 2.17: 137 2.17 - 3.08: 27938 3.08 - 3.99: 109464 3.99 - 4.90: 200943 Warning: very small nonbonded interaction distances. Nonbonded interactions: 338511 Sorted by model distance: nonbonded pdb=" O PRO M 461 " pdb=" N ASN M 465 " model vdw 0.346 3.120 nonbonded pdb=" O LEU Z 506 " pdb=" CB VAL Z 630 " model vdw 0.513 3.470 nonbonded pdb=" O LYS M 282 " pdb=" CZ PHE M 561 " model vdw 0.668 3.340 nonbonded pdb=" CD1 LEU M 425 " pdb=" CD LYS M 555 " model vdw 0.688 3.860 nonbonded pdb=" CD GLN B 72 " pdb=" CE2 TYR Z 203 " model vdw 0.696 3.570 ... (remaining 338506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 56.800 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.005 0.232 41214 Z= 0.312 Angle : 0.856 50.671 56043 Z= 0.521 Chirality : 0.055 0.624 6266 Planarity : 0.005 0.132 6931 Dihedral : 15.137 175.018 15954 Min Nonbonded Distance : 0.346 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.85 % Rotamer: Outliers : 0.43 % Allowed : 1.23 % Favored : 98.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.14 (0.12), residues: 4739 helix: 0.03 (0.14), residues: 1451 sheet: -0.94 (0.19), residues: 687 loop : -1.13 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 70 TYR 0.033 0.002 TYR B 752 PHE 0.032 0.002 PHE Z 558 TRP 0.024 0.002 TRP B 99 HIS 0.007 0.001 HIS Z 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.30 (41209) covalent geometry : angle 0.82757 / 0.51 (56041) SS BOND : bond 0.05942 / 2.97 ( 1) SS BOND : angle 36.55917 / 37.30 ( 2) hydrogen bonds : bond 0.17761 / 19.65 ( 1557) hydrogen bonds : angle 7.21844 / 6.80 ( 4291) metal coordination : bond 0.22339 / 15.99 ( 3) Misc. bond : bond 0.05385 / 2.69 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 359 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8574 (mmm) cc_final: 0.8251 (mmm) REVERT: I 29 ASP cc_start: 0.8671 (t0) cc_final: 0.8457 (t0) REVERT: L 41 TYR cc_start: 0.8257 (t80) cc_final: 0.8031 (t80) REVERT: G 29 LYS cc_start: 0.9316 (tptm) cc_final: 0.8756 (tppt) REVERT: G 104 MET cc_start: 0.6399 (tmm) cc_final: 0.5830 (ttp) REVERT: M 276 MET cc_start: -0.0382 (ttm) cc_final: -0.0810 (ttp) outliers start: 18 outliers final: 1 residues processed: 375 average time/residue: 0.2564 time to fit residues: 161.2920 Evaluate side-chains 235 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 441 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 HIS ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN A1299 GLN B 52 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 593 GLN B 725 GLN ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS I 32 ASN L 23 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN G 111 HIS M 537 ASN Y 12 HIS Y 41 GLN Z 534 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.064664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.039420 restraints weight = 226364.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.040144 restraints weight = 114407.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.040709 restraints weight = 75900.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.041115 restraints weight = 60374.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041195 restraints weight = 53118.163| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 41214 Z= 0.290 Angle : 0.808 19.044 56043 Z= 0.414 Chirality : 0.054 0.999 6266 Planarity : 0.006 0.104 6931 Dihedral : 14.952 167.482 6263 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.49 % Favored : 94.45 % Rotamer: Outliers : 0.80 % Allowed : 7.20 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.75 (0.12), residues: 4739 helix: 0.49 (0.14), residues: 1458 sheet: -0.88 (0.18), residues: 722 loop : -0.93 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 859 TYR 0.031 0.002 TYR Z 203 PHE 0.046 0.002 PHE B 823 TRP 0.023 0.002 TRP B 99 HIS 0.016 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.29 (41209) covalent geometry : angle 0.80794 / 0.41 (56041) SS BOND : bond 0.00629 / 0.31 ( 1) SS BOND : angle 3.91084 / 6.75 ( 2) hydrogen bonds : bond 0.04990 / 5.51 ( 1557) hydrogen bonds : angle 5.69748 / 5.58 ( 4291) metal coordination : bond 0.00460 / 0.44 ( 3) Misc. bond : bond 0.00116 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9338 (tpp) cc_final: 0.8781 (tpp) REVERT: A 317 MET cc_start: 0.9260 (tmm) cc_final: 0.8907 (tmm) REVERT: A 355 MET cc_start: 0.9161 (mmp) cc_final: 0.8837 (mmp) REVERT: A 1102 MET cc_start: 0.8887 (ptp) cc_final: 0.8642 (ptp) REVERT: B 365 LEU cc_start: 0.9893 (OUTLIER) cc_final: 0.9657 (tp) REVERT: B 529 MET cc_start: 0.8601 (mtp) cc_final: 0.8266 (mmt) REVERT: B 603 MET cc_start: 0.8551 (mpp) cc_final: 0.8331 (mpp) REVERT: E 94 MET cc_start: 0.8922 (mmm) cc_final: 0.8664 (tpt) REVERT: I 75 ASP cc_start: 0.9254 (t0) cc_final: 0.9036 (t0) REVERT: K 103 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8494 (pp20) REVERT: M 276 MET cc_start: 0.6197 (ttm) cc_final: 0.5990 (ttm) REVERT: M 396 MET cc_start: 0.3636 (mtt) cc_final: 0.3402 (mtt) REVERT: M 437 MET cc_start: 0.7392 (tmm) cc_final: 0.7174 (tmm) REVERT: M 539 TYR cc_start: 0.7245 (t80) cc_final: 0.6718 (t80) outliers start: 34 outliers final: 18 residues processed: 263 average time/residue: 0.2524 time to fit residues: 113.0211 Evaluate side-chains 232 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 316 ASP Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 496 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 358 optimal weight: 10.0000 chunk 349 optimal weight: 2.9990 chunk 477 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 334 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 422 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 416 optimal weight: 0.0030 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 ASN Z 737 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.065304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040284 restraints weight = 222573.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.040917 restraints weight = 111876.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041528 restraints weight = 74032.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.041954 restraints weight = 58399.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.042050 restraints weight = 51117.838| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41214 Z= 0.155 Angle : 0.673 11.494 56043 Z= 0.346 Chirality : 0.049 0.730 6266 Planarity : 0.004 0.056 6931 Dihedral : 14.706 167.342 6261 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 1.20 % Allowed : 8.97 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.54 (0.12), residues: 4739 helix: 0.68 (0.14), residues: 1468 sheet: -0.66 (0.19), residues: 709 loop : -0.86 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 31 TYR 0.023 0.001 TYR Z 203 PHE 0.022 0.002 PHE K 13 TRP 0.017 0.002 TRP B 99 HIS 0.014 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (41209) covalent geometry : angle 0.67247 / 0.35 (56041) SS BOND : bond 0.00252 / 0.13 ( 1) SS BOND : angle 1.71718 / 2.91 ( 2) hydrogen bonds : bond 0.04288 / 4.78 ( 1557) hydrogen bonds : angle 5.31242 / 5.22 ( 4291) metal coordination : bond 0.00146 / 0.11 ( 3) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9306 (tpp) cc_final: 0.8865 (tpp) REVERT: A 317 MET cc_start: 0.9314 (tmm) cc_final: 0.8826 (tmm) REVERT: A 355 MET cc_start: 0.9192 (mmp) cc_final: 0.8865 (mmp) REVERT: A 930 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9450 (tt) REVERT: A 1085 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 1086 MET cc_start: 0.9072 (mmm) cc_final: 0.8760 (mmm) REVERT: A 1102 MET cc_start: 0.8787 (ptp) cc_final: 0.8532 (ptp) REVERT: A 1228 MET cc_start: 0.8768 (mmm) cc_final: 0.8317 (mmp) REVERT: B 99 TRP cc_start: 0.2780 (m-10) cc_final: 0.2350 (m-10) REVERT: B 403 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9251 (tt) REVERT: B 407 MET cc_start: 0.8754 (mtp) cc_final: 0.8506 (mtp) REVERT: B 603 MET cc_start: 0.8680 (mpp) cc_final: 0.8354 (mpp) REVERT: B 744 MET cc_start: 0.9091 (tpp) cc_final: 0.8841 (mmm) REVERT: E 94 MET cc_start: 0.8802 (mmm) cc_final: 0.8561 (mmm) REVERT: H 95 LYS cc_start: 0.9352 (ptmm) cc_final: 0.9051 (ptmm) REVERT: I 23 MET cc_start: 0.8330 (ttp) cc_final: 0.8117 (tmm) REVERT: K 1 MET cc_start: 0.7100 (pmm) cc_final: 0.6814 (pmm) REVERT: L 42 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7614 (mtt-85) REVERT: L 44 MET cc_start: 0.8688 (tpp) cc_final: 0.7796 (mmt) REVERT: L 47 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8693 (mmmm) REVERT: M 276 MET cc_start: 0.5555 (ttm) cc_final: 0.5342 (ttm) REVERT: M 437 MET cc_start: 0.7294 (tmm) cc_final: 0.7036 (tmm) REVERT: Z 451 MET cc_start: 0.8841 (mmm) cc_final: 0.8611 (mmm) outliers start: 51 outliers final: 26 residues processed: 263 average time/residue: 0.2270 time to fit residues: 101.4757 Evaluate side-chains 242 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain M residue 316 ASP Chi-restraints excluded: chain M residue 334 ARG Chi-restraints excluded: chain M residue 496 ARG Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain Z residue 508 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 201 optimal weight: 7.9990 chunk 239 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 413 optimal weight: 30.0000 chunk 282 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 36 optimal weight: 0.0470 chunk 387 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 overall best weight: 3.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A1042 ASN A1194 ASN A1303 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN I 32 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.064329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.039220 restraints weight = 223734.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040249 restraints weight = 112992.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040710 restraints weight = 74437.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.041027 restraints weight = 58928.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.041236 restraints weight = 52301.533| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 41214 Z= 0.193 Angle : 0.645 10.346 56043 Z= 0.332 Chirality : 0.047 0.475 6266 Planarity : 0.004 0.049 6931 Dihedral : 14.578 171.458 6261 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 1.63 % Allowed : 9.94 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.37 (0.12), residues: 4739 helix: 0.94 (0.14), residues: 1460 sheet: -0.72 (0.18), residues: 714 loop : -0.76 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 859 TYR 0.028 0.001 TYR M 539 PHE 0.020 0.001 PHE A 113 TRP 0.015 0.001 TRP B 27 HIS 0.012 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (41209) covalent geometry : angle 0.64525 / 0.33 (56041) SS BOND : bond 0.00327 / 0.16 ( 1) SS BOND : angle 1.21281 / 1.92 ( 2) hydrogen bonds : bond 0.04091 / 4.52 ( 1557) hydrogen bonds : angle 5.12408 / 5.12 ( 4291) metal coordination : bond 0.00115 / 0.10 ( 3) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9277 (tpp) cc_final: 0.8750 (tpp) REVERT: A 317 MET cc_start: 0.9379 (tmm) cc_final: 0.8933 (tmm) REVERT: A 1086 MET cc_start: 0.9157 (mmm) cc_final: 0.8842 (mmm) REVERT: A 1102 MET cc_start: 0.8803 (ptp) cc_final: 0.8279 (ptp) REVERT: A 1303 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: B 298 MET cc_start: 0.9251 (mmt) cc_final: 0.9013 (mpp) REVERT: B 603 MET cc_start: 0.8733 (mpp) cc_final: 0.8460 (mpp) REVERT: B 674 MET cc_start: 0.8812 (tpt) cc_final: 0.8535 (tpt) REVERT: H 76 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8857 (p0) REVERT: H 95 LYS cc_start: 0.9411 (ptmm) cc_final: 0.9083 (ptmm) REVERT: I 108 MET cc_start: 0.8244 (mmm) cc_final: 0.7938 (mmm) REVERT: J 57 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8599 (mm-30) REVERT: L 44 MET cc_start: 0.8586 (tpp) cc_final: 0.8055 (tpp) REVERT: L 47 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8777 (tptm) REVERT: G 164 MET cc_start: 0.7819 (mpp) cc_final: 0.7453 (mmt) REVERT: M 346 MET cc_start: -0.1430 (mtp) cc_final: -0.2021 (mtt) REVERT: M 437 MET cc_start: 0.7307 (tmm) cc_final: 0.7049 (tmm) REVERT: M 539 TYR cc_start: 0.6655 (t80) cc_final: 0.6396 (t80) REVERT: Z 563 MET cc_start: 0.5002 (ppp) cc_final: 0.4746 (mtt) outliers start: 69 outliers final: 28 residues processed: 278 average time/residue: 0.2370 time to fit residues: 113.0455 Evaluate side-chains 238 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain M residue 334 ARG Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 302 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 479 optimal weight: 0.0870 chunk 13 optimal weight: 8.9990 chunk 393 optimal weight: 20.0000 chunk 299 optimal weight: 5.9990 chunk 362 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 475 optimal weight: 3.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS A 441 GLN A 606 HIS ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 HIS I 32 ASN ** D 102 ASN ** 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 = 0.3634 r_free = 0.3634 target = 0.064780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.040617 restraints weight = 221752.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.040771 restraints weight = 113455.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041389 restraints weight = 72610.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.041778 restraints weight = 55936.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042047 restraints weight = 48397.165| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41214 Z= 0.139 Angle : 0.631 11.030 56043 Z= 0.322 Chirality : 0.046 0.395 6266 Planarity : 0.004 0.048 6931 Dihedral : 14.527 173.246 6261 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 1.44 % Allowed : 10.91 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.12), residues: 4739 helix: 0.98 (0.14), residues: 1462 sheet: -0.67 (0.18), residues: 714 loop : -0.75 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 16 TYR 0.017 0.001 TYR M 539 PHE 0.020 0.001 PHE A 113 TRP 0.014 0.001 TRP C 49 HIS 0.011 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (41209) covalent geometry : angle 0.63124 / 0.32 (56041) SS BOND : bond 0.00294 / 0.15 ( 1) SS BOND : angle 1.17867 / 2.08 ( 2) hydrogen bonds : bond 0.03863 / 4.31 ( 1557) hydrogen bonds : angle 5.01284 / 5.02 ( 4291) metal coordination : bond 0.00086 / 0.08 ( 3) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9275 (tpp) cc_final: 0.8718 (tpp) REVERT: A 317 MET cc_start: 0.9417 (tmm) cc_final: 0.9006 (tmm) REVERT: A 322 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8848 (mm) REVERT: A 355 MET cc_start: 0.9134 (mmp) cc_final: 0.8804 (mmp) REVERT: A 986 MET cc_start: 0.9300 (mtm) cc_final: 0.9090 (mtm) REVERT: A 1086 MET cc_start: 0.9167 (mmm) cc_final: 0.8875 (mmm) REVERT: A 1102 MET cc_start: 0.8843 (ptp) cc_final: 0.8587 (ptp) REVERT: B 603 MET cc_start: 0.8790 (mpp) cc_final: 0.8435 (mpp) REVERT: B 692 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9061 (p) REVERT: B 744 MET cc_start: 0.9180 (tpp) cc_final: 0.8936 (mmm) REVERT: E 94 MET cc_start: 0.8930 (mmm) cc_final: 0.8578 (tpt) REVERT: H 76 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8867 (p0) REVERT: H 95 LYS cc_start: 0.9458 (ptmm) cc_final: 0.9096 (ptmm) REVERT: I 108 MET cc_start: 0.8158 (mmm) cc_final: 0.7840 (mmm) REVERT: J 57 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8578 (mm-30) REVERT: K 1 MET cc_start: 0.7206 (pmm) cc_final: 0.6748 (pmm) REVERT: K 111 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8726 (p0) REVERT: L 47 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8801 (tptm) REVERT: G 16 ARG cc_start: 0.8779 (ptm-80) cc_final: 0.8132 (ptm-80) REVERT: G 164 MET cc_start: 0.7895 (mpp) cc_final: 0.7499 (mmt) REVERT: M 276 MET cc_start: 0.2449 (OUTLIER) cc_final: 0.1626 (ptp) REVERT: M 346 MET cc_start: -0.3909 (mtp) cc_final: -0.4563 (mtt) REVERT: M 437 MET cc_start: 0.5604 (tmm) cc_final: 0.5022 (tmm) REVERT: Z 563 MET cc_start: 0.4864 (ppp) cc_final: 0.4294 (mtt) outliers start: 61 outliers final: 30 residues processed: 263 average time/residue: 0.2415 time to fit residues: 108.9759 Evaluate side-chains 241 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 334 ARG Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 468 optimal weight: 50.0000 chunk 421 optimal weight: 30.0000 chunk 292 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 290 optimal weight: 7.9990 chunk 348 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A1303 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 592 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.063390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.038142 restraints weight = 223408.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038984 restraints weight = 114128.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.039557 restraints weight = 75277.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039938 restraints weight = 59632.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.040028 restraints weight = 52403.250| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 41214 Z= 0.228 Angle : 0.654 10.950 56043 Z= 0.334 Chirality : 0.046 0.338 6266 Planarity : 0.004 0.048 6931 Dihedral : 14.491 173.182 6261 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 1.72 % Allowed : 11.00 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.25 (0.12), residues: 4739 helix: 1.05 (0.14), residues: 1475 sheet: -0.76 (0.18), residues: 723 loop : -0.68 (0.13), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.019 0.002 TYR M 539 PHE 0.018 0.001 PHE A 113 TRP 0.016 0.001 TRP B 27 HIS 0.044 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (41209) covalent geometry : angle 0.65399 / 0.33 (56041) SS BOND : bond 0.00349 / 0.17 ( 1) SS BOND : angle 0.87191 / 1.30 ( 2) hydrogen bonds : bond 0.04088 / 4.50 ( 1557) hydrogen bonds : angle 4.98212 / 5.04 ( 4291) metal coordination : bond 0.00071 / 0.05 ( 3) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9244 (tpp) cc_final: 0.8666 (tpp) REVERT: A 317 MET cc_start: 0.9409 (tmm) cc_final: 0.9010 (tmm) REVERT: A 399 ILE cc_start: 0.9812 (OUTLIER) cc_final: 0.9586 (mt) REVERT: A 467 MET cc_start: 0.9057 (mpp) cc_final: 0.8795 (mmt) REVERT: A 1086 MET cc_start: 0.9208 (mmm) cc_final: 0.8954 (mmm) REVERT: A 1102 MET cc_start: 0.8845 (ptp) cc_final: 0.8332 (ptp) REVERT: B 603 MET cc_start: 0.8720 (mpp) cc_final: 0.8445 (mpp) REVERT: B 692 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9177 (p) REVERT: B 1158 LEU cc_start: 0.9859 (OUTLIER) cc_final: 0.9260 (tt) REVERT: B 1161 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8962 (mp0) REVERT: H 76 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8817 (p0) REVERT: I 23 MET cc_start: 0.8474 (ttp) cc_final: 0.8200 (tmm) REVERT: I 108 MET cc_start: 0.8037 (mmm) cc_final: 0.7728 (mmm) REVERT: J 57 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8570 (mm-30) REVERT: L 44 MET cc_start: 0.8549 (tpp) cc_final: 0.7767 (mmt) REVERT: G 16 ARG cc_start: 0.8850 (ptm-80) cc_final: 0.8214 (ptm-80) REVERT: M 276 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.4260 (ptp) REVERT: M 312 MET cc_start: -0.5637 (mpp) cc_final: -0.6365 (mtm) REVERT: M 437 MET cc_start: 0.6988 (tmm) cc_final: 0.6606 (tmm) REVERT: Y 63 MET cc_start: 0.3990 (pmm) cc_final: 0.3707 (pmm) REVERT: Z 563 MET cc_start: 0.5200 (ppp) cc_final: 0.4583 (mtt) outliers start: 73 outliers final: 36 residues processed: 266 average time/residue: 0.2365 time to fit residues: 107.8279 Evaluate side-chains 239 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 334 ARG Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 32 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 421 optimal weight: 40.0000 chunk 403 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.063793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.038885 restraints weight = 223316.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.039733 restraints weight = 113426.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.040248 restraints weight = 73507.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.040600 restraints weight = 58571.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.040782 restraints weight = 51764.080| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41214 Z= 0.172 Angle : 0.637 14.072 56043 Z= 0.324 Chirality : 0.046 0.313 6266 Planarity : 0.004 0.048 6931 Dihedral : 14.436 172.631 6261 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 1.39 % Allowed : 11.55 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.22 (0.12), residues: 4739 helix: 1.07 (0.14), residues: 1476 sheet: -0.76 (0.18), residues: 733 loop : -0.65 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 31 TYR 0.017 0.001 TYR M 539 PHE 0.020 0.001 PHE A 113 TRP 0.025 0.001 TRP B 99 HIS 0.011 0.001 HIS A 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (41209) covalent geometry : angle 0.63669 / 0.32 (56041) SS BOND : bond 0.00359 / 0.18 ( 1) SS BOND : angle 1.06089 / 2.03 ( 2) hydrogen bonds : bond 0.03825 / 4.24 ( 1557) hydrogen bonds : angle 4.92460 / 5.00 ( 4291) metal coordination : bond 0.00104 / 0.09 ( 3) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9221 (tpp) cc_final: 0.8635 (tpp) REVERT: A 107 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9540 (mm) REVERT: A 317 MET cc_start: 0.9417 (tmm) cc_final: 0.9014 (tmm) REVERT: A 355 MET cc_start: 0.9135 (mmp) cc_final: 0.8728 (mmp) REVERT: A 399 ILE cc_start: 0.9813 (tt) cc_final: 0.9592 (mt) REVERT: A 467 MET cc_start: 0.9049 (mpp) cc_final: 0.8649 (mmt) REVERT: A 470 MET cc_start: 0.8856 (mtm) cc_final: 0.8531 (mtm) REVERT: A 986 MET cc_start: 0.9046 (mtp) cc_final: 0.8805 (mtt) REVERT: A 1086 MET cc_start: 0.9153 (mmm) cc_final: 0.8924 (mmm) REVERT: A 1102 MET cc_start: 0.8782 (ptp) cc_final: 0.8522 (ptp) REVERT: B 603 MET cc_start: 0.8738 (mpp) cc_final: 0.8462 (mpp) REVERT: B 692 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9187 (p) REVERT: B 744 MET cc_start: 0.9158 (tpp) cc_final: 0.8926 (mmm) REVERT: B 1158 LEU cc_start: 0.9849 (OUTLIER) cc_final: 0.9188 (tt) REVERT: B 1161 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8962 (mp0) REVERT: E 94 MET cc_start: 0.8828 (tpt) cc_final: 0.8530 (tpt) REVERT: H 76 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8788 (p0) REVERT: I 23 MET cc_start: 0.8491 (ttp) cc_final: 0.8088 (tmm) REVERT: I 92 LYS cc_start: 0.9071 (tppt) cc_final: 0.8813 (tppt) REVERT: J 57 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8524 (mm-30) REVERT: K 8 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8674 (mp0) REVERT: L 15 MET cc_start: 0.7749 (ppp) cc_final: 0.7520 (ppp) REVERT: L 44 MET cc_start: 0.8441 (tpp) cc_final: 0.7722 (mmt) REVERT: G 16 ARG cc_start: 0.8898 (ptm-80) cc_final: 0.8252 (ptm-80) REVERT: M 276 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.4039 (ptp) REVERT: M 437 MET cc_start: 0.6345 (tmm) cc_final: 0.5852 (tmm) REVERT: Y 63 MET cc_start: 0.4366 (pmm) cc_final: 0.4033 (pmm) REVERT: Z 563 MET cc_start: 0.4951 (ppp) cc_final: 0.4320 (mtt) outliers start: 59 outliers final: 37 residues processed: 250 average time/residue: 0.2265 time to fit residues: 98.0718 Evaluate side-chains 243 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 413 optimal weight: 0.3980 chunk 183 optimal weight: 20.0000 chunk 322 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 358 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 435 optimal weight: 40.0000 chunk 443 optimal weight: 10.0000 chunk 437 optimal weight: 7.9990 chunk 426 optimal weight: 50.0000 chunk 480 optimal weight: 20.0000 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.064300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.039025 restraints weight = 224685.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040021 restraints weight = 111733.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.040633 restraints weight = 73471.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.040929 restraints weight = 57754.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.041088 restraints weight = 51095.382| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 41214 Z= 0.128 Angle : 0.625 13.093 56043 Z= 0.316 Chirality : 0.045 0.297 6266 Planarity : 0.004 0.049 6931 Dihedral : 14.390 172.295 6261 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 1.46 % Allowed : 11.64 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.20 (0.12), residues: 4739 helix: 1.08 (0.14), residues: 1475 sheet: -0.72 (0.18), residues: 735 loop : -0.64 (0.13), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 33 TYR 0.019 0.001 TYR M 539 PHE 0.018 0.001 PHE A 113 TRP 0.027 0.001 TRP B 99 HIS 0.009 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (41209) covalent geometry : angle 0.62473 / 0.32 (56041) SS BOND : bond 0.00283 / 0.14 ( 1) SS BOND : angle 1.03520 / 2.06 ( 2) hydrogen bonds : bond 0.03646 / 4.07 ( 1557) hydrogen bonds : angle 4.87096 / 4.95 ( 4291) metal coordination : bond 0.00125 / 0.10 ( 3) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9218 (tpp) cc_final: 0.8626 (tpp) REVERT: A 107 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9533 (mm) REVERT: A 317 MET cc_start: 0.9444 (tmm) cc_final: 0.9034 (tmm) REVERT: A 355 MET cc_start: 0.9125 (mmp) cc_final: 0.8816 (mmp) REVERT: A 986 MET cc_start: 0.9048 (mtp) cc_final: 0.8814 (mtt) REVERT: A 1102 MET cc_start: 0.8793 (ptp) cc_final: 0.8280 (ptp) REVERT: A 1228 MET cc_start: 0.8835 (mmm) cc_final: 0.8255 (mtt) REVERT: A 1440 MET cc_start: 0.9280 (mmm) cc_final: 0.8307 (mmm) REVERT: B 133 ILE cc_start: 0.6413 (OUTLIER) cc_final: 0.6185 (tp) REVERT: B 603 MET cc_start: 0.8713 (mpp) cc_final: 0.8445 (mpp) REVERT: B 692 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.9169 (p) REVERT: B 744 MET cc_start: 0.9166 (tpp) cc_final: 0.8927 (mmm) REVERT: B 1158 LEU cc_start: 0.9841 (OUTLIER) cc_final: 0.9186 (tt) REVERT: B 1161 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8950 (mp0) REVERT: E 94 MET cc_start: 0.8884 (tpt) cc_final: 0.8552 (tpt) REVERT: H 76 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8781 (p0) REVERT: I 23 MET cc_start: 0.8466 (ttp) cc_final: 0.8105 (tmm) REVERT: J 57 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8494 (mm-30) REVERT: K 1 MET cc_start: 0.7178 (pmm) cc_final: 0.6691 (pmm) REVERT: K 38 GLU cc_start: 0.8453 (tp30) cc_final: 0.8094 (tp30) REVERT: L 44 MET cc_start: 0.8351 (tpp) cc_final: 0.7703 (mmt) REVERT: G 16 ARG cc_start: 0.8870 (ptm-80) cc_final: 0.8150 (ptm-80) REVERT: M 276 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.3175 (ptp) REVERT: M 437 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.5951 (tmm) REVERT: Y 63 MET cc_start: 0.4314 (pmm) cc_final: 0.3948 (pmm) REVERT: Z 563 MET cc_start: 0.4918 (ppp) cc_final: 0.4325 (mtt) outliers start: 62 outliers final: 40 residues processed: 257 average time/residue: 0.2228 time to fit residues: 98.8591 Evaluate side-chains 249 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 334 ARG Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain Z residue 474 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 359 optimal weight: 0.2980 chunk 357 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 406 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 441 optimal weight: 50.0000 chunk 136 optimal weight: 5.9990 chunk 232 optimal weight: 0.4980 chunk 317 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 347 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.064573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.040603 restraints weight = 221411.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041903 restraints weight = 119131.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041612 restraints weight = 72828.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.041979 restraints weight = 55897.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.042060 restraints weight = 50080.755| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41214 Z= 0.118 Angle : 0.633 17.040 56043 Z= 0.318 Chirality : 0.045 0.282 6266 Planarity : 0.004 0.050 6931 Dihedral : 14.335 172.283 6261 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 1.44 % Allowed : 11.85 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.14 (0.12), residues: 4739 helix: 1.13 (0.14), residues: 1462 sheet: -0.64 (0.18), residues: 732 loop : -0.61 (0.13), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 42 TYR 0.017 0.001 TYR M 539 PHE 0.018 0.001 PHE A 113 TRP 0.023 0.001 TRP B 99 HIS 0.008 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (41209) covalent geometry : angle 0.63312 / 0.32 (56041) SS BOND : bond 0.00265 / 0.13 ( 1) SS BOND : angle 1.02079 / 2.06 ( 2) hydrogen bonds : bond 0.03550 / 3.96 ( 1557) hydrogen bonds : angle 4.81669 / 4.91 ( 4291) metal coordination : bond 0.00110 / 0.08 ( 3) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9236 (tpp) cc_final: 0.8663 (tpp) REVERT: A 107 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9531 (mm) REVERT: A 317 MET cc_start: 0.9412 (tmm) cc_final: 0.9019 (tmm) REVERT: A 355 MET cc_start: 0.9165 (mmp) cc_final: 0.8850 (mmp) REVERT: A 1085 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 1102 MET cc_start: 0.8866 (ptp) cc_final: 0.8308 (ptp) REVERT: A 1228 MET cc_start: 0.8869 (mmm) cc_final: 0.8212 (mtt) REVERT: B 133 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5937 (tp) REVERT: B 590 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9343 (tp) REVERT: B 603 MET cc_start: 0.8728 (mpp) cc_final: 0.8427 (mpp) REVERT: B 744 MET cc_start: 0.9191 (tpp) cc_final: 0.8952 (mmm) REVERT: B 795 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9285 (mm) REVERT: B 1158 LEU cc_start: 0.9831 (OUTLIER) cc_final: 0.9194 (tt) REVERT: B 1161 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8956 (mp0) REVERT: E 94 MET cc_start: 0.8903 (tpt) cc_final: 0.8546 (tpt) REVERT: H 76 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8807 (p0) REVERT: I 23 MET cc_start: 0.8520 (ttp) cc_final: 0.8122 (tmm) REVERT: J 57 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8501 (mm-30) REVERT: K 1 MET cc_start: 0.7159 (pmm) cc_final: 0.6701 (pmm) REVERT: K 8 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8630 (mp0) REVERT: K 38 GLU cc_start: 0.8478 (tp30) cc_final: 0.8096 (tp30) REVERT: K 61 TYR cc_start: 0.9257 (p90) cc_final: 0.8986 (p90) REVERT: L 44 MET cc_start: 0.8387 (tpp) cc_final: 0.7704 (mmt) REVERT: G 16 ARG cc_start: 0.8896 (ptm-80) cc_final: 0.8182 (ptm-80) REVERT: M 276 MET cc_start: 0.1471 (OUTLIER) cc_final: 0.1099 (ptp) REVERT: M 437 MET cc_start: 0.3771 (OUTLIER) cc_final: 0.3278 (tmm) REVERT: Y 63 MET cc_start: 0.3889 (pmm) cc_final: 0.3609 (pmm) REVERT: Z 563 MET cc_start: 0.5170 (ppp) cc_final: 0.4416 (mtt) outliers start: 61 outliers final: 39 residues processed: 258 average time/residue: 0.2252 time to fit residues: 100.6734 Evaluate side-chains 252 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 334 ARG Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain Z residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 465 optimal weight: 8.9990 chunk 221 optimal weight: 0.0020 chunk 464 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 chunk 262 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 414 optimal weight: 40.0000 chunk 274 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 479 optimal weight: 8.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.064413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.039723 restraints weight = 221193.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.040408 restraints weight = 110981.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.040987 restraints weight = 72457.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.041359 restraints weight = 57033.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041566 restraints weight = 49894.897| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41214 Z= 0.126 Angle : 0.631 16.692 56043 Z= 0.316 Chirality : 0.045 0.273 6266 Planarity : 0.004 0.050 6931 Dihedral : 14.295 172.864 6261 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 1.16 % Allowed : 12.30 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.09 (0.12), residues: 4739 helix: 1.17 (0.14), residues: 1464 sheet: -0.65 (0.18), residues: 735 loop : -0.57 (0.13), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.018 0.001 TYR M 539 PHE 0.016 0.001 PHE A 113 TRP 0.019 0.001 TRP B 99 HIS 0.009 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (41209) covalent geometry : angle 0.63084 / 0.32 (56041) SS BOND : bond 0.00261 / 0.13 ( 1) SS BOND : angle 0.86135 / 1.66 ( 2) hydrogen bonds : bond 0.03526 / 3.92 ( 1557) hydrogen bonds : angle 4.77332 / 4.89 ( 4291) metal coordination : bond 0.00129 / 0.10 ( 3) Misc. bond : bond 0.00009 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9478 Ramachandran restraints generated. 4739 Oldfield, 0 Emsley, 4739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9218 (tpp) cc_final: 0.8680 (tpp) REVERT: A 107 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9541 (mm) REVERT: A 317 MET cc_start: 0.9449 (tmm) cc_final: 0.9060 (tmm) REVERT: A 355 MET cc_start: 0.9136 (mmp) cc_final: 0.8934 (mmp) REVERT: A 1085 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7901 (mt-10) REVERT: A 1102 MET cc_start: 0.8795 (ptp) cc_final: 0.8281 (ptp) REVERT: A 1228 MET cc_start: 0.8833 (mmm) cc_final: 0.8214 (mtt) REVERT: A 1440 MET cc_start: 0.9288 (mmm) cc_final: 0.8339 (mmm) REVERT: B 133 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5931 (tp) REVERT: B 407 MET cc_start: 0.8672 (mtm) cc_final: 0.8442 (ttm) REVERT: B 590 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9327 (tp) REVERT: B 603 MET cc_start: 0.8754 (mpp) cc_final: 0.8492 (mpp) REVERT: B 744 MET cc_start: 0.9179 (tpp) cc_final: 0.8943 (mmm) REVERT: B 1158 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9197 (tt) REVERT: B 1161 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8975 (mp0) REVERT: E 18 MET cc_start: 0.8961 (mmm) cc_final: 0.8737 (tpt) REVERT: E 94 MET cc_start: 0.8875 (tpt) cc_final: 0.8570 (mmm) REVERT: H 76 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8782 (p0) REVERT: H 92 MET cc_start: 0.8806 (mtm) cc_final: 0.8600 (mtm) REVERT: I 23 MET cc_start: 0.8496 (ttp) cc_final: 0.8120 (tmm) REVERT: J 57 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8355 (mm-30) REVERT: K 1 MET cc_start: 0.7164 (pmm) cc_final: 0.6704 (pmm) REVERT: K 38 GLU cc_start: 0.8487 (tp30) cc_final: 0.8116 (tp30) REVERT: K 61 TYR cc_start: 0.9318 (p90) cc_final: 0.9111 (p90) REVERT: L 44 MET cc_start: 0.8219 (tpp) cc_final: 0.7657 (mmt) REVERT: G 16 ARG cc_start: 0.8870 (ptm-80) cc_final: 0.8193 (ptm-80) REVERT: M 276 MET cc_start: 0.2963 (ttm) cc_final: 0.2392 (ptp) REVERT: M 437 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5433 (tmm) REVERT: Y 63 MET cc_start: 0.4546 (pmm) cc_final: 0.4160 (pmm) REVERT: Z 563 MET cc_start: 0.5114 (ppp) cc_final: 0.4328 (mtt) outliers start: 49 outliers final: 38 residues processed: 248 average time/residue: 0.2161 time to fit residues: 92.6949 Evaluate side-chains 250 residues out of total 4255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 334 ARG Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain Z residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 371 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 281 optimal weight: 0.8980 chunk 454 optimal weight: 50.0000 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 333 optimal weight: 7.9990 chunk 342 optimal weight: 2.9990 chunk 414 optimal weight: 50.0000 chunk 58 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.064573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.040651 restraints weight = 222585.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042012 restraints weight = 119876.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.041619 restraints weight = 70487.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.042018 restraints weight = 54910.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042059 restraints weight = 50402.064| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41214 Z= 0.120 Angle : 0.626 15.861 56043 Z= 0.315 Chirality : 0.045 0.267 6266 Planarity : 0.004 0.050 6931 Dihedral : 14.257 173.359 6261 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 1.13 % Allowed : 12.42 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.06 (0.12), residues: 4739 helix: 1.19 (0.14), residues: 1456 sheet: -0.57 (0.19), residues: 715 loop : -0.55 (0.13), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 31 TYR 0.024 0.001 TYR M 289 PHE 0.018 0.001 PHE A 113 TRP 0.019 0.001 TRP C 49 HIS 0.008 0.001 HIS M 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (41209) covalent geometry : angle 0.62585 / 0.31 (56041) SS BOND : bond 0.00264 / 0.13 ( 1) SS BOND : angle 0.95116 / 1.91 ( 2) hydrogen bonds : bond 0.03499 / 3.92 ( 1557) hydrogen bonds : angle 4.76196 / 4.89 ( 4291) metal coordination : bond 0.00142 / 0.11 ( 3) Misc. bond : bond 0.00001 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8494.37 seconds wall clock time: 147 minutes 32.34 seconds (8852.34 seconds total)