Starting phenix.real_space_refine (version: dev) on Mon Feb 27 21:08:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hls_0241/02_2023/6hls_0241.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hls_0241/02_2023/6hls_0241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hls_0241/02_2023/6hls_0241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hls_0241/02_2023/6hls_0241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hls_0241/02_2023/6hls_0241.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hls_0241/02_2023/6hls_0241.pdb" } resolution = 3.21 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 Process input model Symmetric amino acids flipped Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A ARG 1223": "NH1" <-> "NH2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1494": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1580": "NH1" <-> "NH2" Residue "A ARG 1640": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ARG 909": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1023": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1129": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "B PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30954 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 11308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1431, 11308 Classifications: {'peptide': 1431} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1371} Chain breaks: 10 Chain: "B" Number of atoms: 9248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 9248 Classifications: {'peptide': 1163} Link IDs: {'PTRANS': 59, 'TRANS': 1103} Chain breaks: 4 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2415 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain breaks: 1 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 62.136 51.274 56.118 1.00 58.45 S ATOM 480 SG CYS A 65 65.634 49.840 55.871 1.00 53.69 S ATOM 535 SG CYS A 72 64.578 51.492 59.046 1.00 50.91 S ATOM 781 SG CYS A 102 62.369 101.530 43.631 1.00 74.18 S ATOM 806 SG CYS A 105 65.742 99.891 40.778 1.00 73.06 S ATOM 1575 SG CYS A 233 66.792 102.720 42.781 1.00 81.47 S ATOM 1597 SG CYS A 236 63.853 102.893 40.174 1.00 89.19 S ATOM 19886 SG CYS B1104 76.730 60.405 48.595 1.00 36.57 S ATOM 19912 SG CYS B1107 74.219 63.051 48.457 1.00 43.96 S ATOM 20059 SG CYS B1128 73.130 59.669 48.583 1.00 51.13 S ATOM 28535 SG CYS I 13 33.169 126.428 107.591 1.00 63.09 S ATOM 28655 SG CYS I 30 34.090 128.049 104.458 1.00 77.26 S ATOM 28973 SG CYS I 89 71.399 86.317 155.587 1.00136.54 S ATOM 29171 SG CYS I 114 68.717 87.322 151.553 1.00108.04 S ATOM 29314 SG CYS J 7 79.156 42.644 128.480 1.00 25.29 S ATOM 29337 SG CYS J 10 82.641 42.009 129.097 1.00 24.78 S ATOM 29617 SG CYS J 45 82.811 45.659 129.920 1.00 23.47 S ATOM 29623 SG CYS J 46 80.569 43.167 131.777 1.00 23.27 S ATOM 30638 SG CYS L 31 37.873 42.965 112.755 1.00 47.42 S ATOM 30658 SG CYS L 34 36.247 41.491 115.808 1.00 49.32 S ATOM 30762 SG CYS L 48 34.804 40.130 112.736 1.00 69.01 S ATOM 30785 SG CYS L 51 34.029 44.387 114.355 1.00 68.98 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I3002 " occ=0.75 Time building chain proxies: 17.25, per 1000 atoms: 0.56 Number of scatterers: 30954 At special positions: 0 Unit cell: (158.08, 162.24, 171.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 166 16.00 O 5825 8.00 N 5376 7.00 C 19580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.43 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN I3002 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 89 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 114 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " Number of angles added : 21 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7316 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 51 sheets defined 35.6% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.977A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 90 through 99 removed outlier: 4.191A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.740A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.559A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 199 removed outlier: 3.697A pdb=" N SER A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 229 removed outlier: 3.613A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.516A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.536A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.683A pdb=" N ARG A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.503A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 439 removed outlier: 3.676A pdb=" N PHE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.172A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.659A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.515A pdb=" N ASN A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.528A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.954A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 802 removed outlier: 3.810A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.642A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.786A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 847 Processing helix chain 'A' and resid 848 through 851 removed outlier: 3.894A pdb=" N VAL A 851 " --> pdb=" O LYS A 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 884 removed outlier: 3.629A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 891 Processing helix chain 'A' and resid 894 through 912 removed outlier: 3.685A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.561A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1008 removed outlier: 3.558A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 removed outlier: 3.775A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.733A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 3.555A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 4.194A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.566A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.695A pdb=" N ASP A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.794A pdb=" N PHE A1166 " --> pdb=" O ASN A1162 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.875A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1195 " --> pdb=" O GLN A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1248 through 1256 removed outlier: 3.553A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.081A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A1306 " --> pdb=" O TYR A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.507A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A1319 " --> pdb=" O ASN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.525A pdb=" N VAL A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1454 removed outlier: 3.608A pdb=" N ASP A1445 " --> pdb=" O LYS A1441 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A1446 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1451 " --> pdb=" O GLN A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.897A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 3.852A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1554 removed outlier: 3.829A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1566 removed outlier: 3.576A pdb=" N ASN A1560 " --> pdb=" O GLU A1556 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1572 Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.747A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.637A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 removed outlier: 3.582A pdb=" N ASP A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1643 removed outlier: 3.763A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 removed outlier: 4.289A pdb=" N ASN B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.035A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.049A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 55 through 59 removed outlier: 4.136A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 69 removed outlier: 3.915A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.529A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.665A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.545A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.515A pdb=" N GLY B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.526A pdb=" N THR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.824A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.703A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.815A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 406 through 435 removed outlier: 3.774A pdb=" N LEU B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.573A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.835A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 614 removed outlier: 3.594A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.557A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.584A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.508A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.321A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 833 through 839 removed outlier: 3.928A pdb=" N TRP B 836 " --> pdb=" O PRO B 833 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 833 through 839' Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.968A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.808A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.686A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1093 removed outlier: 3.559A pdb=" N GLN B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1193 removed outlier: 3.609A pdb=" N ALA B1191 " --> pdb=" O SER B1187 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.533A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.671A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.557A pdb=" N HIS C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.820A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 179' Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.598A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 3.714A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.641A pdb=" N ARG C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 282' Processing helix chain 'C' and resid 283 through 286 removed outlier: 3.899A pdb=" N ALA C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.567A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 82 through 94 removed outlier: 4.143A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 4.151A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.656A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.781A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.609A pdb=" N LEU E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.992A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.826A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.573A pdb=" N LEU F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 4.129A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 removed outlier: 3.885A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.640A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 67 removed outlier: 3.770A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.569A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 4.283A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.721A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.608A pdb=" N LYS K 122 " --> pdb=" O GLN K 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU K 132 " --> pdb=" O CYS K 128 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR K 136 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA2, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 7.344A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 86 removed outlier: 3.595A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 11.486A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.967A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.641A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.980A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.578A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB2, first strand: chain 'A' and resid 1507 through 1508 Processing sheet with id=AB3, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 7.139A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.841A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG G 40 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.841A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG G 40 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TRP G 117 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 104 removed outlier: 5.948A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB9, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC1, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.355A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.418A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 236 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.705A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC5, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.803A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.501A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.501A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 752 through 753 removed outlier: 3.527A pdb=" N LYS B 753 " --> pdb=" O GLN B 979 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 768 through 775 removed outlier: 8.462A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.684A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD3, first strand: chain 'B' and resid 1010 through 1011 Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD5, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AD6, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.686A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.686A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C 232 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 168 through 169 removed outlier: 6.677A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.400A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE4, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.105A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.703A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.913A pdb=" N PHE G 231 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AF1, first strand: chain 'G' and resid 167 through 169 removed outlier: 4.009A pdb=" N HIS G 216 " --> pdb=" O VAL G 169 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.945A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 107 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.853A pdb=" N LEU I 7 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 28 through 29 Processing sheet with id=AF5, first strand: chain 'I' and resid 95 through 99 Processing sheet with id=AF6, first strand: chain 'K' and resid 47 through 49 1078 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.28 Time building geometry restraints manager: 12.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9549 1.33 - 1.46: 5634 1.46 - 1.58: 16108 1.58 - 1.70: 0 1.70 - 1.82: 260 Bond restraints: 31551 Sorted by residual: bond pdb=" C GLY B 844 " pdb=" N LEU B 845 " ideal model delta sigma weight residual 1.331 1.257 0.074 2.83e-02 1.25e+03 6.76e+00 bond pdb=" CG1 ILE B 276 " pdb=" CD1 ILE B 276 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.68e+00 bond pdb=" CB MET B 936 " pdb=" CG MET B 936 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.12e+00 bond pdb=" CG LEU B1087 " pdb=" CD1 LEU B1087 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.98e+00 bond pdb=" CG LEU A1584 " pdb=" CD1 LEU A1584 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.91e+00 ... (remaining 31546 not shown) Histogram of bond angle deviations from ideal: 95.66 - 103.84: 474 103.84 - 112.02: 14595 112.02 - 120.20: 14554 120.20 - 128.39: 12803 128.39 - 136.57: 207 Bond angle restraints: 42633 Sorted by residual: angle pdb=" N ILE A 793 " pdb=" CA ILE A 793 " pdb=" C ILE A 793 " ideal model delta sigma weight residual 112.96 108.02 4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" N ILE B 417 " pdb=" CA ILE B 417 " pdb=" C ILE B 417 " ideal model delta sigma weight residual 112.29 107.74 4.55 9.40e-01 1.13e+00 2.35e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ARG L 42 " pdb=" N THR L 43 " pdb=" CA THR L 43 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C THR B 18 " pdb=" N LEU B 19 " pdb=" CA LEU B 19 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 ... (remaining 42628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 18068 15.30 - 30.59: 929 30.59 - 45.89: 206 45.89 - 61.19: 8 61.19 - 76.48: 21 Dihedral angle restraints: 19232 sinusoidal: 7905 harmonic: 11327 Sorted by residual: dihedral pdb=" CA ASP B 794 " pdb=" C ASP B 794 " pdb=" N GLU B 795 " pdb=" CA GLU B 795 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA CYS J 7 " pdb=" C CYS J 7 " pdb=" N PHE J 8 " pdb=" CA PHE J 8 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA LEU A 781 " pdb=" C LEU A 781 " pdb=" N ASP A 782 " pdb=" CA ASP A 782 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 19229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4241 0.094 - 0.188: 482 0.188 - 0.282: 28 0.282 - 0.375: 3 0.375 - 0.469: 2 Chirality restraints: 4756 Sorted by residual: chirality pdb=" CB ILE B 207 " pdb=" CA ILE B 207 " pdb=" CG1 ILE B 207 " pdb=" CG2 ILE B 207 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CB ILE A1219 " pdb=" CA ILE A1219 " pdb=" CG1 ILE A1219 " pdb=" CG2 ILE A1219 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE D 22 " pdb=" CA ILE D 22 " pdb=" CG1 ILE D 22 " pdb=" CG2 ILE D 22 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 4753 not shown) Planarity restraints: 5519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO E 151 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " -0.024 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR B1033 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 67 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO G 68 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 68 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 68 " -0.039 5.00e-02 4.00e+02 ... (remaining 5516 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5424 2.76 - 3.30: 27483 3.30 - 3.83: 50649 3.83 - 4.37: 62084 4.37 - 4.90: 106492 Nonbonded interactions: 252132 Sorted by model distance: nonbonded pdb=" O PHE B 963 " pdb=" OH TYR B1027 " model vdw 2.231 2.440 nonbonded pdb=" OD2 ASP B 843 " pdb=" OH TYR L 29 " model vdw 2.262 2.440 nonbonded pdb=" OD1 ASP B1186 " pdb=" OH TYR B1198 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR A 621 " pdb=" O ALA A 626 " model vdw 2.289 2.440 nonbonded pdb=" OD2 ASP E 25 " pdb=" OH TYR E 187 " model vdw 2.301 2.440 ... (remaining 252127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 166 5.16 5 C 19580 2.51 5 N 5376 2.21 5 O 5825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.540 Check model and map are aligned: 0.500 Process input model: 87.320 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.250 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.007 0.104 31551 Z= 0.449 Angle : 0.943 11.110 42633 Z= 0.495 Chirality : 0.060 0.469 4756 Planarity : 0.007 0.082 5519 Dihedral : 10.209 76.484 11916 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.10), residues: 3836 helix: -4.39 (0.06), residues: 1228 sheet: -2.49 (0.19), residues: 600 loop : -2.19 (0.12), residues: 2008 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 979 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 986 average time/residue: 0.5058 time to fit residues: 771.3365 Evaluate side-chains 559 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 557 time to evaluate : 3.954 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3013 time to fit residues: 6.6517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 8.9990 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 348 optimal weight: 0.0000 overall best weight: 1.8168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 116 HIS A 380 ASN A 553 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 673 HIS A 798 HIS A 880 GLN A 939 ASN A1047 GLN A1062 HIS A1108 HIS A1293 HIS A1447 GLN B 27 ASN B 433 ASN B 473 GLN B 679 GLN B 684 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 745 GLN B 767 ASN B 921 HIS B1115 GLN C 175 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN G 56 ASN G 64 GLN G 121 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 21 ASN K 106 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 31551 Z= 0.220 Angle : 0.631 9.502 42633 Z= 0.332 Chirality : 0.046 0.232 4756 Planarity : 0.005 0.076 5519 Dihedral : 5.611 26.141 4231 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.12), residues: 3836 helix: -2.74 (0.11), residues: 1271 sheet: -2.04 (0.19), residues: 633 loop : -1.62 (0.13), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 628 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 60 residues processed: 685 average time/residue: 0.4633 time to fit residues: 510.1398 Evaluate side-chains 581 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 521 time to evaluate : 3.788 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2961 time to fit residues: 39.2580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 377 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 346 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 93 GLN A 603 HIS A 656 GLN A 863 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN B 679 GLN B 710 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 207 HIS C 234 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN E 101 GLN E 136 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 119 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 11 GLN J 53 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 31551 Z= 0.371 Angle : 0.666 11.007 42633 Z= 0.344 Chirality : 0.048 0.274 4756 Planarity : 0.005 0.069 5519 Dihedral : 5.440 24.014 4231 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.12), residues: 3836 helix: -1.74 (0.13), residues: 1277 sheet: -1.74 (0.19), residues: 629 loop : -1.32 (0.14), residues: 1930 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 545 time to evaluate : 3.755 Fit side-chains revert: symmetry clash outliers start: 95 outliers final: 56 residues processed: 615 average time/residue: 0.4814 time to fit residues: 472.6839 Evaluate side-chains 543 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 487 time to evaluate : 3.810 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2977 time to fit residues: 36.8716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 234 optimal weight: 0.4980 chunk 350 optimal weight: 0.9990 chunk 371 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 332 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 553 GLN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1447 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN D 29 GLN D 49 ASN E 101 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 31551 Z= 0.159 Angle : 0.543 9.328 42633 Z= 0.284 Chirality : 0.044 0.249 4756 Planarity : 0.004 0.064 5519 Dihedral : 4.977 23.078 4231 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 3836 helix: -1.06 (0.14), residues: 1277 sheet: -1.46 (0.19), residues: 646 loop : -1.08 (0.14), residues: 1913 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 542 time to evaluate : 3.957 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 576 average time/residue: 0.4731 time to fit residues: 434.5032 Evaluate side-chains 510 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 490 time to evaluate : 3.974 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2925 time to fit residues: 16.8103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 316 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 553 GLN A1336 GLN A1629 ASN B 547 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN B 702 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 31551 Z= 0.377 Angle : 0.641 10.326 42633 Z= 0.330 Chirality : 0.048 0.264 4756 Planarity : 0.005 0.060 5519 Dihedral : 5.148 22.995 4231 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3836 helix: -0.90 (0.14), residues: 1279 sheet: -1.49 (0.19), residues: 636 loop : -0.98 (0.14), residues: 1921 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 507 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 49 residues processed: 561 average time/residue: 0.4764 time to fit residues: 427.4445 Evaluate side-chains 530 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 481 time to evaluate : 3.919 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2904 time to fit residues: 32.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 9.9990 chunk 334 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 371 optimal weight: 0.1980 chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 592 GLN A1629 ASN B 101 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 31551 Z= 0.260 Angle : 0.583 10.007 42633 Z= 0.301 Chirality : 0.045 0.249 4756 Planarity : 0.004 0.059 5519 Dihedral : 4.983 22.229 4231 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 3836 helix: -0.66 (0.14), residues: 1287 sheet: -1.36 (0.19), residues: 633 loop : -0.86 (0.14), residues: 1916 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 494 time to evaluate : 4.292 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 518 average time/residue: 0.4968 time to fit residues: 409.6823 Evaluate side-chains 499 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 473 time to evaluate : 3.895 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3007 time to fit residues: 20.1499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 271 optimal weight: 8.9990 chunk 210 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 370 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 489 ASN A 515 ASN A 553 GLN A1629 ASN B 251 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS C 99 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 31551 Z= 0.330 Angle : 0.620 10.146 42633 Z= 0.318 Chirality : 0.047 0.261 4756 Planarity : 0.004 0.053 5519 Dihedral : 5.058 22.289 4231 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3836 helix: -0.57 (0.14), residues: 1290 sheet: -1.32 (0.19), residues: 629 loop : -0.87 (0.14), residues: 1917 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 485 time to evaluate : 4.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 35 residues processed: 514 average time/residue: 0.4877 time to fit residues: 398.4625 Evaluate side-chains 506 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 471 time to evaluate : 3.786 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3088 time to fit residues: 25.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS A1629 ASN B 251 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN I 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 31551 Z= 0.227 Angle : 0.569 12.277 42633 Z= 0.293 Chirality : 0.045 0.255 4756 Planarity : 0.004 0.051 5519 Dihedral : 4.863 21.564 4231 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 3836 helix: -0.33 (0.14), residues: 1290 sheet: -1.23 (0.19), residues: 639 loop : -0.79 (0.15), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 486 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 499 average time/residue: 0.4858 time to fit residues: 387.1861 Evaluate side-chains 484 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 471 time to evaluate : 3.725 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2828 time to fit residues: 12.3043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 20.0000 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 270 optimal weight: 0.3980 chunk 105 optimal weight: 9.9990 chunk 311 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 343 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31551 Z= 0.205 Angle : 0.552 11.859 42633 Z= 0.284 Chirality : 0.044 0.258 4756 Planarity : 0.004 0.049 5519 Dihedral : 4.710 20.541 4231 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3836 helix: -0.16 (0.15), residues: 1290 sheet: -1.17 (0.20), residues: 639 loop : -0.73 (0.15), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 493 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 503 average time/residue: 0.4947 time to fit residues: 395.3638 Evaluate side-chains 485 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 471 time to evaluate : 3.900 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4132 time to fit residues: 15.5653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 9.9990 chunk 364 optimal weight: 7.9990 chunk 222 optimal weight: 0.0970 chunk 173 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 352 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN B 251 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN I 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 31551 Z= 0.284 Angle : 0.589 12.171 42633 Z= 0.302 Chirality : 0.046 0.260 4756 Planarity : 0.004 0.048 5519 Dihedral : 4.813 21.068 4231 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3836 helix: -0.13 (0.14), residues: 1279 sheet: -1.18 (0.20), residues: 641 loop : -0.74 (0.14), residues: 1916 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 471 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 480 average time/residue: 0.4923 time to fit residues: 375.9263 Evaluate side-chains 471 residues out of total 3445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 465 time to evaluate : 3.656 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3651 time to fit residues: 9.4659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.9980 chunk 324 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 305 optimal weight: 0.8980 chunk 127 optimal weight: 0.1980 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1629 ASN B 251 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN B 745 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.120807 restraints weight = 42408.782| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.64 r_work: 0.3188 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 31551 Z= 0.143 Angle : 0.523 11.319 42633 Z= 0.270 Chirality : 0.043 0.238 4756 Planarity : 0.003 0.045 5519 Dihedral : 4.500 18.706 4231 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3836 helix: 0.18 (0.15), residues: 1262 sheet: -1.11 (0.20), residues: 651 loop : -0.63 (0.14), residues: 1923 =============================================================================== Job complete usr+sys time: 8264.93 seconds wall clock time: 150 minutes 31.48 seconds (9031.48 seconds total)