Starting phenix.real_space_refine (version: dev) on Mon May 16 05:10:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/05_2022/6bcj_7081.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/05_2022/6bcj_7081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/05_2022/6bcj_7081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/05_2022/6bcj_7081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/05_2022/6bcj_7081.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/05_2022/6bcj_7081.pdb" } resolution = 3.14 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= 0.010 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 888": "NH1" <-> "NH2" Residue "B ARG 949": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 993": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1118": "NH1" <-> "NH2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1063": "NH1" <-> "NH2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 611": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 878": "NH1" <-> "NH2" Residue "C ARG 888": "NH1" <-> "NH2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C ARG 953": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 1063": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 826": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 888": "NH1" <-> "NH2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 993": "NH1" <-> "NH2" Residue "D ARG 1063": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1137": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 29868 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "C" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "D" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' NA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 17.44, per 1000 atoms: 0.58 Number of scatterers: 29868 At special positions: 0 Unit cell: (150.87, 150.87, 163.71, 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) S 136 16.00 Na 4 11.00 O 5252 8.00 N 5216 7.00 C 19260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.03 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.03 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: 12.11 Conformation dependent library (CDL) restraints added in 4.5 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 68.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.706A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 202 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.544A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.783A pdb=" N ILE B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 406 through 416 removed outlier: 4.246A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 3.720A pdb=" N TYR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 4.113A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 668' Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 704' Processing helix chain 'B' and resid 766 through 772 Processing helix chain 'B' and resid 774 through 799 Processing helix chain 'B' and resid 807 through 830 Processing helix chain 'B' and resid 849 through 858 removed outlier: 3.889A pdb=" N ASP B 858 " --> pdb=" O LEU B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 removed outlier: 3.815A pdb=" N VAL B 926 " --> pdb=" O MET B 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Proline residue: B 966 - end of helix Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1012 through 1029 removed outlier: 3.967A pdb=" N VAL B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1089 Processing helix chain 'B' and resid 1113 through 1141 Processing helix chain 'B' and resid 1142 through 1162 Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.705A pdb=" N SER A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET A 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.545A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.720A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.112A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.613A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.564A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.570A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 774 through 799 Processing helix chain 'A' and resid 807 through 830 Processing helix chain 'A' and resid 849 through 858 removed outlier: 3.889A pdb=" N ASP A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 920 removed outlier: 4.649A pdb=" N LYS A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG A 965 " --> pdb=" O ARG A 961 " (cutoff:3.500A) Proline residue: A 966 - end of helix Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1142 through 1162 Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.705A pdb=" N SER C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 202 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN C 261 " --> pdb=" O TYR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 344 through 358 removed outlier: 3.543A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 362 removed outlier: 3.762A pdb=" N LEU C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 359 through 362' Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.721A pdb=" N TYR C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 removed outlier: 4.113A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 663 through 668' Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 704' Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 774 through 799 Processing helix chain 'C' and resid 807 through 830 Processing helix chain 'C' and resid 849 through 858 removed outlier: 3.890A pdb=" N ASP C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR C 880 " --> pdb=" O GLY C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 900 removed outlier: 3.538A pdb=" N GLY C 887 " --> pdb=" O LEU C 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 892 " --> pdb=" O ARG C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL C 926 " --> pdb=" O MET C 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 948 " --> pdb=" O THR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG C 965 " --> pdb=" O ARG C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1089 Processing helix chain 'C' and resid 1113 through 1141 Processing helix chain 'C' and resid 1142 through 1162 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.991A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.706A pdb=" N SER D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET D 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 202 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.623A pdb=" N GLN D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.750A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.545A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.692A pdb=" N VAL D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 removed outlier: 3.721A pdb=" N TYR D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 4.112A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 484 " --> pdb=" O GLN D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU D 562 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 removed outlier: 3.838A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 663 through 668' Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 700 through 704' Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 774 through 799 Processing helix chain 'D' and resid 807 through 830 Processing helix chain 'D' and resid 849 through 858 removed outlier: 3.890A pdb=" N ASP D 858 " --> pdb=" O LEU D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY D 887 " --> pdb=" O LEU D 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS D 892 " --> pdb=" O ARG D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS D 915 " --> pdb=" O GLN D 911 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 919 " --> pdb=" O LYS D 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL D 926 " --> pdb=" O MET D 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG D 965 " --> pdb=" O ARG D 961 " (cutoff:3.500A) Proline residue: D 966 - end of helix Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL D1016 " --> pdb=" O ALA D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D1056 " --> pdb=" O LEU D1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1089 Processing helix chain 'D' and resid 1113 through 1141 Processing helix chain 'D' and resid 1142 through 1162 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 211 removed outlier: 6.835A pdb=" N ALA B 210 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP B 78 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 92 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B 154 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 189 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR B 156 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 119 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 277 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER B 121 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 302 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR B 365 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 301 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 987 removed outlier: 3.947A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 987 " --> pdb=" O TRP B 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP B 996 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.833A pdb=" N ALA A 210 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP A 78 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 92 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 154 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A 189 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 156 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 119 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 277 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER A 121 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 302 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR A 365 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 301 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.948A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 987 " --> pdb=" O TRP A 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP A 996 " --> pdb=" O GLY A 987 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 210 through 211 removed outlier: 6.834A pdb=" N ALA C 210 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP C 78 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 92 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE C 154 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL C 189 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 156 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 119 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 277 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER C 121 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 302 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR C 365 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 301 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.948A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 987 " --> pdb=" O TRP C 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP C 996 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 210 through 211 removed outlier: 6.834A pdb=" N ALA D 210 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP D 78 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 92 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE D 154 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL D 189 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR D 156 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL D 119 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU D 277 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER D 121 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 302 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR D 365 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU D 301 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 987 removed outlier: 3.946A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 987 " --> pdb=" O TRP D 996 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP D 996 " --> pdb=" O GLY D 987 " (cutoff:3.500A) 1698 hydrogen bonds defined for protein. 5034 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: 12.40 Time building geometry restraints manager: 13.09 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: 8037 1.33 - 1.46: 6828 1.46 - 1.58: 15459 1.58 - 1.70: 0 1.70 - 1.83: 204 Bond restraints: 30528 Sorted by residual: bond pdb=" CB VAL C 776 " pdb=" CG1 VAL C 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB VAL A 776 " pdb=" CG1 VAL A 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" C PHE C 340 " pdb=" N PRO C 341 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.36e+00 bond pdb=" C PHE A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.36e+00 bond pdb=" CB VAL B 776 " pdb=" CG1 VAL B 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 30523 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.46: 569 105.46 - 112.62: 15874 112.62 - 119.78: 10630 119.78 - 126.94: 13846 126.94 - 134.09: 453 Bond angle restraints: 41372 Sorted by residual: angle pdb=" N PRO B1073 " pdb=" CA PRO B1073 " pdb=" C PRO B1073 " ideal model delta sigma weight residual 110.70 117.10 -6.40 1.22e+00 6.72e-01 2.75e+01 angle pdb=" N PRO D1073 " pdb=" CA PRO D1073 " pdb=" C PRO D1073 " ideal model delta sigma weight residual 110.70 117.08 -6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N PRO A1073 " pdb=" CA PRO A1073 " pdb=" C PRO A1073 " ideal model delta sigma weight residual 110.70 117.08 -6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N PRO C1073 " pdb=" CA PRO C1073 " pdb=" C PRO C1073 " ideal model delta sigma weight residual 110.70 117.05 -6.35 1.22e+00 6.72e-01 2.71e+01 angle pdb=" CB ARG C 965 " pdb=" CG ARG C 965 " pdb=" CD ARG C 965 " ideal model delta sigma weight residual 111.30 100.48 10.82 2.30e+00 1.89e-01 2.21e+01 ... (remaining 41367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 17373 16.49 - 32.98: 619 32.98 - 49.46: 96 49.46 - 65.95: 8 65.95 - 82.44: 20 Dihedral angle restraints: 18116 sinusoidal: 7320 harmonic: 10796 Sorted by residual: dihedral pdb=" CB CYS B 989 " pdb=" SG CYS B 989 " pdb=" SG CYS B1007 " pdb=" CB CYS B1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 989 " pdb=" SG CYS A 989 " pdb=" SG CYS A1007 " pdb=" CB CYS A1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.43 82.43 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS C 989 " pdb=" SG CYS C 989 " pdb=" SG CYS C1007 " pdb=" CB CYS C1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 18113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2983 0.048 - 0.096: 1377 0.096 - 0.143: 273 0.143 - 0.191: 39 0.191 - 0.239: 4 Chirality restraints: 4676 Sorted by residual: chirality pdb=" CB ILE B 279 " pdb=" CA ILE B 279 " pdb=" CG1 ILE B 279 " pdb=" CG2 ILE B 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE C 279 " pdb=" CA ILE C 279 " pdb=" CG1 ILE C 279 " pdb=" CG2 ILE C 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4673 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.030 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP B 816 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.030 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 816 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 816 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP D 816 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 816 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 816 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 816 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 816 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 816 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 816 " 0.008 2.00e-02 2.50e+03 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8780 2.82 - 3.34: 26099 3.34 - 3.86: 46204 3.86 - 4.38: 53211 4.38 - 4.90: 93129 Nonbonded interactions: 227423 Sorted by model distance: nonbonded pdb=" O LEU D 948 " pdb=" CD1 LEU D 948 " model vdw 2.301 3.460 nonbonded pdb=" O LEU B 948 " pdb=" CD1 LEU B 948 " model vdw 2.303 3.460 nonbonded pdb=" O LEU A 948 " pdb=" CD1 LEU A 948 " model vdw 2.306 3.460 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.331 2.440 nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.332 2.440 ... (remaining 227418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 1162) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 S 136 5.16 5 Na 4 4.78 5 C 19260 2.51 5 N 5216 2.21 5 O 5252 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=1.00 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.520 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.270 Process input model: 78.600 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.070 30528 Z= 0.527 Angle : 0.968 10.821 41372 Z= 0.531 Chirality : 0.053 0.239 4676 Planarity : 0.007 0.071 5208 Dihedral : 9.603 77.213 11112 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.83 (0.09), residues: 3672 helix: -3.23 (0.06), residues: 2348 sheet: -1.40 (0.29), residues: 216 loop : -3.00 (0.15), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 566 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 578 average time/residue: 0.4854 time to fit residues: 418.8813 Evaluate side-chains 293 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 ASN B1010 GLN B1013 ASN B1080 HIS A 261 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN A1010 GLN A1013 ASN A1080 HIS C 261 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 ASN C1010 GLN C1013 ASN C1080 HIS D 261 GLN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 ASN D1010 GLN D1013 ASN D1080 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 30528 Z= 0.319 Angle : 0.651 11.469 41372 Z= 0.335 Chirality : 0.040 0.176 4676 Planarity : 0.006 0.079 5208 Dihedral : 4.776 21.840 4092 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.73 (0.12), residues: 3672 helix: -0.40 (0.10), residues: 2360 sheet: -0.99 (0.31), residues: 208 loop : -2.65 (0.16), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 357 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 34 residues processed: 390 average time/residue: 0.4526 time to fit residues: 273.2651 Evaluate side-chains 302 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 3.563 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2548 time to fit residues: 21.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 338 optimal weight: 0.7980 chunk 365 optimal weight: 0.8980 chunk 301 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 271 optimal weight: 0.0870 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 30528 Z= 0.192 Angle : 0.580 15.701 41372 Z= 0.296 Chirality : 0.037 0.165 4676 Planarity : 0.005 0.085 5208 Dihedral : 4.246 19.551 4092 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.13), residues: 3672 helix: 0.94 (0.11), residues: 2368 sheet: -0.94 (0.32), residues: 216 loop : -2.50 (0.16), residues: 1088 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 296 time to evaluate : 3.858 Fit side-chains outliers start: 57 outliers final: 14 residues processed: 338 average time/residue: 0.4351 time to fit residues: 236.3000 Evaluate side-chains 262 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 3.770 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2717 time to fit residues: 12.4984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 339 optimal weight: 0.9990 chunk 359 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 321 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 30528 Z= 0.299 Angle : 0.647 14.269 41372 Z= 0.329 Chirality : 0.040 0.180 4676 Planarity : 0.005 0.071 5208 Dihedral : 4.266 19.141 4092 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.14), residues: 3672 helix: 1.30 (0.11), residues: 2368 sheet: -0.51 (0.33), residues: 208 loop : -2.48 (0.16), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 263 time to evaluate : 3.827 Fit side-chains outliers start: 52 outliers final: 27 residues processed: 297 average time/residue: 0.4887 time to fit residues: 224.6289 Evaluate side-chains 270 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 243 time to evaluate : 3.838 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2752 time to fit residues: 19.4057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 306 optimal weight: 0.4980 chunk 248 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 322 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 30528 Z= 0.164 Angle : 0.536 15.119 41372 Z= 0.276 Chirality : 0.037 0.172 4676 Planarity : 0.004 0.110 5208 Dihedral : 3.933 18.702 4092 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.14), residues: 3672 helix: 1.86 (0.11), residues: 2360 sheet: -1.08 (0.32), residues: 236 loop : -2.28 (0.17), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 307 time to evaluate : 3.710 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 319 average time/residue: 0.4486 time to fit residues: 226.2002 Evaluate side-chains 269 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 3.928 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2667 time to fit residues: 9.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 20.0000 chunk 323 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 211 optimal weight: 50.0000 chunk 88 optimal weight: 0.9990 chunk 359 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 480 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.171 30528 Z= 0.194 Angle : 0.555 19.288 41372 Z= 0.287 Chirality : 0.037 0.173 4676 Planarity : 0.004 0.074 5208 Dihedral : 3.820 18.380 4092 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.14), residues: 3672 helix: 2.02 (0.11), residues: 2368 sheet: -0.96 (0.32), residues: 236 loop : -2.23 (0.17), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 3.902 Fit side-chains outliers start: 42 outliers final: 15 residues processed: 301 average time/residue: 0.4556 time to fit residues: 216.0748 Evaluate side-chains 275 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 3.466 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2613 time to fit residues: 12.6816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 262 optimal weight: 0.4980 chunk 203 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.350 30528 Z= 0.480 Angle : 0.746 26.790 41372 Z= 0.386 Chirality : 0.044 0.176 4676 Planarity : 0.005 0.063 5208 Dihedral : 4.399 20.126 4092 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.14), residues: 3672 helix: 1.51 (0.11), residues: 2368 sheet: -0.88 (0.32), residues: 236 loop : -2.32 (0.16), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 267 time to evaluate : 3.906 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 303 average time/residue: 0.4573 time to fit residues: 217.3082 Evaluate side-chains 270 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 246 time to evaluate : 3.918 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2689 time to fit residues: 17.4554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 227 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 480 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 480 GLN D1013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.121 30528 Z= 0.198 Angle : 0.578 15.358 41372 Z= 0.299 Chirality : 0.038 0.188 4676 Planarity : 0.004 0.056 5208 Dihedral : 4.023 19.597 4092 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.14), residues: 3672 helix: 1.94 (0.11), residues: 2372 sheet: -0.43 (0.34), residues: 216 loop : -2.36 (0.17), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 3.493 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 274 average time/residue: 0.4734 time to fit residues: 201.5292 Evaluate side-chains 260 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 3.727 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2702 time to fit residues: 9.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 20.0000 chunk 313 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 301 optimal weight: 0.5980 chunk 316 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.041 30528 Z= 0.477 Angle : 0.884 88.187 41372 Z= 0.398 Chirality : 0.039 0.184 4676 Planarity : 0.004 0.070 5208 Dihedral : 4.008 18.931 4092 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.14), residues: 3672 helix: 1.98 (0.11), residues: 2368 sheet: -0.42 (0.34), residues: 216 loop : -2.36 (0.16), residues: 1088 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 248 time to evaluate : 3.801 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 252 average time/residue: 0.5015 time to fit residues: 197.0520 Evaluate side-chains 245 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3136 time to fit residues: 7.2337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 6.9990 chunk 353 optimal weight: 0.0000 chunk 215 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 370 optimal weight: 7.9990 chunk 341 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 overall best weight: 2.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.060 30528 Z= 0.507 Angle : 0.885 84.368 41372 Z= 0.400 Chirality : 0.040 0.214 4676 Planarity : 0.004 0.064 5208 Dihedral : 4.116 20.170 4092 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.14), residues: 3672 helix: 1.86 (0.11), residues: 2372 sheet: -0.37 (0.34), residues: 216 loop : -2.35 (0.16), residues: 1084 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 3.730 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.4719 time to fit residues: 183.2306 Evaluate side-chains 244 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2562 time to fit residues: 5.4301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 295 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 303 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136847 restraints weight = 40645.540| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.47 r_work: 0.3577 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3435 rms_B_bonded: 3.14 restraints_weight: 0.1250 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.062 30528 Z= 0.448 Angle : 0.811 82.239 41372 Z= 0.364 Chirality : 0.037 0.214 4676 Planarity : 0.004 0.053 5208 Dihedral : 3.847 22.021 4092 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.14), residues: 3672 helix: 2.21 (0.11), residues: 2380 sheet: -0.30 (0.34), residues: 216 loop : -2.27 (0.17), residues: 1076 =============================================================================== Job complete usr+sys time: 5023.52 seconds wall clock time: 92 minutes 20.31 seconds (5540.31 seconds total)