Starting phenix.real_space_refine (version: dev) on Fri Apr 8 09:25:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsk_10564/04_2022/6tsk_10564_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsk_10564/04_2022/6tsk_10564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsk_10564/04_2022/6tsk_10564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsk_10564/04_2022/6tsk_10564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsk_10564/04_2022/6tsk_10564_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsk_10564/04_2022/6tsk_10564_updated.pdb" } resolution = 2.3 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= 0.002 sd= 0.020 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 "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 630": "NH1" <-> "NH2" Residue "B GLU 667": "OE1" <-> "OE2" Residue "B ARG 755": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B GLU 797": "OE1" <-> "OE2" Residue "B GLU 871": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 630": "NH1" <-> "NH2" Residue "C GLU 667": "OE1" <-> "OE2" Residue "C ARG 755": "NH1" <-> "NH2" Residue "C ARG 781": "NH1" <-> "NH2" Residue "C GLU 797": "OE1" <-> "OE2" Residue "C GLU 871": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ARG 630": "NH1" <-> "NH2" Residue "D GLU 667": "OE1" <-> "OE2" Residue "D ARG 755": "NH1" <-> "NH2" Residue "D ARG 781": "NH1" <-> "NH2" Residue "D GLU 797": "OE1" <-> "OE2" Residue "D GLU 871": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 33632 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 8156 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 57, 'CIS': 3, 'TRANS': 949, 'PCIS': 5} Chain: "B" Number of atoms: 8156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 8156 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 57, 'CIS': 3, 'TRANS': 949, 'PCIS': 5} Chain: "C" Number of atoms: 8156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 8156 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 57, 'CIS': 3, 'TRANS': 949, 'PCIS': 5} Chain: "D" Number of atoms: 8156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 8156 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 57, 'CIS': 3, 'TRANS': 949, 'PCIS': 5} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, '0MK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, '0MK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, '0MK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, '0MK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Chain: "C" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Chain: "D" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Time building chain proxies: 17.22, per 1000 atoms: 0.51 Number of scatterers: 33632 At special positions: 0 Unit cell: (101.32, 150.28, 195.16, 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 152 16.00 Mg 4 11.99 O 7040 8.00 N 5780 7.00 C 20656 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: 14.10 Conformation dependent library (CDL) restraints added in 4.7 seconds 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 52 sheets defined 14.1% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.770A pdb=" N GLN A 135 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.960A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Proline residue: A 434 - end of helix removed outlier: 3.608A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.523A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 549 through 558 Processing helix chain 'A' and resid 599 through 602 removed outlier: 4.248A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 599 through 602' Processing helix chain 'A' and resid 615 through 623 Processing helix chain 'A' and resid 790 through 793 No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 922 through 925 Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 973 through 975 No H-bonds generated for 'chain 'A' and resid 973 through 975' Processing helix chain 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'B' and resid 10 through 13 No H-bonds generated for 'chain 'B' and resid 10 through 13' Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.770A pdb=" N GLN B 135 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 396 through 405 removed outlier: 3.960A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 447 Proline residue: B 434 - end of helix removed outlier: 3.608A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 478 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.523A pdb=" N LEU B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 525' Processing helix chain 'B' and resid 549 through 558 Processing helix chain 'B' and resid 599 through 602 removed outlier: 4.248A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 599 through 602' Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 790 through 793 No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 806 through 813 Processing helix chain 'B' and resid 922 through 925 Processing helix chain 'B' and resid 964 through 969 Processing helix chain 'B' and resid 973 through 975 No H-bonds generated for 'chain 'B' and resid 973 through 975' Processing helix chain 'B' and resid 1005 through 1007 No H-bonds generated for 'chain 'B' and resid 1005 through 1007' Processing helix chain 'C' and resid 10 through 13 No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 90 through 93 Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.770A pdb=" N GLN C 135 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 396 through 405 removed outlier: 3.960A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 447 Proline residue: C 434 - end of helix removed outlier: 3.608A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 478 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.523A pdb=" N LEU C 524 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 558 Processing helix chain 'C' and resid 599 through 602 removed outlier: 4.248A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 599 through 602' Processing helix chain 'C' and resid 615 through 623 Processing helix chain 'C' and resid 790 through 793 No H-bonds generated for 'chain 'C' and resid 790 through 793' Processing helix chain 'C' and resid 806 through 813 Processing helix chain 'C' and resid 922 through 925 Processing helix chain 'C' and resid 964 through 969 Processing helix chain 'C' and resid 973 through 975 No H-bonds generated for 'chain 'C' and resid 973 through 975' Processing helix chain 'C' and resid 1005 through 1007 No H-bonds generated for 'chain 'C' and resid 1005 through 1007' Processing helix chain 'D' and resid 10 through 13 No H-bonds generated for 'chain 'D' and resid 10 through 13' Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.769A pdb=" N GLN D 135 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.959A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 447 Proline residue: D 434 - end of helix removed outlier: 3.608A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 478 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.522A pdb=" N LEU D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 525' Processing helix chain 'D' and resid 549 through 558 Processing helix chain 'D' and resid 599 through 602 removed outlier: 4.249A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 599 through 602' Processing helix chain 'D' and resid 615 through 623 Processing helix chain 'D' and resid 790 through 793 No H-bonds generated for 'chain 'D' and resid 790 through 793' Processing helix chain 'D' and resid 806 through 813 Processing helix chain 'D' and resid 922 through 925 Processing helix chain 'D' and resid 964 through 969 Processing helix chain 'D' and resid 973 through 975 No H-bonds generated for 'chain 'D' and resid 973 through 975' Processing helix chain 'D' and resid 1005 through 1007 No H-bonds generated for 'chain 'D' and resid 1005 through 1007' Processing sheet with id= A, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= B, first strand: chain 'A' and resid 82 through 86 removed outlier: 8.850A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 160 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS A 154 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TRP A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.554A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 288 through 296 removed outlier: 3.582A pdb=" N ASP A 224 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.769A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU A 254 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 335 through 338 Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.019A pdb=" N ILE A 351 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 567 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY A 353 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA A 386 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG A 356 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG A 388 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 408 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS A 389 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 410 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP A 411 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP A 456 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 575 through 578 Processing sheet with id= I, first strand: chain 'A' and resid 627 through 632 Processing sheet with id= J, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.794A pdb=" N VAL A 656 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A 665 " --> pdb=" O TRP A 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP A 654 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 667 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 652 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.315A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 781 through 783 removed outlier: 6.962A pdb=" N LEU A 884 " --> pdb=" O ASP A 987 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP A 987 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS A 886 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN A 985 " --> pdb=" O CYS A 886 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 888 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP A 983 " --> pdb=" O LEU A 888 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 914 through 921 removed outlier: 3.535A pdb=" N GLU A 943 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP A 842 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 851 " --> pdb=" O HIS A 840 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS A 840 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG A 853 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 838 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A 855 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 836 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG A 857 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 834 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 824 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= O, first strand: chain 'B' and resid 82 through 86 removed outlier: 8.850A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 160 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS B 154 " --> pdb=" O TRP B 158 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TRP B 158 " --> pdb=" O CYS B 154 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.554A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 288 through 296 removed outlier: 3.581A pdb=" N ASP B 224 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.769A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU B 254 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 335 through 338 Processing sheet with id= T, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.019A pdb=" N ILE B 351 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL B 567 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY B 353 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 386 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG B 356 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG B 388 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 408 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS B 389 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL B 410 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP B 411 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP B 456 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 575 through 578 Processing sheet with id= V, first strand: chain 'B' and resid 627 through 632 Processing sheet with id= W, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.794A pdb=" N VAL B 656 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER B 665 " --> pdb=" O TRP B 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP B 654 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 667 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 652 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.316A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 781 through 783 removed outlier: 6.962A pdb=" N LEU B 884 " --> pdb=" O ASP B 987 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP B 987 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS B 886 " --> pdb=" O ASN B 985 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B 985 " --> pdb=" O CYS B 886 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 888 " --> pdb=" O TRP B 983 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP B 983 " --> pdb=" O LEU B 888 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 914 through 921 removed outlier: 3.535A pdb=" N GLU B 943 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP B 842 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 851 " --> pdb=" O HIS B 840 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS B 840 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG B 853 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 838 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 855 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 836 " --> pdb=" O THR B 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B 857 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 834 " --> pdb=" O ARG B 857 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 824 " --> pdb=" O ALA B 839 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 51 through 53 Processing sheet with id= AB, first strand: chain 'C' and resid 82 through 86 removed outlier: 8.850A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY C 160 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS C 154 " --> pdb=" O TRP C 158 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TRP C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.554A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 288 through 296 removed outlier: 3.582A pdb=" N ASP C 224 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.769A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU C 254 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 335 through 338 Processing sheet with id= AG, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.019A pdb=" N ILE C 351 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL C 567 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY C 353 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA C 386 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG C 356 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG C 388 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR C 408 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS C 389 " --> pdb=" O TYR C 408 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL C 410 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP C 411 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP C 456 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 575 through 578 Processing sheet with id= AI, first strand: chain 'C' and resid 627 through 632 Processing sheet with id= AJ, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.794A pdb=" N VAL C 656 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER C 665 " --> pdb=" O TRP C 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP C 654 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU C 667 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 652 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.316A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 781 through 783 removed outlier: 6.962A pdb=" N LEU C 884 " --> pdb=" O ASP C 987 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP C 987 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS C 886 " --> pdb=" O ASN C 985 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN C 985 " --> pdb=" O CYS C 886 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 888 " --> pdb=" O TRP C 983 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP C 983 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 914 through 921 removed outlier: 3.535A pdb=" N GLU C 943 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP C 842 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE C 851 " --> pdb=" O HIS C 840 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS C 840 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG C 853 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 838 " --> pdb=" O ARG C 853 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR C 855 " --> pdb=" O ILE C 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 836 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG C 857 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 834 " --> pdb=" O ARG C 857 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 824 " --> pdb=" O ALA C 839 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 51 through 53 Processing sheet with id= AO, first strand: chain 'D' and resid 82 through 86 removed outlier: 8.850A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 160 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS D 154 " --> pdb=" O TRP D 158 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TRP D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.555A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'D' and resid 288 through 296 removed outlier: 3.583A pdb=" N ASP D 224 " --> pdb=" O GLN D 245 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.769A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU D 254 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'D' and resid 335 through 338 Processing sheet with id= AT, first strand: chain 'D' and resid 564 through 567 removed outlier: 6.018A pdb=" N ILE D 351 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL D 567 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY D 353 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA D 386 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG D 356 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG D 388 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR D 408 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS D 389 " --> pdb=" O TYR D 408 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 410 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP D 411 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP D 456 " --> pdb=" O ASP D 411 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 575 through 578 Processing sheet with id= AV, first strand: chain 'D' and resid 627 through 632 Processing sheet with id= AW, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.794A pdb=" N VAL D 656 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER D 665 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP D 654 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU D 667 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 652 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.315A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'D' and resid 781 through 783 removed outlier: 6.961A pdb=" N LEU D 884 " --> pdb=" O ASP D 987 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP D 987 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS D 886 " --> pdb=" O ASN D 985 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN D 985 " --> pdb=" O CYS D 886 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 888 " --> pdb=" O TRP D 983 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP D 983 " --> pdb=" O LEU D 888 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'D' and resid 914 through 921 removed outlier: 3.536A pdb=" N GLU D 943 " --> pdb=" O LEU D 898 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP D 842 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 851 " --> pdb=" O HIS D 840 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS D 840 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG D 853 " --> pdb=" O THR D 838 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR D 838 " --> pdb=" O ARG D 853 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR D 855 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 836 " --> pdb=" O THR D 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG D 857 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 834 " --> pdb=" O ARG D 857 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 824 " --> pdb=" O ALA D 839 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) 956 hydrogen bonds defined for protein. 2484 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: 16.42 Time building geometry restraints manager: 15.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7648 1.33 - 1.47: 9341 1.47 - 1.60: 16403 1.60 - 1.74: 0 1.74 - 1.88: 240 Bond restraints: 33632 Sorted by residual: bond pdb=" N ASP C 164 " pdb=" CA ASP C 164 " ideal model delta sigma weight residual 1.457 1.550 -0.093 1.29e-02 6.01e+03 5.17e+01 bond pdb=" N ASP B 164 " pdb=" CA ASP B 164 " ideal model delta sigma weight residual 1.457 1.550 -0.092 1.29e-02 6.01e+03 5.12e+01 bond pdb=" N ASP A 164 " pdb=" CA ASP A 164 " ideal model delta sigma weight residual 1.457 1.550 -0.092 1.29e-02 6.01e+03 5.12e+01 bond pdb=" N ASP D 164 " pdb=" CA ASP D 164 " ideal model delta sigma weight residual 1.457 1.549 -0.092 1.29e-02 6.01e+03 5.07e+01 bond pdb=" N VAL A 421 " pdb=" CA VAL A 421 " ideal model delta sigma weight residual 1.454 1.499 -0.045 7.70e-03 1.69e+04 3.39e+01 ... (remaining 33627 not shown) Histogram of bond angle deviations from ideal: 94.90 - 102.84: 172 102.84 - 110.78: 10043 110.78 - 118.72: 16574 118.72 - 126.66: 18215 126.66 - 134.61: 884 Bond angle restraints: 45888 Sorted by residual: angle pdb=" C GLN A 625 " pdb=" CA GLN A 625 " pdb=" CB GLN A 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C GLN D 625 " pdb=" CA GLN D 625 " pdb=" CB GLN D 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C GLN B 625 " pdb=" CA GLN B 625 " pdb=" CB GLN B 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C GLN C 625 " pdb=" CA GLN C 625 " pdb=" CB GLN C 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C LYS D 661 " pdb=" N PRO D 662 " pdb=" CA PRO D 662 " ideal model delta sigma weight residual 119.76 126.73 -6.97 1.03e+00 9.43e-01 4.58e+01 ... (remaining 45883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17683 17.77 - 35.55: 1417 35.55 - 53.32: 320 53.32 - 71.10: 132 71.10 - 88.87: 124 Dihedral angle restraints: 19676 sinusoidal: 7944 harmonic: 11732 Sorted by residual: dihedral pdb=" C GLN A 625 " pdb=" N GLN A 625 " pdb=" CA GLN A 625 " pdb=" CB GLN A 625 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C GLN D 625 " pdb=" N GLN D 625 " pdb=" CA GLN D 625 " pdb=" CB GLN D 625 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C GLN B 625 " pdb=" N GLN B 625 " pdb=" CA GLN B 625 " pdb=" CB GLN B 625 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 ... (remaining 19673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2776 0.090 - 0.181: 1512 0.181 - 0.271: 416 0.271 - 0.361: 84 0.361 - 0.451: 8 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CA GLN A 625 " pdb=" N GLN A 625 " pdb=" C GLN A 625 " pdb=" CB GLN A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA GLN D 625 " pdb=" N GLN D 625 " pdb=" C GLN D 625 " pdb=" CB GLN D 625 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA GLN B 625 " pdb=" N GLN B 625 " pdb=" C GLN B 625 " pdb=" CB GLN B 625 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.09e+00 ... (remaining 4793 not shown) Planarity restraints: 6056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 553 " 0.085 2.00e-02 2.50e+03 4.06e-02 4.11e+01 pdb=" CG TRP C 553 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP C 553 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 553 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP C 553 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP C 553 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 553 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 553 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 553 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP C 553 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 553 " 0.085 2.00e-02 2.50e+03 4.05e-02 4.11e+01 pdb=" CG TRP A 553 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 553 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 553 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 553 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 553 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 553 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 553 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 553 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP A 553 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 553 " -0.085 2.00e-02 2.50e+03 4.05e-02 4.10e+01 pdb=" CG TRP D 553 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 553 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 553 " 0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP D 553 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 553 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 553 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 553 " -0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 553 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP D 553 " -0.033 2.00e-02 2.50e+03 ... (remaining 6053 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 30 2.21 - 2.88: 11783 2.88 - 3.55: 44353 3.55 - 4.23: 92011 4.23 - 4.90: 146667 Nonbonded interactions: 294844 Sorted by model distance: nonbonded pdb=" O HOH C3184 " pdb=" O HOH D3184 " model vdw 1.535 2.440 nonbonded pdb=" O HOH A3184 " pdb=" O HOH B3184 " model vdw 1.535 2.440 nonbonded pdb=" O HOH C3107 " pdb=" O HOH C3108 " model vdw 1.614 2.440 nonbonded pdb=" O HOH B3107 " pdb=" O HOH B3108 " model vdw 1.614 2.440 nonbonded pdb=" O HOH A3107 " pdb=" O HOH A3108 " model vdw 1.615 2.440 ... (remaining 294839 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' 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 Mg 4 5.21 5 S 152 5.16 5 C 20656 2.51 5 N 5780 2.21 5 O 7040 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: 0.800 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: 5.410 Check model and map are aligned: 0.440 Convert atoms to be neutral: 0.240 Process input model: 88.290 Find NCS groups from input model: 2.190 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: 0.000 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9365 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 : 0.012 0.093 33632 Z= 0.780 Angle : 1.544 15.519 45888 Z= 0.996 Chirality : 0.114 0.451 4796 Planarity : 0.016 0.223 6056 Dihedral : 16.570 88.872 12124 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 (0.12), residues: 4052 helix: -1.84 (0.19), residues: 480 sheet: 0.13 (0.14), residues: 1268 loop : -0.83 (0.11), residues: 2304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 584 time to evaluate : 4.306 Fit side-chains outliers start: 84 outliers final: 24 residues processed: 632 average time/residue: 1.7230 time to fit residues: 1269.7850 Evaluate side-chains 458 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 434 time to evaluate : 3.942 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.4821 time to fit residues: 8.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 266 GLN A 294 ASN A 365 GLN A 583 ASN A 624 GLN A 625 GLN A 634 GLN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A 702 GLN A 739 HIS A 890 GLN B 226 HIS B 266 GLN B 294 ASN B 365 GLN B 583 ASN B 624 GLN B 625 GLN B 634 GLN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN B 702 GLN B 739 HIS B 890 GLN C 226 HIS C 266 GLN C 294 ASN C 365 GLN C 583 ASN C 624 GLN C 625 GLN C 634 GLN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN C 702 GLN C 739 HIS C 890 GLN D 226 HIS D 266 GLN D 294 ASN D 365 GLN D 583 ASN D 624 GLN D 625 GLN D 634 GLN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 702 GLN D 739 HIS D 890 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 33632 Z= 0.202 Angle : 0.625 7.355 45888 Z= 0.335 Chirality : 0.047 0.164 4796 Planarity : 0.005 0.033 6056 Dihedral : 5.475 23.926 4448 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.08 (0.13), residues: 4052 helix: -0.42 (0.22), residues: 480 sheet: 0.85 (0.13), residues: 1376 loop : -0.31 (0.13), residues: 2196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 462 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 36 residues processed: 505 average time/residue: 1.6330 time to fit residues: 971.7742 Evaluate side-chains 497 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 461 time to evaluate : 4.138 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 20 residues processed: 16 average time/residue: 0.3295 time to fit residues: 14.9481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 305 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 chunk 367 optimal weight: 20.0000 chunk 397 optimal weight: 8.9990 chunk 327 optimal weight: 8.9990 chunk 364 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN B 226 HIS B 604 ASN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN C 226 HIS ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN D 226 HIS ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 33632 Z= 0.215 Angle : 0.608 7.337 45888 Z= 0.325 Chirality : 0.047 0.150 4796 Planarity : 0.005 0.036 6056 Dihedral : 5.252 22.914 4448 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.33 (0.13), residues: 4052 helix: -0.19 (0.22), residues: 480 sheet: 1.07 (0.14), residues: 1380 loop : -0.18 (0.13), residues: 2192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 496 time to evaluate : 4.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 38 residues processed: 528 average time/residue: 1.6865 time to fit residues: 1052.0554 Evaluate side-chains 523 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 485 time to evaluate : 4.037 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 24 residues processed: 14 average time/residue: 0.5659 time to fit residues: 17.1897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 0.0870 chunk 276 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 40 optimal weight: 50.0000 chunk 175 optimal weight: 10.0000 chunk 246 optimal weight: 30.0000 chunk 368 optimal weight: 9.9990 chunk 390 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 349 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN B 226 HIS ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN C 226 HIS ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN D 226 HIS ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9269 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 33632 Z= 0.207 Angle : 0.593 7.180 45888 Z= 0.314 Chirality : 0.046 0.143 4796 Planarity : 0.004 0.031 6056 Dihedral : 5.144 22.445 4448 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.41 (0.13), residues: 4052 helix: -0.12 (0.23), residues: 480 sheet: 1.15 (0.14), residues: 1388 loop : -0.16 (0.13), residues: 2184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 474 time to evaluate : 4.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 38 residues processed: 506 average time/residue: 1.6656 time to fit residues: 989.9153 Evaluate side-chains 495 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 457 time to evaluate : 4.238 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 24 residues processed: 14 average time/residue: 1.0174 time to fit residues: 23.6598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 161 optimal weight: 0.0570 chunk 333 optimal weight: 40.0000 chunk 269 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 199 optimal weight: 20.0000 chunk 350 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN A 653 HIS A 739 HIS A 761 GLN A 863 GLN B 226 HIS B 653 HIS B 739 HIS ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN C 226 HIS C 653 HIS C 739 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 653 HIS D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9257 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 33632 Z= 0.177 Angle : 0.558 7.130 45888 Z= 0.295 Chirality : 0.045 0.137 4796 Planarity : 0.004 0.030 6056 Dihedral : 4.941 21.509 4448 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.51 (0.13), residues: 4052 helix: -0.01 (0.23), residues: 480 sheet: 1.21 (0.14), residues: 1392 loop : -0.10 (0.13), residues: 2180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 462 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 45 residues processed: 505 average time/residue: 1.6970 time to fit residues: 1004.8686 Evaluate side-chains 507 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 462 time to evaluate : 4.040 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 10 average time/residue: 0.4424 time to fit residues: 12.5830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 40.0000 chunk 351 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 229 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 390 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 180 optimal weight: 40.0000 chunk 32 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN A 604 ASN A 761 GLN A 863 GLN B 226 HIS B 583 ASN B 739 HIS B 761 GLN B 863 GLN C 226 HIS C 583 ASN C 604 ASN C 739 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 583 ASN D 604 ASN D 739 HIS ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 33632 Z= 0.277 Angle : 0.650 7.899 45888 Z= 0.344 Chirality : 0.049 0.150 4796 Planarity : 0.005 0.041 6056 Dihedral : 5.262 22.212 4448 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.36 (0.13), residues: 4052 helix: -0.33 (0.22), residues: 500 sheet: 1.13 (0.14), residues: 1392 loop : -0.15 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 456 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 46 residues processed: 493 average time/residue: 1.7136 time to fit residues: 993.9742 Evaluate side-chains 495 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 449 time to evaluate : 4.178 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 34 residues processed: 13 average time/residue: 0.8438 time to fit residues: 20.4184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 0.8980 chunk 44 optimal weight: 30.0000 chunk 222 optimal weight: 30.0000 chunk 285 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 329 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 chunk 389 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 overall best weight: 6.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN A 761 GLN A 863 GLN B 226 HIS B 583 ASN B 739 HIS B 761 GLN B 863 GLN C 226 HIS C 583 ASN C 739 HIS C 761 GLN D 226 HIS D 583 ASN D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9269 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 33632 Z= 0.225 Angle : 0.603 7.394 45888 Z= 0.319 Chirality : 0.047 0.146 4796 Planarity : 0.004 0.032 6056 Dihedral : 5.125 21.884 4448 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.40 (0.13), residues: 4052 helix: -0.27 (0.22), residues: 500 sheet: 1.14 (0.14), residues: 1392 loop : -0.13 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 466 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 43 residues processed: 502 average time/residue: 1.6952 time to fit residues: 1000.2185 Evaluate side-chains 497 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 454 time to evaluate : 4.005 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 33 residues processed: 11 average time/residue: 0.6238 time to fit residues: 15.2746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 232 optimal weight: 40.0000 chunk 117 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 247 optimal weight: 30.0000 chunk 265 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN A 863 GLN B 226 HIS B 583 ASN B 739 HIS ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN C 226 HIS C 583 ASN C 739 HIS C 761 GLN C 863 GLN D 226 HIS D 583 ASN D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 33632 Z= 0.263 Angle : 0.636 7.747 45888 Z= 0.337 Chirality : 0.048 0.149 4796 Planarity : 0.005 0.037 6056 Dihedral : 5.232 21.946 4448 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.34 (0.13), residues: 4052 helix: -0.34 (0.22), residues: 500 sheet: 1.00 (0.13), residues: 1432 loop : -0.10 (0.13), residues: 2120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 454 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 36 residues processed: 497 average time/residue: 1.7024 time to fit residues: 998.0358 Evaluate side-chains 479 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 443 time to evaluate : 4.169 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.3295 time to fit residues: 8.0892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 340 optimal weight: 6.9990 chunk 362 optimal weight: 30.0000 chunk 372 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 327 optimal weight: 3.9990 chunk 343 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN A 863 GLN B 226 HIS B 583 ASN B 739 HIS ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN C 226 HIS C 583 ASN C 739 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN D 226 HIS D 583 ASN D 739 HIS ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9270 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 33632 Z= 0.232 Angle : 0.612 7.651 45888 Z= 0.324 Chirality : 0.047 0.147 4796 Planarity : 0.004 0.033 6056 Dihedral : 5.143 21.605 4448 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.40 (0.13), residues: 4052 helix: -0.26 (0.22), residues: 500 sheet: 1.13 (0.14), residues: 1392 loop : -0.13 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 454 time to evaluate : 3.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 36 residues processed: 486 average time/residue: 1.6461 time to fit residues: 945.9876 Evaluate side-chains 486 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 450 time to evaluate : 4.317 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.3191 time to fit residues: 8.1710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 383 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 chunk 402 optimal weight: 6.9990 chunk 370 optimal weight: 8.9990 chunk 320 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN A 845 GLN A 863 GLN B 226 HIS B 583 ASN B 739 HIS ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B 863 GLN C 226 HIS C 583 ASN C 739 HIS C 845 GLN C 863 GLN D 226 HIS D 583 ASN D 739 HIS D 845 GLN D 863 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 33632 Z= 0.263 Angle : 0.638 7.959 45888 Z= 0.338 Chirality : 0.048 0.149 4796 Planarity : 0.005 0.037 6056 Dihedral : 5.228 21.872 4448 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.35 (0.13), residues: 4052 helix: -0.32 (0.22), residues: 500 sheet: 1.00 (0.13), residues: 1432 loop : -0.10 (0.13), residues: 2120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 453 time to evaluate : 4.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 489 average time/residue: 1.6979 time to fit residues: 979.0273 Evaluate side-chains 478 residues out of total 3472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 446 time to evaluate : 3.913 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 5.5781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 321 optimal weight: 20.0000 chunk 134 optimal weight: 0.0000 chunk 329 optimal weight: 7.9990 chunk 40 optimal weight: 40.0000 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 583 ASN A 845 GLN A 863 GLN B 226 HIS B 583 ASN B 739 HIS B 845 GLN B 863 GLN C 226 HIS C 583 ASN C 739 HIS C 845 GLN C 863 GLN D 226 HIS D 583 ASN D 739 HIS D 845 GLN D 863 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.115611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.096471 restraints weight = 33320.402| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.11 r_work: 0.2963 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2923 rms_B_bonded: 1.21 restraints_weight: 0.1250 r_work: 0.2895 rms_B_bonded: 1.50 restraints_weight: 0.0625 r_work: 0.2858 rms_B_bonded: 1.96 restraints_weight: 0.0312 r_work: 0.2808 rms_B_bonded: 2.66 restraints_weight: 0.0156 r_work: 0.2740 rms_B_bonded: 3.75 restraints_weight: 0.0078 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 33632 Z= 0.213 Angle : 0.597 8.040 45888 Z= 0.315 Chirality : 0.047 0.145 4796 Planarity : 0.004 0.031 6056 Dihedral : 5.085 21.450 4448 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.43 (0.13), residues: 4052 helix: -0.23 (0.22), residues: 500 sheet: 1.15 (0.14), residues: 1392 loop : -0.11 (0.13), residues: 2160 =============================================================================== Job complete usr+sys time: 13317.85 seconds wall clock time: 236 minutes 38.17 seconds (14198.17 seconds total)