Starting phenix.real_space_refine (version: 1.19rc7) on Wed Jan 6 20:35:41 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/01_2021/6djv_7943_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/01_2021/6djv_7943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/01_2021/6djv_7943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/01_2021/6djv_7943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/01_2021/6djv_7943_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/01_2021/6djv_7943_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 27318 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4649 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4657 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 586} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 4678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4678 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4289 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 23, 'TRANS': 534} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.14, per 1000 atoms: 0.52 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'B' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'C' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'D' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'E' and resid 159 through 845) selection = (chain 'F' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 845)) } Number of scatterers: 27318 At special positions: 0 Unit cell: (138.546, 147.138, 134.25, 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 64 16.00 P 34 15.00 O 5269 8.00 N 4966 7.00 C 16985 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 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.60 Conformation dependent library (CDL) restraints added in 4.3 seconds 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 22 sheets defined 40.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.824A pdb=" N TYR A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 164' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.839A pdb=" N ARG A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.579A pdb=" N HIS A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.609A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.723A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 430 Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.566A pdb=" N LEU A 449 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 455 " --> pdb=" O GLN A 452 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 456 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 4.095A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 561 No H-bonds generated for 'chain 'A' and resid 558 through 561' Processing helix chain 'A' and resid 564 through 570 removed outlier: 4.233A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.822A pdb=" N ASP A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.539A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 729 through 738 removed outlier: 3.840A pdb=" N ARG A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 744 No H-bonds generated for 'chain 'A' and resid 741 through 744' Processing helix chain 'A' and resid 759 through 775 removed outlier: 4.462A pdb=" N ARG A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.884A pdb=" N ALA A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 795 " --> pdb=" O ARG A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 823 removed outlier: 3.676A pdb=" N ARG A 809 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 172 No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.595A pdb=" N SER B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.196A pdb=" N ALA B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 306' Processing helix chain 'B' and resid 317 through 323 removed outlier: 3.888A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.984A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 removed outlier: 4.429A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 377 removed outlier: 3.692A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 406 Processing helix chain 'B' and resid 412 through 430 Processing helix chain 'B' and resid 444 through 468 removed outlier: 3.566A pdb=" N LEU B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 451 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 455 " --> pdb=" O GLN B 452 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 456 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 459 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 removed outlier: 3.604A pdb=" N ALA B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 576 through 590 removed outlier: 3.693A pdb=" N VAL B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 665 through 668 No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 689 through 695 removed outlier: 4.436A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 695 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 758 through 775 removed outlier: 3.803A pdb=" N VAL B 762 " --> pdb=" O PRO B 758 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.779A pdb=" N LEU B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 795 " --> pdb=" O ARG B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 814 removed outlier: 4.914A pdb=" N VAL B 811 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 814 " --> pdb=" O VAL B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.877A pdb=" N LYS B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 4.096A pdb=" N TYR C 164 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 No H-bonds generated for 'chain 'C' and resid 170 through 173' Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.659A pdb=" N SER C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 304 No H-bonds generated for 'chain 'C' and resid 301 through 304' Processing helix chain 'C' and resid 320 through 323 No H-bonds generated for 'chain 'C' and resid 320 through 323' Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.537A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 361 No H-bonds generated for 'chain 'C' and resid 358 through 361' Processing helix chain 'C' and resid 368 through 379 removed outlier: 4.267A pdb=" N THR C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 406 removed outlier: 3.700A pdb=" N GLU C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 444 through 468 removed outlier: 3.566A pdb=" N LEU C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 451 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 455 " --> pdb=" O GLN C 452 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 456 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 459 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.738A pdb=" N ALA C 539 " --> pdb=" O PRO C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 562 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 576 through 591 removed outlier: 3.568A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 619 removed outlier: 3.863A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.682A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 668 No H-bonds generated for 'chain 'C' and resid 665 through 668' Processing helix chain 'C' and resid 732 through 738 removed outlier: 3.934A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 732 through 738' Processing helix chain 'C' and resid 741 through 744 No H-bonds generated for 'chain 'C' and resid 741 through 744' Processing helix chain 'C' and resid 758 through 777 removed outlier: 3.867A pdb=" N VAL C 762 " --> pdb=" O PRO C 758 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 777 " --> pdb=" O GLY C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 removed outlier: 3.830A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 814 Proline residue: C 806 - end of helix removed outlier: 4.456A pdb=" N VAL C 811 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 184 through 194 removed outlier: 4.540A pdb=" N GLN D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.908A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.822A pdb=" N ALA D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 306' Processing helix chain 'D' and resid 317 through 320 No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 368 through 377 Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 558 through 562 Processing helix chain 'D' and resid 565 through 570 removed outlier: 4.030A pdb=" N LYS D 570 " --> pdb=" O ASP D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 589 removed outlier: 3.591A pdb=" N ALA D 585 " --> pdb=" O ALA D 581 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 586 " --> pdb=" O VAL D 582 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG D 588 " --> pdb=" O ASP D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 623 Processing helix chain 'D' and resid 642 through 647 removed outlier: 3.898A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 642 through 647' Processing helix chain 'D' and resid 663 through 669 removed outlier: 4.156A pdb=" N VAL D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'D' and resid 692 through 695 No H-bonds generated for 'chain 'D' and resid 692 through 695' Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 760 through 775 removed outlier: 4.135A pdb=" N ILE D 764 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 803 through 805 No H-bonds generated for 'chain 'D' and resid 803 through 805' Processing helix chain 'D' and resid 807 through 824 removed outlier: 4.303A pdb=" N ASP D 817 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 212 through 225 removed outlier: 3.782A pdb=" N ALA E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 257 through 267 removed outlier: 3.777A pdb=" N ALA E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 317 through 321 removed outlier: 3.652A pdb=" N ARG E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 317 through 321' Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 368 through 381 removed outlier: 4.363A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 393 removed outlier: 3.825A pdb=" N ALA E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.625A pdb=" N MET E 404 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 405 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 546 removed outlier: 4.094A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR E 546 " --> pdb=" O VAL E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 585 Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 615 through 624 removed outlier: 3.564A pdb=" N ASP E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 648 Processing helix chain 'E' and resid 665 through 667 No H-bonds generated for 'chain 'E' and resid 665 through 667' Processing helix chain 'E' and resid 681 through 683 No H-bonds generated for 'chain 'E' and resid 681 through 683' Processing helix chain 'E' and resid 689 through 695 removed outlier: 3.682A pdb=" N GLN E 694 " --> pdb=" O ASP E 690 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 695 " --> pdb=" O VAL E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 738 Processing helix chain 'E' and resid 742 through 745 No H-bonds generated for 'chain 'E' and resid 742 through 745' Processing helix chain 'E' and resid 760 through 773 removed outlier: 3.624A pdb=" N ILE E 764 " --> pdb=" O LEU E 761 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 773 " --> pdb=" O ALA E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 775 through 777 No H-bonds generated for 'chain 'E' and resid 775 through 777' Processing helix chain 'E' and resid 787 through 797 removed outlier: 4.122A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 825 removed outlier: 4.154A pdb=" N GLN E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE E 815 " --> pdb=" O VAL E 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 185 through 194 Processing helix chain 'F' and resid 213 through 225 Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 254 through 266 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.380A pdb=" N ALA F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 301 through 306' Processing helix chain 'F' and resid 319 through 321 No H-bonds generated for 'chain 'F' and resid 319 through 321' Processing helix chain 'F' and resid 324 through 326 No H-bonds generated for 'chain 'F' and resid 324 through 326' Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.343A pdb=" N ARG F 332 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 353 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 368 through 377 removed outlier: 3.975A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 405 removed outlier: 4.145A pdb=" N LEU F 394 " --> pdb=" O LYS F 390 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 542 Processing helix chain 'F' and resid 558 through 562 Processing helix chain 'F' and resid 568 through 570 No H-bonds generated for 'chain 'F' and resid 568 through 570' Processing helix chain 'F' and resid 576 through 591 removed outlier: 3.551A pdb=" N ALA F 581 " --> pdb=" O ALA F 577 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG F 590 " --> pdb=" O VAL F 586 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 591 " --> pdb=" O ARG F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 624 removed outlier: 3.824A pdb=" N ALA F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP F 622 " --> pdb=" O LYS F 618 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 647 removed outlier: 4.204A pdb=" N VAL F 645 " --> pdb=" O LYS F 642 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 670 removed outlier: 3.875A pdb=" N VAL F 668 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG F 670 " --> pdb=" O GLU F 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 695 removed outlier: 4.446A pdb=" N GLN F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL F 695 " --> pdb=" O VAL F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 736 Processing helix chain 'F' and resid 761 through 777 removed outlier: 3.538A pdb=" N LEU F 776 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 777 " --> pdb=" O GLY F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 795 removed outlier: 3.858A pdb=" N ALA F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 805 through 814 removed outlier: 3.659A pdb=" N ARG F 809 " --> pdb=" O ARG F 805 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN F 812 " --> pdb=" O ARG F 808 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 825 removed outlier: 3.857A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA F 825 " --> pdb=" O LYS F 821 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.926A pdb=" N GLY A 313 " --> pdb=" O LEU A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 601 through 605 removed outlier: 3.756A pdb=" N LEU A 718 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 634 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 679 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.839A pdb=" N VAL A 834 " --> pdb=" O GLN A 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 335 through 338 removed outlier: 6.092A pdb=" N LEU B 311 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 204 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY B 313 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLY B 206 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR B 315 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG B 310 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 314 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE B 276 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASP B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 601 through 604 removed outlier: 6.848A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP B 679 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 782 through 785 Processing sheet with id= G, first strand: chain 'C' and resid 335 through 338 removed outlier: 7.021A pdb=" N GLY C 313 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLY C 206 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 315 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 601 through 605 removed outlier: 6.871A pdb=" N VAL C 632 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASP C 679 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE C 634 " --> pdb=" O ASP C 679 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 700 through 702 Processing sheet with id= J, first strand: chain 'C' and resid 783 through 785 removed outlier: 7.269A pdb=" N VAL C 834 " --> pdb=" O GLN C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 837 through 839 Processing sheet with id= L, first strand: chain 'D' and resid 204 through 206 removed outlier: 6.317A pdb=" N VAL D 337 " --> pdb=" O ILE D 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 276 through 278 removed outlier: 6.160A pdb=" N VAL D 312 " --> pdb=" O ILE D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 632 through 635 removed outlier: 3.573A pdb=" N ASP D 679 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 715 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE D 678 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE D 717 " --> pdb=" O PHE D 678 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 335 through 338 removed outlier: 6.355A pdb=" N LEU E 311 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU E 204 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY E 313 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY E 206 " --> pdb=" O GLY E 313 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR E 315 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR E 275 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ALA E 314 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 277 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N THR E 316 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 631 through 635 removed outlier: 7.108A pdb=" N VAL E 675 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 634 " --> pdb=" O VAL E 675 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU E 677 " --> pdb=" O ILE E 634 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE E 715 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE E 678 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE E 717 " --> pdb=" O PHE E 678 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 700 through 702 Processing sheet with id= R, first strand: chain 'F' and resid 335 through 338 removed outlier: 6.766A pdb=" N GLY F 313 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLY F 206 " --> pdb=" O GLY F 313 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR F 315 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA F 314 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 236 through 238 Processing sheet with id= T, first strand: chain 'F' and resid 601 through 605 removed outlier: 6.907A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE F 634 " --> pdb=" O ASP F 679 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 700 through 702 Processing sheet with id= V, first strand: chain 'F' and resid 837 through 839 removed outlier: 3.911A pdb=" N SER F 839 " --> pdb=" O ALA F 842 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1800 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: 8.40 Time building geometry restraints manager: 12.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 10804 1.39 - 1.56: 16734 1.56 - 1.73: 38 1.73 - 1.90: 108 1.90 - 2.08: 10 Bond restraints: 27694 Sorted by residual: bond pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.27e+01 bond pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.15e+01 bond pdb=" C5 AGS D 901 " pdb=" C6 AGS D 901 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 AGS F 901 " pdb=" C6 AGS F 901 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" PG AGS F 901 " pdb=" S1G AGS F 901 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 27689 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.98: 661 105.98 - 114.07: 16016 114.07 - 122.15: 15590 122.15 - 130.24: 5106 130.24 - 138.33: 104 Bond angle restraints: 37477 Sorted by residual: angle pdb=" C5 AGS F 901 " pdb=" C4 AGS F 901 " pdb=" N3 AGS F 901 " ideal model delta sigma weight residual 126.80 118.65 8.15 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS D 901 " pdb=" C4 AGS D 901 " pdb=" N3 AGS D 901 " ideal model delta sigma weight residual 126.80 118.71 8.09 7.41e-01 1.82e+00 1.19e+02 angle pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " pdb=" N7 AGS F 901 " ideal model delta sigma weight residual 110.73 106.56 4.17 4.52e-01 4.89e+00 8.50e+01 angle pdb=" C SER C 594 " pdb=" N ASP C 595 " pdb=" CA ASP C 595 " ideal model delta sigma weight residual 120.94 138.33 -17.39 1.90e+00 2.77e-01 8.38e+01 angle pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " pdb=" N7 AGS D 901 " ideal model delta sigma weight residual 110.73 106.60 4.13 4.52e-01 4.89e+00 8.33e+01 ... (remaining 37472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 16621 32.67 - 65.33: 290 65.33 - 98.00: 25 98.00 - 130.67: 3 130.67 - 163.34: 3 Dihedral angle restraints: 16942 sinusoidal: 6906 harmonic: 10036 Sorted by residual: dihedral pdb=" CA SER C 839 " pdb=" C SER C 839 " pdb=" N PRO C 840 " pdb=" CA PRO C 840 " ideal model delta harmonic sigma weight residual 180.00 -134.77 -45.23 0 5.00e+00 4.00e-02 8.18e+01 dihedral pdb=" CA SER E 839 " pdb=" C SER E 839 " pdb=" N PRO E 840 " pdb=" CA PRO E 840 " ideal model delta harmonic sigma weight residual 180.00 -135.46 -44.54 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA LEU C 387 " pdb=" C LEU C 387 " pdb=" N PRO C 388 " pdb=" CA PRO C 388 " ideal model delta harmonic sigma weight residual 180.00 135.83 44.17 0 5.00e+00 4.00e-02 7.80e+01 ... (remaining 16939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3696 0.082 - 0.164: 572 0.164 - 0.245: 27 0.245 - 0.327: 3 0.327 - 0.409: 2 Chirality restraints: 4300 Sorted by residual: chirality pdb=" CB ILE D 681 " pdb=" CA ILE D 681 " pdb=" CG1 ILE D 681 " pdb=" CG2 ILE D 681 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ARG E 805 " pdb=" N ARG E 805 " pdb=" C ARG E 805 " pdb=" CB ARG E 805 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB VAL F 180 " pdb=" CA VAL F 180 " pdb=" CG1 VAL F 180 " pdb=" CG2 VAL F 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4297 not shown) Planarity restraints: 4894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 409 " 0.094 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO B 410 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 410 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 410 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 387 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 388 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 387 " -0.080 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO D 388 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO D 388 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO D 388 " -0.066 5.00e-02 4.00e+02 ... (remaining 4891 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 138 2.51 - 3.11: 18861 3.11 - 3.71: 39545 3.71 - 4.30: 52840 4.30 - 4.90: 87354 Nonbonded interactions: 198738 Sorted by model distance: nonbonded pdb=" O TRP F 545 " pdb=" N GLY F 547 " model vdw 1.913 2.520 nonbonded pdb=" NH1 ARG B 418 " pdb=" OD1 ASP C 184 " model vdw 1.981 2.520 nonbonded pdb=" O LYS B 301 " pdb=" NH1 ARG B 333 " model vdw 1.986 2.520 nonbonded pdb=" NZ LYS E 199 " pdb=" O ARG E 332 " model vdw 2.082 2.520 nonbonded pdb=" O GLU B 412 " pdb=" N GLU B 415 " model vdw 2.148 2.520 ... (remaining 198733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 27318 True True 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 P 34 5.49 5 S 64 5.16 5 C 16985 2.51 5 N 4966 2.21 5 O 5269 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 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: 1.080 Set model interpretation parameters: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.220 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.130 Process input model: 73.760 Set up NCS constraints: 0.140 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:2.370 Internal consistency checks: 0.000 Total: 85.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.126 27694 Angle : 1.110 17.391 37477 Chirality : 0.056 0.409 4300 Planarity : 0.009 0.146 4894 Dihedral : 12.812 163.336 10478 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.49 % Favored : 87.08 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.34 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.11), residues: 3484 helix: -3.40 (0.09), residues: 1474 sheet: -2.81 (0.24), residues: 352 loop : -3.23 (0.13), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 20 poor density : 762 time to evaluate : 3.456 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 781 average time/residue: 0.5367 time to fit residues: 424.7619 Evaluate side-chains 357 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 10 poor density : 347 time to evaluate : 3.222 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 10 average time/residue: 0.3285 time to fit residues: 7.6643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 40.0000 chunk 265 optimal weight: 0.8980 chunk 147 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 106 optimal weight: 0.0040 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 317 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 361 HIS A 643 HIS B 361 HIS B 643 HIS B 757 ASN C 361 HIS C 575 GLN C 721 ASN C 771 GLN C 784 GLN D 192 GLN D 361 HIS ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 HIS F 643 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS F 745 ASN F 827 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.034 27694 Angle : 0.621 13.285 37477 Chirality : 0.042 0.230 4300 Planarity : 0.006 0.097 4894 Dihedral : 9.135 160.505 3991 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.18 % Favored : 90.67 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.82 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.13), residues: 3484 helix: -1.87 (0.12), residues: 1441 sheet: -2.11 (0.27), residues: 321 loop : -2.76 (0.14), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 9 poor density : 545 time to evaluate : 3.343 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 554 average time/residue: 0.4403 time to fit residues: 249.2547 Evaluate side-chains 315 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 8 poor density : 307 time to evaluate : 3.457 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 8 average time/residue: 0.2507 time to fit residues: 6.5962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 343 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 315 optimal weight: 0.0020 chunk 108 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 335 GLN A 336 GLN ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN B 685 HIS ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 597 ASN C 643 HIS D 192 GLN D 336 GLN ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 GLN E 159 GLN E 336 GLN E 362 HIS E 575 GLN E 685 HIS E 705 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS F 827 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.031 27694 Angle : 0.630 13.309 37477 Chirality : 0.043 0.227 4300 Planarity : 0.005 0.103 4894 Dihedral : 8.888 170.326 3991 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.48 % Favored : 89.38 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.82 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.13), residues: 3484 helix: -1.20 (0.13), residues: 1470 sheet: -2.04 (0.28), residues: 312 loop : -2.62 (0.14), residues: 1702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 430 time to evaluate : 3.365 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 440 average time/residue: 0.4080 time to fit residues: 184.9389 Evaluate side-chains 281 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 10 poor density : 271 time to evaluate : 3.331 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 10 average time/residue: 0.2670 time to fit residues: 7.0181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 319 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 302 optimal weight: 20.0000 chunk 91 optimal weight: 0.0370 overall best weight: 2.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 663 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 597 ASN D 192 GLN D 336 GLN ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 GLN E 705 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.037 27694 Angle : 0.668 13.798 37477 Chirality : 0.045 0.229 4300 Planarity : 0.005 0.106 4894 Dihedral : 8.821 170.074 3991 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.59 % Favored : 89.27 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.14), residues: 3484 helix: -0.79 (0.14), residues: 1486 sheet: -2.04 (0.27), residues: 332 loop : -2.48 (0.15), residues: 1666 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 11 poor density : 387 time to evaluate : 3.412 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 397 average time/residue: 0.4141 time to fit residues: 170.2884 Evaluate side-chains 266 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 10 poor density : 256 time to evaluate : 3.767 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 10 average time/residue: 0.3155 time to fit residues: 8.0022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 288 optimal weight: 0.6980 chunk 233 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 597 ASN D 192 GLN ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN E 705 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 827 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.033 27694 Angle : 0.621 13.681 37477 Chirality : 0.043 0.222 4300 Planarity : 0.005 0.111 4894 Dihedral : 8.651 176.781 3991 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.13 % Favored : 89.72 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.14), residues: 3484 helix: -0.53 (0.14), residues: 1493 sheet: -1.91 (0.28), residues: 327 loop : -2.33 (0.15), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 387 time to evaluate : 3.471 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 397 average time/residue: 0.3983 time to fit residues: 163.6274 Evaluate side-chains 275 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 10 poor density : 265 time to evaluate : 3.322 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 10 average time/residue: 0.2482 time to fit residues: 6.8841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 338 optimal weight: 0.6980 chunk 281 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS A 336 GLN ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN D 192 GLN ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.046 27694 Angle : 0.613 14.203 37477 Chirality : 0.043 0.205 4300 Planarity : 0.005 0.111 4894 Dihedral : 8.418 167.846 3991 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.87 % Favored : 89.98 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.15), residues: 3484 helix: -0.32 (0.14), residues: 1479 sheet: -1.70 (0.29), residues: 314 loop : -2.20 (0.15), residues: 1691 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 378 time to evaluate : 3.731 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 389 average time/residue: 0.4200 time to fit residues: 169.1545 Evaluate side-chains 271 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 11 poor density : 260 time to evaluate : 3.306 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 11 average time/residue: 0.2662 time to fit residues: 7.3809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 192 optimal weight: 0.6980 chunk 247 optimal weight: 7.9990 chunk 191 optimal weight: 0.6980 chunk 285 optimal weight: 0.0170 chunk 189 optimal weight: 4.9990 chunk 337 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 705 HIS ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 GLN D 597 ASN E 159 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN E 705 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 827 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.028 27694 Angle : 0.592 19.687 37477 Chirality : 0.041 0.185 4300 Planarity : 0.005 0.188 4894 Dihedral : 7.937 150.870 3991 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.93 % Favored : 90.93 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.71 (0.15), residues: 3484 helix: -0.11 (0.14), residues: 1490 sheet: -1.44 (0.30), residues: 303 loop : -2.04 (0.15), residues: 1691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 423 time to evaluate : 3.398 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 434 average time/residue: 0.3931 time to fit residues: 176.3541 Evaluate side-chains 296 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 11 poor density : 285 time to evaluate : 3.279 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 11 average time/residue: 0.2564 time to fit residues: 7.2952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 265 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 336 GLN A 705 HIS C 597 ASN ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.040 27694 Angle : 0.592 14.362 37477 Chirality : 0.042 0.174 4300 Planarity : 0.005 0.107 4894 Dihedral : 7.782 135.285 3991 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.98 % Favored : 90.87 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.54 (0.15), residues: 3484 helix: 0.03 (0.14), residues: 1490 sheet: -1.38 (0.30), residues: 308 loop : -1.94 (0.16), residues: 1686 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 13 poor density : 397 time to evaluate : 3.469 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 409 average time/residue: 0.4396 time to fit residues: 185.2729 Evaluate side-chains 277 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 11 poor density : 266 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 11 average time/residue: 0.2820 time to fit residues: 7.9272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 chunk 294 optimal weight: 0.7980 chunk 314 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 284 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 313 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 201 ASN C 597 ASN D 336 GLN E 159 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.100 27694 Angle : 0.613 14.304 37477 Chirality : 0.043 0.173 4300 Planarity : 0.005 0.129 4894 Dihedral : 7.752 120.316 3991 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.70 % Favored : 90.15 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.51 (0.15), residues: 3484 helix: 0.04 (0.14), residues: 1497 sheet: -1.36 (0.30), residues: 312 loop : -1.92 (0.16), residues: 1675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 14 poor density : 379 time to evaluate : 3.504 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 391 average time/residue: 0.4282 time to fit residues: 173.2850 Evaluate side-chains 274 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 11 poor density : 263 time to evaluate : 3.526 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 11 average time/residue: 0.2653 time to fit residues: 7.6987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 0.7980 chunk 332 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 348 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 277 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 214 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 705 HIS A 721 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN E 159 GLN E 336 GLN E 705 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 663 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.092 27694 Angle : 0.602 11.805 37477 Chirality : 0.042 0.173 4300 Planarity : 0.005 0.114 4894 Dihedral : 7.562 107.925 3991 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.16 % Favored : 90.70 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.42 (0.15), residues: 3484 helix: 0.10 (0.14), residues: 1501 sheet: -1.31 (0.30), residues: 314 loop : -1.86 (0.16), residues: 1669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield and 0 Emsley and 3484 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 14 poor density : 362 time to evaluate : 3.344 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 375 average time/residue: 0.3942 time to fit residues: 153.4118 Evaluate side-chains 284 residues out of total 2852 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 11 poor density : 273 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 11 average time/residue: 0.2753 time to fit residues: 7.7989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 4.9990 chunk 295 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 256 optimal weight: 0.0050 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 285 optimal weight: 0.0000 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 0.0370 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS A 336 GLN A 705 HIS A 721 ASN B 201 ASN C 281 HIS C 597 ASN E 159 GLN E 336 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123050 restraints weight = 56436.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123070 restraints weight = 57373.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124156 restraints weight = 48176.118| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.079 27694 ANGLE : 0.584 11.217 37477 CHIRALITY : 0.041 0.176 4300 PLANARITY : 0.005 0.106 4894 DIHEDRAL : 7.196 99.119 3991 MIN NONBONDED DISTANCE : 2.156 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 7.80 RAMACHANDRAN PLOT: OUTLIERS : 0.14 % ALLOWED : 8.98 % FAVORED : 90.87 % ROTAMER OUTLIERS : 0.57 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 1.41 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -1.25 (0.15), RESIDUES: 3484 HELIX: 0.25 (0.14), RESIDUES: 1490 SHEET: -1.17 (0.30), RESIDUES: 318 LOOP : -1.77 (0.16), RESIDUES: 1676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.079 27694 Angle : 0.584 11.217 37477 Chirality : 0.041 0.176 4300 Planarity : 0.005 0.106 4894 Dihedral : 7.196 99.119 3991 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.98 % Favored : 90.87 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3484 helix: 0.25 (0.14), residues: 1490 sheet: -1.17 (0.30), residues: 318 loop : -1.77 (0.16), residues: 1676 =============================================================================== Job complete usr+sys time: 4907.90 seconds wall clock time: 90 minutes 20.27 seconds (5420.27 seconds total)