Starting phenix.real_space_refine (version: dev) on Fri Mar 17 11:52:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/03_2023/6sjl_10218.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/03_2023/6sjl_10218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/03_2023/6sjl_10218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/03_2023/6sjl_10218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/03_2023/6sjl_10218.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjl_10218/03_2023/6sjl_10218.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ASP 508": "OD1" <-> "OD2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A ASP 657": "OD1" <-> "OD2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 804": "OD1" <-> "OD2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B ASP 657": "OD1" <-> "OD2" Residue "B ASP 711": "OD1" <-> "OD2" Residue "B TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 804": "OD1" <-> "OD2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C GLU 542": "OE1" <-> "OE2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ASP 565": "OD1" <-> "OD2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C GLU 585": "OE1" <-> "OE2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ASP 426": "OD1" <-> "OD2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ASP 497": "OD1" <-> "OD2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 226": "NH1" <-> "NH2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ASP 348": "OD1" <-> "OD2" Residue "E ASP 415": "OD1" <-> "OD2" Residue "E ASP 426": "OD1" <-> "OD2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E ASP 456": "OD1" <-> "OD2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E GLU 478": "OE1" <-> "OE2" Residue "E TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E ASP 497": "OD1" <-> "OD2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 11": "OD1" <-> "OD2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 152": "OD1" <-> "OD2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 231": "OD1" <-> "OD2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 343": "OD1" <-> "OD2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F ASP 415": "OD1" <-> "OD2" Residue "F ASP 426": "OD1" <-> "OD2" Residue "F GLU 436": "OE1" <-> "OE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 497": "OD1" <-> "OD2" Residue "F ARG 513": "NH1" <-> "NH2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 530": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19459 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "B" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "C" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "D" Number of atoms: 4105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4105 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 22, 'TRANS': 498} Chain breaks: 2 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4113 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 2 Chain: "F" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4113 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 2 Time building chain proxies: 10.92, per 1000 atoms: 0.56 Number of scatterers: 19459 At special positions: 0 Unit cell: (149.504, 154.624, 136.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3734 8.00 N 3455 7.00 C 12174 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: 7.85 Conformation dependent library (CDL) restraints added in 3.4 seconds 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 28 sheets defined 28.9% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 577 through 601 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.718A pdb=" N GLN A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 577 through 601 Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.821A pdb=" N GLN B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'C' and resid 567 through 571 Processing helix chain 'C' and resid 577 through 601 Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.711A pdb=" N GLN C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.544A pdb=" N SER D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 179 Processing helix chain 'D' and resid 198 through 212 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.601A pdb=" N ALA D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.509A pdb=" N ILE D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 348 Processing helix chain 'D' and resid 349 through 365 Processing helix chain 'D' and resid 366 through 369 Processing helix chain 'D' and resid 371 through 375 removed outlier: 3.534A pdb=" N HIS D 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 394 removed outlier: 3.513A pdb=" N ALA D 394 " --> pdb=" O ASN D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 431 Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.818A pdb=" N GLN D 446 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 451 through 467 Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.539A pdb=" N ILE D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.817A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.535A pdb=" N ILE E 85 " --> pdb=" O PHE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 109 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 155 through 178 Processing helix chain 'E' and resid 198 through 212 Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.546A pdb=" N ALA E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 345 through 348 Processing helix chain 'E' and resid 349 through 365 Processing helix chain 'E' and resid 366 through 369 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 388 through 394 Processing helix chain 'E' and resid 416 through 431 Processing helix chain 'E' and resid 442 through 446 removed outlier: 3.998A pdb=" N GLN E 446 " --> pdb=" O THR E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 467 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.559A pdb=" N LYS E 484 " --> pdb=" O TYR E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.743A pdb=" N ILE E 533 " --> pdb=" O ASP E 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.822A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.510A pdb=" N ILE F 85 " --> pdb=" O PHE F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 155 through 179 Processing helix chain 'F' and resid 198 through 212 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.502A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 315 Processing helix chain 'F' and resid 345 through 348 Processing helix chain 'F' and resid 349 through 365 Processing helix chain 'F' and resid 366 through 369 Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 388 through 394 Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 442 through 446 removed outlier: 3.693A pdb=" N GLN F 446 " --> pdb=" O THR F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 451 through 467 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.778A pdb=" N LYS F 484 " --> pdb=" O TYR F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.523A pdb=" N ILE F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 9.898A pdb=" N TRP B 551 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU A 542 " --> pdb=" O TRP B 551 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER B 553 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 544 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG B 555 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 546 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 552 " --> pdb=" O PHE C 561 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER C 563 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE B 554 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 560 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N HIS C 629 " --> pdb=" O ILE C 560 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 562 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY A 635 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 642 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET C 654 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 644 " --> pdb=" O MET C 654 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN A 685 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER C 679 " --> pdb=" O GLN A 685 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 687 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N MET A 684 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN B 696 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 686 " --> pdb=" O GLN B 696 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP A 711 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER C 706 " --> pdb=" O ASP A 711 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN A 713 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 710 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER B 722 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 712 " --> pdb=" O SER B 722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 493 through 497 removed outlier: 6.712A pdb=" N GLN C 526 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 546 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 528 " --> pdb=" O ALA C 544 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 544 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 530 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU C 542 " --> pdb=" O GLY C 530 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN C 532 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 552 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 563 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE A 554 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 560 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS B 629 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 562 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG A 643 " --> pdb=" O MET C 636 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N SER C 638 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA A 645 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 667 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 678 " --> pdb=" O PHE A 667 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 669 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 675 " --> pdb=" O GLN C 685 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU C 687 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 677 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 693 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N SER B 705 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 695 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR A 720 " --> pdb=" O ILE C 712 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER C 714 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER A 722 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 719 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA B 730 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 721 " --> pdb=" O ALA B 730 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 743 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS C 754 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 745 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 493 through 497 removed outlier: 6.791A pdb=" N GLN B 526 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 546 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B 528 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 544 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 530 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 542 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 532 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N TRP C 551 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU B 542 " --> pdb=" O TRP C 551 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER C 553 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 544 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ARG C 555 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 546 " --> pdb=" O ARG C 555 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY A 559 " --> pdb=" O ILE C 552 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C 554 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 561 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY C 556 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 563 " --> pdb=" O GLY C 556 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 560 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N HIS A 629 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 562 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 651 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR B 662 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 653 " --> pdb=" O THR B 662 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET B 684 " --> pdb=" O ASN C 694 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN C 696 " --> pdb=" O MET B 684 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 686 " --> pdb=" O GLN C 696 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU A 726 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL C 721 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 728 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA C 723 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 730 " --> pdb=" O ALA C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 9 removed outlier: 4.322A pdb=" N TYR D 4 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP D 8 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS D 28 " --> pdb=" O ASP D 8 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS D 185 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG D 33 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA D 187 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 35 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 189 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 37 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE D 191 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE D 39 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL D 193 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE D 41 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY D 195 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 43 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N GLU D 237 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 189 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG D 239 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE D 191 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 241 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 193 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU D 243 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY D 195 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU D 304 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN D 281 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU D 306 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR D 283 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 805 through 809 removed outlier: 3.501A pdb=" N VAL A 829 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 799 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 783 through 784 removed outlier: 3.807A pdb=" N ALA E 27 " --> pdb=" O THR B 784 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 9 removed outlier: 4.307A pdb=" N TYR E 4 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE E 184 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG E 33 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE E 186 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL E 35 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS E 188 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N GLU E 237 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE E 189 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG E 239 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE E 191 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU E 241 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 193 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU E 243 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY E 195 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU E 304 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN E 281 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E 306 " --> pdb=" O GLN E 281 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR E 283 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 805 through 809 removed outlier: 3.620A pdb=" N VAL B 829 " --> pdb=" O ARG B 797 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 783 through 785 removed outlier: 3.673A pdb=" N ALA F 27 " --> pdb=" O THR C 784 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 9 removed outlier: 4.252A pdb=" N TYR F 4 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS F 28 " --> pdb=" O ASP F 8 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N CYS F 185 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG F 33 " --> pdb=" O CYS F 185 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA F 187 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL F 35 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE F 189 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU F 37 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE F 191 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 39 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL F 193 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE F 41 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY F 195 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE F 43 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N GLU F 237 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 189 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG F 239 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE F 191 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU F 241 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL F 193 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU F 243 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY F 195 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N LYS F 278 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG F 239 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE F 280 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU F 241 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE F 282 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU F 243 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ALA F 284 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU F 304 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN F 281 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU F 306 " --> pdb=" O GLN F 281 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR F 283 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 795 through 799 Processing sheet with id=AB4, first strand: chain 'C' and resid 826 through 827 removed outlier: 3.545A pdb=" N HIS F 14 " --> pdb=" O VAL C 826 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 294 through 295 removed outlier: 6.345A pdb=" N LEU D 294 " --> pdb=" O TRP D 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 328 through 331 Processing sheet with id=AB7, first strand: chain 'D' and resid 328 through 331 removed outlier: 4.419A pdb=" N GLN D 398 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 495 through 497 Processing sheet with id=AB9, first strand: chain 'D' and resid 500 through 502 Processing sheet with id=AC1, first strand: chain 'E' and resid 294 through 295 removed outlier: 6.431A pdb=" N LEU E 294 " --> pdb=" O TRP E 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 328 through 331 removed outlier: 3.595A pdb=" N GLU E 336 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 328 through 331 removed outlier: 4.421A pdb=" N GLN E 398 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 495 through 497 Processing sheet with id=AC5, first strand: chain 'E' and resid 500 through 502 Processing sheet with id=AC6, first strand: chain 'F' and resid 294 through 295 removed outlier: 6.310A pdb=" N LEU F 294 " --> pdb=" O TRP F 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 328 through 331 Processing sheet with id=AC8, first strand: chain 'F' and resid 328 through 331 removed outlier: 4.599A pdb=" N GLN F 398 " --> pdb=" O VAL F 386 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 495 through 497 Processing sheet with id=AD1, first strand: chain 'F' and resid 500 through 502 810 hydrogen bonds defined for protein. 2250 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: 7.24 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4813 1.32 - 1.44: 3715 1.44 - 1.57: 11096 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 19789 Sorted by residual: bond pdb=" CB ARG B 547 " pdb=" CG ARG B 547 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.09e+00 bond pdb=" CB ARG A 547 " pdb=" CG ARG A 547 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.12e+00 bond pdb=" C SER D 197 " pdb=" N ARG D 198 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.41e-02 5.03e+03 5.93e+00 bond pdb=" CG ARG B 547 " pdb=" CD ARG B 547 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.84e+00 bond pdb=" C SER E 197 " pdb=" N ARG E 198 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.41e-02 5.03e+03 5.77e+00 ... (remaining 19784 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.58: 261 103.58 - 111.77: 9273 111.77 - 119.95: 7924 119.95 - 128.13: 9112 128.13 - 136.32: 143 Bond angle restraints: 26713 Sorted by residual: angle pdb=" C ALA F 411 " pdb=" N VAL F 412 " pdb=" CA VAL F 412 " ideal model delta sigma weight residual 122.59 119.08 3.51 7.20e-01 1.93e+00 2.38e+01 angle pdb=" C GLU B 812 " pdb=" N ASN B 813 " pdb=" CA ASN B 813 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N ARG D 198 " pdb=" CA ARG D 198 " pdb=" C ARG D 198 " ideal model delta sigma weight residual 114.75 109.19 5.56 1.26e+00 6.30e-01 1.95e+01 angle pdb=" N ARG E 198 " pdb=" CA ARG E 198 " pdb=" C ARG E 198 " ideal model delta sigma weight residual 114.75 109.35 5.40 1.26e+00 6.30e-01 1.83e+01 angle pdb=" C LYS E 29 " pdb=" N LYS E 30 " pdb=" CA LYS E 30 " ideal model delta sigma weight residual 121.59 136.32 -14.73 3.54e+00 7.98e-02 1.73e+01 ... (remaining 26708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10764 17.96 - 35.93: 943 35.93 - 53.89: 182 53.89 - 71.85: 46 71.85 - 89.81: 12 Dihedral angle restraints: 11947 sinusoidal: 4777 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ASP A 811 " pdb=" C ASP A 811 " pdb=" N GLU A 812 " pdb=" CA GLU A 812 " ideal model delta harmonic sigma weight residual 180.00 147.36 32.64 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA VAL D 24 " pdb=" C VAL D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG D 198 " pdb=" C ARG D 198 " pdb=" N GLY D 199 " pdb=" CA GLY D 199 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 11944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2276 0.064 - 0.128: 625 0.128 - 0.193: 59 0.193 - 0.257: 0 0.257 - 0.321: 2 Chirality restraints: 2962 Sorted by residual: chirality pdb=" CG LEU A 783 " pdb=" CB LEU A 783 " pdb=" CD1 LEU A 783 " pdb=" CD2 LEU A 783 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE C 823 " pdb=" CA ILE C 823 " pdb=" CG1 ILE C 823 " pdb=" CG2 ILE C 823 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 642 " pdb=" CB LEU A 642 " pdb=" CD1 LEU A 642 " pdb=" CD2 LEU A 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2959 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 81 " 0.029 2.00e-02 2.50e+03 2.99e-02 1.56e+01 pdb=" CG PHE E 81 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE E 81 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE E 81 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 81 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 81 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE E 81 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 81 " 0.032 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE F 81 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE F 81 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE F 81 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 81 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 81 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 81 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 81 " -0.026 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE D 81 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE D 81 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE D 81 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 81 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 81 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 81 " -0.002 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 216 2.57 - 3.15: 16243 3.15 - 3.73: 31551 3.73 - 4.32: 49900 4.32 - 4.90: 79453 Nonbonded interactions: 177363 Sorted by model distance: nonbonded pdb=" NH2 ARG D 422 " pdb=" O LEU D 445 " model vdw 1.985 2.520 nonbonded pdb=" NH2 ARG E 422 " pdb=" O LEU E 445 " model vdw 2.050 2.520 nonbonded pdb=" NH2 ARG F 422 " pdb=" O LEU F 445 " model vdw 2.050 2.520 nonbonded pdb=" O ARG A 640 " pdb=" OG SER B 646 " model vdw 2.088 2.440 nonbonded pdb=" O ARG B 640 " pdb=" OG SER C 646 " model vdw 2.110 2.440 ... (remaining 177358 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' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 3 through 133 or resid 143 through 539)) selection = (chain 'F' and (resid 3 through 133 or resid 143 through 539)) } 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 12174 2.51 5 N 3455 2.21 5 O 3734 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: 0.010 Normalize map: mean=0, sd=1: 2.570 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: 0.010 Extract box with map and model: 10.930 Check model and map are aligned: 0.320 Process input model: 53.030 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.013 0.124 19789 Z= 0.865 Angle : 0.866 14.729 26713 Z= 0.481 Chirality : 0.055 0.321 2962 Planarity : 0.005 0.045 3524 Dihedral : 14.603 89.815 7353 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.06 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.82 (0.14), residues: 2507 helix: -1.54 (0.17), residues: 621 sheet: -1.80 (0.22), residues: 418 loop : -2.08 (0.14), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 2.517 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 1.6678 time to fit residues: 488.8950 Evaluate side-chains 186 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A 583 GLN A 605 GLN A 694 ASN A 696 GLN B 502 ASN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS B 583 GLN B 615 ASN B 725 GLN B 791 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN C 571 GLN C 583 GLN C 615 ASN C 813 ASN D 49 ASN D 76 GLN D 179 ASN D 208 ASN D 213 GLN D 281 GLN D 295 ASN D 370 HIS D 487 HIS D 493 ASN D 512 HIS E 14 HIS E 76 GLN E 179 ASN E 190 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 213 GLN E 281 GLN E 286 ASN E 370 HIS E 429 GLN E 442 ASN E 446 GLN E 472 GLN E 487 HIS E 493 ASN E 512 HIS F 20 ASN F 76 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 213 GLN F 281 GLN F 286 ASN F 487 HIS F 493 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 19789 Z= 0.232 Angle : 0.580 7.800 26713 Z= 0.315 Chirality : 0.045 0.230 2962 Planarity : 0.004 0.044 3524 Dihedral : 6.112 30.787 2711 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.63 (0.16), residues: 2507 helix: 0.18 (0.19), residues: 633 sheet: -1.39 (0.22), residues: 432 loop : -1.59 (0.16), residues: 1442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 235 time to evaluate : 2.446 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 17 residues processed: 262 average time/residue: 1.5322 time to fit residues: 446.3588 Evaluate side-chains 207 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 5 average time/residue: 0.6341 time to fit residues: 7.2432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 0.0980 chunk 204 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 19789 Z= 0.231 Angle : 0.552 7.634 26713 Z= 0.297 Chirality : 0.044 0.217 2962 Planarity : 0.004 0.037 3524 Dihedral : 5.825 31.092 2711 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.12 (0.16), residues: 2507 helix: 0.93 (0.20), residues: 633 sheet: -1.06 (0.22), residues: 446 loop : -1.44 (0.16), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 204 time to evaluate : 2.533 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 26 residues processed: 241 average time/residue: 1.4458 time to fit residues: 391.3359 Evaluate side-chains 212 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 2.510 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.9614 time to fit residues: 11.0549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 6.9990 chunk 172 optimal weight: 0.0000 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 230 optimal weight: 0.1980 chunk 243 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 ASN C 696 GLN C 725 GLN D 49 ASN D 106 ASN D 123 GLN E 170 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 19789 Z= 0.168 Angle : 0.516 6.918 26713 Z= 0.277 Chirality : 0.043 0.212 2962 Planarity : 0.003 0.037 3524 Dihedral : 5.473 31.563 2711 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.76 (0.16), residues: 2507 helix: 1.53 (0.20), residues: 628 sheet: -0.88 (0.23), residues: 446 loop : -1.36 (0.16), residues: 1433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 24 residues processed: 242 average time/residue: 1.4889 time to fit residues: 404.0953 Evaluate side-chains 223 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 2.522 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.9581 time to fit residues: 11.1724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN A 707 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 ASN C 696 GLN C 725 GLN D 49 ASN D 123 GLN E 5 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 19789 Z= 0.484 Angle : 0.642 7.400 26713 Z= 0.342 Chirality : 0.047 0.226 2962 Planarity : 0.004 0.042 3524 Dihedral : 5.943 28.702 2711 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2507 helix: 1.22 (0.20), residues: 635 sheet: -0.82 (0.23), residues: 440 loop : -1.32 (0.16), residues: 1432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 33 residues processed: 243 average time/residue: 1.4658 time to fit residues: 400.5464 Evaluate side-chains 224 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 2.392 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 0.7806 time to fit residues: 10.9955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.5980 chunk 219 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 243 optimal weight: 0.0020 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 750 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 791 GLN D 49 ASN E 5 GLN E 170 GLN E 429 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19789 Z= 0.161 Angle : 0.520 6.694 26713 Z= 0.279 Chirality : 0.043 0.210 2962 Planarity : 0.003 0.044 3524 Dihedral : 5.473 31.326 2711 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.60 (0.16), residues: 2507 helix: 1.68 (0.20), residues: 628 sheet: -0.72 (0.24), residues: 413 loop : -1.28 (0.16), residues: 1466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 207 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 32 residues processed: 243 average time/residue: 1.4751 time to fit residues: 402.9534 Evaluate side-chains 227 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 0.8003 time to fit residues: 9.1789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 19789 Z= 0.252 Angle : 0.552 8.187 26713 Z= 0.294 Chirality : 0.044 0.209 2962 Planarity : 0.004 0.050 3524 Dihedral : 5.527 29.363 2711 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2507 helix: 1.75 (0.20), residues: 626 sheet: -0.59 (0.23), residues: 431 loop : -1.25 (0.16), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 197 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 34 residues processed: 231 average time/residue: 1.5067 time to fit residues: 389.3142 Evaluate side-chains 229 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 28 residues processed: 6 average time/residue: 0.7829 time to fit residues: 8.9127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 750 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 HIS E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 19789 Z= 0.253 Angle : 0.553 8.587 26713 Z= 0.295 Chirality : 0.044 0.212 2962 Planarity : 0.004 0.052 3524 Dihedral : 5.526 28.877 2711 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2507 helix: 1.78 (0.20), residues: 626 sheet: -0.54 (0.23), residues: 437 loop : -1.23 (0.16), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 200 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 34 residues processed: 237 average time/residue: 1.5246 time to fit residues: 405.8505 Evaluate side-chains 228 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 2.472 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 7 average time/residue: 0.6078 time to fit residues: 8.6138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 49 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 19789 Z= 0.435 Angle : 0.631 8.850 26713 Z= 0.335 Chirality : 0.046 0.215 2962 Planarity : 0.004 0.063 3524 Dihedral : 5.836 27.656 2711 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2507 helix: 1.34 (0.20), residues: 646 sheet: -0.65 (0.23), residues: 462 loop : -1.26 (0.16), residues: 1399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 195 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 35 residues processed: 232 average time/residue: 1.4992 time to fit residues: 389.3756 Evaluate side-chains 226 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 2.405 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 29 residues processed: 6 average time/residue: 0.7595 time to fit residues: 8.9884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 0.2980 chunk 199 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN A 725 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 750 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 ASN C 696 GLN C 725 GLN D 49 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19789 Z= 0.205 Angle : 0.546 8.646 26713 Z= 0.291 Chirality : 0.044 0.211 2962 Planarity : 0.004 0.061 3524 Dihedral : 5.488 29.513 2711 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2507 helix: 1.79 (0.20), residues: 626 sheet: -0.55 (0.23), residues: 456 loop : -1.22 (0.16), residues: 1425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 29 residues processed: 230 average time/residue: 1.4269 time to fit residues: 370.2763 Evaluate side-chains 221 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 0.7825 time to fit residues: 5.2707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN A 725 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 ASN C 696 GLN C 725 GLN D 49 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN E 170 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 469 GLN E 472 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095016 restraints weight = 19517.072| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.52 r_work: 0.3059 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2141 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: