Starting phenix.real_space_refine (version: dev) on Fri Dec 16 02:57:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2022/6o72_0638_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2022/6o72_0638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2022/6o72_0638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2022/6o72_0638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2022/6o72_0638_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2022/6o72_0638_updated.pdb" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 775": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 880": "NH1" <-> "NH2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C GLU 653": "OE1" <-> "OE2" Residue "C ARG 655": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 880": "NH1" <-> "NH2" Residue "C GLU 1041": "OE1" <-> "OE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D GLU 649": "OE1" <-> "OE2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 775": "NH1" <-> "NH2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 875": "NH1" <-> "NH2" Residue "D ARG 880": "NH1" <-> "NH2" Residue "D GLU 1041": "OE1" <-> "OE2" Residue "D GLU 1051": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 28592 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "B" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "D" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 140 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 3, 'Y01': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 15.86, per 1000 atoms: 0.55 Number of scatterers: 28592 At special positions: 0 Unit cell: (128.139, 128.139, 145.083, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 148 16.00 P 4 15.00 Na 8 11.00 F 24 9.00 O 5028 8.00 N 4604 7.00 C 18776 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.64 Conformation dependent library (CDL) restraints added in 3.9 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 4 sheets defined 59.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 166 removed outlier: 4.184A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 3.614A pdb=" N GLY A 184 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.710A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 354 through 357 No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 362 through 374 removed outlier: 4.091A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.624A pdb=" N GLN A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.520A pdb=" N PHE A 522 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.798A pdb=" N LYS A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 592 removed outlier: 3.650A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 626 removed outlier: 3.729A pdb=" N GLU A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.504A pdb=" N GLN A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.527A pdb=" N VAL A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 684 through 691 removed outlier: 3.888A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.529A pdb=" N GLY A 697 " --> pdb=" O PRO A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 725 through 748 Processing helix chain 'A' and resid 757 through 765 Processing helix chain 'A' and resid 767 through 774 removed outlier: 3.689A pdb=" N GLU A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 786 No H-bonds generated for 'chain 'A' and resid 784 through 786' Processing helix chain 'A' and resid 791 through 805 removed outlier: 3.621A pdb=" N TYR A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 841 removed outlier: 3.537A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.900A pdb=" N ILE A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 878 Processing helix chain 'A' and resid 890 through 893 No H-bonds generated for 'chain 'A' and resid 890 through 893' Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 946 through 956 removed outlier: 4.609A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 980 through 996 removed outlier: 3.733A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1007 through 1013 removed outlier: 4.323A pdb=" N PHE A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1058 removed outlier: 3.530A pdb=" N ASN A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1090 through 1093 No H-bonds generated for 'chain 'A' and resid 1090 through 1093' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 166 removed outlier: 4.184A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.613A pdb=" N GLY B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.709A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 354 through 357 No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 362 through 374 removed outlier: 4.091A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 394 through 408 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.624A pdb=" N GLN B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 removed outlier: 3.519A pdb=" N PHE B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 565 through 574 removed outlier: 3.797A pdb=" N LYS B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 592 removed outlier: 3.650A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 626 removed outlier: 3.730A pdb=" N GLU B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 removed outlier: 3.504A pdb=" N GLN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 removed outlier: 3.527A pdb=" N VAL B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 663 through 674 Processing helix chain 'B' and resid 684 through 691 removed outlier: 3.888A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 697 removed outlier: 3.529A pdb=" N GLY B 697 " --> pdb=" O PRO B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 725 through 748 Processing helix chain 'B' and resid 757 through 765 Processing helix chain 'B' and resid 767 through 774 removed outlier: 3.689A pdb=" N GLU B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 791 through 805 removed outlier: 3.622A pdb=" N TYR B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 841 removed outlier: 3.537A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 removed outlier: 3.900A pdb=" N ILE B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 878 Processing helix chain 'B' and resid 890 through 893 No H-bonds generated for 'chain 'B' and resid 890 through 893' Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 946 through 956 removed outlier: 4.609A pdb=" N CYS B 951 " --> pdb=" O ILE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 969 Processing helix chain 'B' and resid 980 through 996 removed outlier: 3.733A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 994 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1005 No H-bonds generated for 'chain 'B' and resid 1003 through 1005' Processing helix chain 'B' and resid 1007 through 1013 removed outlier: 4.323A pdb=" N PHE B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1058 removed outlier: 3.530A pdb=" N ASN B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1086 Processing helix chain 'B' and resid 1090 through 1093 No H-bonds generated for 'chain 'B' and resid 1090 through 1093' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 166 removed outlier: 4.184A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.613A pdb=" N GLY C 184 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 276 Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.711A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 354 through 357 No H-bonds generated for 'chain 'C' and resid 354 through 357' Processing helix chain 'C' and resid 362 through 374 removed outlier: 4.092A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 394 through 408 Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 450 through 458 Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 475 through 478 No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 504 removed outlier: 3.624A pdb=" N GLN C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.520A pdb=" N PHE C 522 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 561 Processing helix chain 'C' and resid 565 through 574 removed outlier: 3.798A pdb=" N LYS C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.650A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 626 removed outlier: 3.729A pdb=" N GLU C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 635 removed outlier: 3.504A pdb=" N GLN C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 653 removed outlier: 3.527A pdb=" N VAL C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 663 through 674 Processing helix chain 'C' and resid 684 through 691 removed outlier: 3.889A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 697 removed outlier: 3.529A pdb=" N GLY C 697 " --> pdb=" O PRO C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 721 Processing helix chain 'C' and resid 725 through 748 Processing helix chain 'C' and resid 757 through 765 Processing helix chain 'C' and resid 767 through 774 removed outlier: 3.689A pdb=" N GLU C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 786 No H-bonds generated for 'chain 'C' and resid 784 through 786' Processing helix chain 'C' and resid 791 through 805 removed outlier: 3.621A pdb=" N TYR C 799 " --> pdb=" O LEU C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 841 removed outlier: 3.537A pdb=" N SER C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 849 removed outlier: 3.900A pdb=" N ILE C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 878 Processing helix chain 'C' and resid 890 through 893 No H-bonds generated for 'chain 'C' and resid 890 through 893' Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 946 through 956 removed outlier: 4.609A pdb=" N CYS C 951 " --> pdb=" O ILE C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 969 Processing helix chain 'C' and resid 980 through 996 removed outlier: 3.732A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 994 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 995 " --> pdb=" O LEU C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1005 No H-bonds generated for 'chain 'C' and resid 1003 through 1005' Processing helix chain 'C' and resid 1007 through 1013 removed outlier: 4.324A pdb=" N PHE C1012 " --> pdb=" O PHE C1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1058 removed outlier: 3.529A pdb=" N ASN C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1086 Processing helix chain 'C' and resid 1090 through 1093 No H-bonds generated for 'chain 'C' and resid 1090 through 1093' Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 150 through 166 removed outlier: 4.185A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 removed outlier: 3.614A pdb=" N GLY D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 276 Processing helix chain 'D' and resid 301 through 312 removed outlier: 3.710A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 344 through 352 Processing helix chain 'D' and resid 354 through 357 No H-bonds generated for 'chain 'D' and resid 354 through 357' Processing helix chain 'D' and resid 362 through 374 removed outlier: 4.091A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 394 through 408 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'D' and resid 430 through 436 Processing helix chain 'D' and resid 450 through 458 Processing helix chain 'D' and resid 462 through 470 Processing helix chain 'D' and resid 475 through 478 No H-bonds generated for 'chain 'D' and resid 475 through 478' Processing helix chain 'D' and resid 481 through 489 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.624A pdb=" N GLN D 501 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 removed outlier: 3.520A pdb=" N PHE D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 561 Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.798A pdb=" N LYS D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 592 removed outlier: 3.650A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 626 removed outlier: 3.730A pdb=" N GLU D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 removed outlier: 3.505A pdb=" N GLN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 653 removed outlier: 3.527A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 663 through 674 Processing helix chain 'D' and resid 684 through 691 removed outlier: 3.888A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 697 removed outlier: 3.529A pdb=" N GLY D 697 " --> pdb=" O PRO D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 725 through 748 Processing helix chain 'D' and resid 757 through 765 Processing helix chain 'D' and resid 767 through 774 removed outlier: 3.689A pdb=" N GLU D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 786 No H-bonds generated for 'chain 'D' and resid 784 through 786' Processing helix chain 'D' and resid 791 through 805 removed outlier: 3.622A pdb=" N TYR D 799 " --> pdb=" O LEU D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 841 removed outlier: 3.537A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 849 removed outlier: 3.900A pdb=" N ILE D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 878 Processing helix chain 'D' and resid 890 through 893 No H-bonds generated for 'chain 'D' and resid 890 through 893' Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 946 through 956 removed outlier: 4.609A pdb=" N CYS D 951 " --> pdb=" O ILE D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 980 through 996 removed outlier: 3.733A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 994 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 995 " --> pdb=" O LEU D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1005 No H-bonds generated for 'chain 'D' and resid 1003 through 1005' Processing helix chain 'D' and resid 1007 through 1013 removed outlier: 4.323A pdb=" N PHE D1012 " --> pdb=" O PHE D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1058 removed outlier: 3.530A pdb=" N ASN D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1086 Processing helix chain 'D' and resid 1090 through 1093 No H-bonds generated for 'chain 'D' and resid 1090 through 1093' Processing sheet with id= A, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.609A pdb=" N HIS A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS A 317 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA A 296 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 319 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.609A pdb=" N HIS B 250 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS B 317 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA B 296 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 319 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 107 through 110 removed outlier: 3.609A pdb=" N HIS C 250 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS C 317 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA C 296 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 319 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 107 through 110 removed outlier: 3.610A pdb=" N HIS D 250 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS D 317 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA D 296 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL D 319 " --> pdb=" O ALA D 296 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3696 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: 10.51 Time building geometry restraints manager: 12.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4480 1.31 - 1.44: 8218 1.44 - 1.56: 16246 1.56 - 1.69: 48 1.69 - 1.82: 244 Bond restraints: 29236 Sorted by residual: bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" C19 T14 C1305 " pdb=" N20 T14 C1305 " ideal model delta sigma weight residual 1.274 1.446 -0.172 2.00e-02 2.50e+03 7.35e+01 ... (remaining 29231 not shown) Histogram of bond angle deviations from ideal: 95.27 - 104.60: 340 104.60 - 113.93: 16864 113.93 - 123.26: 21043 123.26 - 132.59: 1161 132.59 - 141.92: 108 Bond angle restraints: 39516 Sorted by residual: angle pdb=" C PHE B1003 " pdb=" N PRO B1004 " pdb=" CA PRO B1004 " ideal model delta sigma weight residual 119.87 108.20 11.67 1.04e+00 9.25e-01 1.26e+02 angle pdb=" C PHE A1003 " pdb=" N PRO A1004 " pdb=" CA PRO A1004 " ideal model delta sigma weight residual 119.87 108.22 11.65 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE C1003 " pdb=" N PRO C1004 " pdb=" CA PRO C1004 " ideal model delta sigma weight residual 119.87 108.23 11.64 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE D1003 " pdb=" N PRO D1004 " pdb=" CA PRO D1004 " ideal model delta sigma weight residual 119.87 108.25 11.62 1.04e+00 9.25e-01 1.25e+02 angle pdb=" N HIS B 412 " pdb=" CA HIS B 412 " pdb=" C HIS B 412 " ideal model delta sigma weight residual 112.92 99.93 12.99 1.23e+00 6.61e-01 1.12e+02 ... (remaining 39511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.81: 15358 18.81 - 37.62: 1446 37.62 - 56.43: 276 56.43 - 75.25: 52 75.25 - 94.06: 24 Dihedral angle restraints: 17156 sinusoidal: 7088 harmonic: 10068 Sorted by residual: dihedral pdb=" CA SER D 638 " pdb=" C SER D 638 " pdb=" N CYS D 639 " pdb=" CA CYS D 639 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER A 638 " pdb=" C SER A 638 " pdb=" N CYS A 639 " pdb=" CA CYS A 639 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER C 638 " pdb=" C SER C 638 " pdb=" N CYS C 639 " pdb=" CA CYS C 639 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 17153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4117 0.101 - 0.202: 255 0.202 - 0.304: 19 0.304 - 0.405: 5 0.405 - 0.506: 4 Chirality restraints: 4400 Sorted by residual: chirality pdb=" CBI Y01 B1301 " pdb=" CAU Y01 B1301 " pdb=" CBE Y01 B1301 " pdb=" CBG Y01 B1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 D1301 " pdb=" CAU Y01 D1301 " pdb=" CBE Y01 D1301 " pdb=" CBG Y01 D1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 C1301 " pdb=" CAU Y01 C1301 " pdb=" CBE Y01 C1301 " pdb=" CBG Y01 C1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 4397 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 947 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO D 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 947 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO C 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 947 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO A 948 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 948 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 948 " 0.047 5.00e-02 4.00e+02 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 309 2.63 - 3.20: 24548 3.20 - 3.76: 45110 3.76 - 4.33: 65337 4.33 - 4.90: 101779 Nonbonded interactions: 237083 Sorted by model distance: nonbonded pdb=" O TYR D 286 " pdb=" O GLY D 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR C 286 " pdb=" O GLY C 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR A 286 " pdb=" O GLY A 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR B 286 " pdb=" O GLY B 288 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR B 115 " pdb=" OD1 ASP B 116 " model vdw 2.291 2.440 ... (remaining 237078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'B' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'C' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'D' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ } 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 148 5.16 5 Na 8 4.78 5 C 18776 2.51 5 N 4604 2.21 5 O 5028 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.980 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.240 Process input model: 71.700 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.170 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.009 0.357 29236 Z= 0.568 Angle : 1.197 23.439 39516 Z= 0.617 Chirality : 0.059 0.506 4400 Planarity : 0.007 0.084 4816 Dihedral : 15.627 94.057 10604 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.00 % 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: -6.25 (0.08), residues: 3336 helix: -4.15 (0.05), residues: 2240 sheet: -2.60 (0.35), residues: 176 loop : -3.67 (0.15), residues: 920 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 837 time to evaluate : 3.696 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 837 average time/residue: 1.1443 time to fit residues: 1145.1465 Evaluate side-chains 600 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 598 time to evaluate : 3.302 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2910 time to fit residues: 5.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 266 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1070 HIS B 248 HIS B 250 HIS B 297 GLN B 418 ASN B 429 GLN B 491 ASN B 597 ASN B 851 GLN B 987 GLN B1070 HIS C 248 HIS C 250 HIS C 297 GLN C 429 GLN C 491 ASN C 597 ASN C 851 GLN C 987 GLN C1070 HIS D 248 HIS D 250 HIS D 297 GLN D 429 GLN D 491 ASN D 597 ASN D 851 GLN D 987 GLN D1070 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 29236 Z= 0.229 Angle : 0.667 9.591 39516 Z= 0.342 Chirality : 0.042 0.200 4400 Planarity : 0.005 0.059 4816 Dihedral : 9.760 78.783 3936 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 3.81 % 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: -3.68 (0.12), residues: 3336 helix: -1.97 (0.09), residues: 2212 sheet: -2.29 (0.35), residues: 176 loop : -3.18 (0.16), residues: 948 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 687 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 60 residues processed: 735 average time/residue: 1.1153 time to fit residues: 988.1235 Evaluate side-chains 646 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 586 time to evaluate : 3.217 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 19 residues processed: 43 average time/residue: 0.5822 time to fit residues: 39.6784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.1980 chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 309 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 306 optimal weight: 0.9980 chunk 105 optimal weight: 0.0770 chunk 248 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 429 GLN A 597 ASN B 297 GLN C 297 GLN D 297 GLN D 418 ASN D 993 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 29236 Z= 0.192 Angle : 0.603 10.146 39516 Z= 0.309 Chirality : 0.041 0.184 4400 Planarity : 0.004 0.050 4816 Dihedral : 9.148 81.704 3936 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 4.46 % 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: -2.16 (0.13), residues: 3336 helix: -0.73 (0.10), residues: 2232 sheet: -2.02 (0.35), residues: 176 loop : -2.80 (0.18), residues: 928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 654 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 58 residues processed: 716 average time/residue: 1.0877 time to fit residues: 940.8713 Evaluate side-chains 633 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 575 time to evaluate : 3.467 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 29 residues processed: 30 average time/residue: 0.3700 time to fit residues: 22.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 418 ASN A 835 HIS A 993 GLN B 297 GLN B 501 GLN C 190 ASN C 297 GLN C 418 ASN C 501 GLN C 835 HIS D 297 GLN D 501 GLN D 562 GLN D 835 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 29236 Z= 0.259 Angle : 0.627 8.743 39516 Z= 0.322 Chirality : 0.042 0.180 4400 Planarity : 0.004 0.064 4816 Dihedral : 8.981 89.870 3936 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 5.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3336 helix: -0.18 (0.11), residues: 2256 sheet: -1.75 (0.37), residues: 176 loop : -2.58 (0.19), residues: 904 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 676 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 94 residues processed: 761 average time/residue: 1.0509 time to fit residues: 978.7427 Evaluate side-chains 683 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 589 time to evaluate : 3.380 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 49 residues processed: 49 average time/residue: 0.3706 time to fit residues: 34.1949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 250 HIS A 297 GLN A 993 GLN B 297 GLN B 490 ASN B 657 GLN C 297 GLN C 993 GLN D 190 ASN D 297 GLN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 29236 Z= 0.321 Angle : 0.660 9.440 39516 Z= 0.335 Chirality : 0.043 0.177 4400 Planarity : 0.004 0.071 4816 Dihedral : 9.084 89.628 3936 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 5.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3336 helix: 0.05 (0.11), residues: 2272 sheet: -1.66 (0.37), residues: 176 loop : -2.41 (0.20), residues: 888 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 641 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 100 residues processed: 731 average time/residue: 1.1129 time to fit residues: 995.7006 Evaluate side-chains 691 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 591 time to evaluate : 3.305 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 53 residues processed: 47 average time/residue: 0.4360 time to fit residues: 36.5134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 192 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 328 optimal weight: 8.9990 chunk 273 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 108 optimal weight: 0.0770 chunk 172 optimal weight: 0.4980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 987 GLN A 993 GLN B 190 ASN B 297 GLN C 190 ASN C 297 GLN C 987 GLN C 993 GLN D 297 GLN D 562 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 29236 Z= 0.183 Angle : 0.607 8.080 39516 Z= 0.307 Chirality : 0.041 0.188 4400 Planarity : 0.004 0.054 4816 Dihedral : 8.705 89.395 3936 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 4.79 % 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: -0.46 (0.15), residues: 3336 helix: 0.59 (0.11), residues: 2224 sheet: -1.49 (0.38), residues: 176 loop : -2.16 (0.20), residues: 936 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 650 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 70 residues processed: 745 average time/residue: 1.0770 time to fit residues: 977.4386 Evaluate side-chains 659 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 589 time to evaluate : 3.336 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 43 residues processed: 28 average time/residue: 0.3590 time to fit residues: 21.0731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 308 ASN A 550 HIS A 987 GLN B 297 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN C 297 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 851 GLN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN C 993 GLN D 297 GLN D 562 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 29236 Z= 0.379 Angle : 0.706 9.955 39516 Z= 0.358 Chirality : 0.045 0.195 4400 Planarity : 0.005 0.070 4816 Dihedral : 8.885 84.495 3936 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 4.26 % 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: -0.70 (0.15), residues: 3336 helix: 0.39 (0.11), residues: 2232 sheet: -1.49 (0.39), residues: 176 loop : -2.27 (0.20), residues: 928 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 640 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 84 residues processed: 711 average time/residue: 1.0846 time to fit residues: 944.8361 Evaluate side-chains 676 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 592 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 52 residues processed: 36 average time/residue: 0.6097 time to fit residues: 34.8950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 195 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 987 GLN B 297 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN C 297 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN D 297 GLN D 562 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 29236 Z= 0.197 Angle : 0.644 10.257 39516 Z= 0.321 Chirality : 0.041 0.190 4400 Planarity : 0.004 0.056 4816 Dihedral : 8.489 89.997 3936 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 3.35 % 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: -0.31 (0.15), residues: 3336 helix: 0.75 (0.11), residues: 2212 sheet: -1.39 (0.39), residues: 176 loop : -2.21 (0.20), residues: 948 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 631 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 64 residues processed: 703 average time/residue: 1.0084 time to fit residues: 871.6269 Evaluate side-chains 648 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 584 time to evaluate : 3.395 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 48 residues processed: 16 average time/residue: 0.4533 time to fit residues: 15.5758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 133 optimal weight: 0.1980 chunk 239 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 288 optimal weight: 0.5980 chunk 304 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 501 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN C 297 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN D 297 GLN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 29236 Z= 0.225 Angle : 0.662 9.480 39516 Z= 0.331 Chirality : 0.042 0.196 4400 Planarity : 0.004 0.060 4816 Dihedral : 8.292 89.967 3936 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 3.39 % 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: -0.20 (0.15), residues: 3336 helix: 0.85 (0.11), residues: 2224 sheet: -1.46 (0.39), residues: 176 loop : -2.22 (0.20), residues: 936 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 626 time to evaluate : 3.271 Fit side-chains revert: symmetry clash outliers start: 104 outliers final: 78 residues processed: 696 average time/residue: 1.0606 time to fit residues: 908.4630 Evaluate side-chains 671 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 593 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 51 residues processed: 28 average time/residue: 0.4656 time to fit residues: 24.8519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 2.9990 chunk 322 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 224 optimal weight: 0.5980 chunk 338 optimal weight: 0.2980 chunk 311 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 208 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 297 GLN C 993 GLN D 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 29236 Z= 0.213 Angle : 0.680 10.750 39516 Z= 0.337 Chirality : 0.042 0.197 4400 Planarity : 0.004 0.058 4816 Dihedral : 8.090 89.446 3936 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3336 helix: 0.98 (0.11), residues: 2216 sheet: -1.42 (0.38), residues: 176 loop : -2.24 (0.20), residues: 944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 614 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 59 residues processed: 671 average time/residue: 1.1095 time to fit residues: 919.7251 Evaluate side-chains 639 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 580 time to evaluate : 3.061 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 49 residues processed: 10 average time/residue: 0.5265 time to fit residues: 12.2376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.7980 chunk 287 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 270 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 277 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 835 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132671 restraints weight = 36011.659| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.34 r_work: 0.3367 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 29236 Z= 0.212 Angle : 0.687 12.730 39516 Z= 0.340 Chirality : 0.042 0.204 4400 Planarity : 0.004 0.060 4816 Dihedral : 7.905 89.167 3936 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 2.67 % 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: 0.02 (0.15), residues: 3336 helix: 1.07 (0.11), residues: 2212 sheet: -1.43 (0.38), residues: 176 loop : -2.25 (0.20), residues: 948 =============================================================================== Job complete usr+sys time: 12820.91 seconds wall clock time: 227 minutes 18.40 seconds (13638.40 seconds total)