Starting phenix.real_space_refine (version: dev) on Wed Apr 6 16:28:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/04_2022/7kfu_22856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/04_2022/7kfu_22856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/04_2022/7kfu_22856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/04_2022/7kfu_22856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/04_2022/7kfu_22856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/04_2022/7kfu_22856.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 21848 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "C" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 7401 Classifications: {'peptide': 909} Link IDs: {'PTRANS': 33, 'TRANS': 875} Chain breaks: 6 Chain: "D" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "E" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 7401 Classifications: {'peptide': 909} Link IDs: {'PTRANS': 33, 'TRANS': 875} Chain breaks: 6 Chain: "F" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Time building chain proxies: 11.55, per 1000 atoms: 0.53 Number of scatterers: 21848 At special positions: 0 Unit cell: (148.375, 142.44, 179.237, 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 46 16.00 O 3902 8.00 N 3988 7.00 C 13912 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: 8.22 Conformation dependent library (CDL) restraints added in 3.2 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 20 sheets defined 49.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.832A pdb=" N LYS A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.953A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 removed outlier: 3.661A pdb=" N LYS B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.510A pdb=" N ILE B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 41 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 150 removed outlier: 4.004A pdb=" N TRP C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.510A pdb=" N LEU C 227 " --> pdb=" O HIS C 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.542A pdb=" N CYS C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 370 removed outlier: 3.782A pdb=" N THR C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 420 Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 430 through 445 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.646A pdb=" N ASP C 456 " --> pdb=" O ASP C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.798A pdb=" N LEU C 466 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.371A pdb=" N LEU C 515 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 523 removed outlier: 3.546A pdb=" N ASP C 523 " --> pdb=" O ILE C 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 620 through 628 removed outlier: 4.118A pdb=" N ALA C 624 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 709 Processing helix chain 'C' and resid 736 through 746 Processing helix chain 'C' and resid 748 through 771 Processing helix chain 'C' and resid 772 through 773 No H-bonds generated for 'chain 'C' and resid 772 through 773' Processing helix chain 'C' and resid 774 through 780 removed outlier: 3.538A pdb=" N HIS C 777 " --> pdb=" O ARG C 774 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS C 779 " --> pdb=" O ALA C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 796 removed outlier: 3.636A pdb=" N LEU C 785 " --> pdb=" O LEU C 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 817 removed outlier: 4.508A pdb=" N ASN C 805 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY C 806 " --> pdb=" O SER C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 828 removed outlier: 3.737A pdb=" N HIS C 828 " --> pdb=" O GLU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 864 removed outlier: 3.700A pdb=" N VAL C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU C 844 " --> pdb=" O PRO C 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 887 Processing helix chain 'C' and resid 896 through 904 Processing helix chain 'C' and resid 927 through 944 Processing helix chain 'C' and resid 951 through 968 removed outlier: 4.033A pdb=" N GLN C 957 " --> pdb=" O GLN C 953 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 709 Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 748 through 773 removed outlier: 3.710A pdb=" N VAL D 760 " --> pdb=" O ALA D 756 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 771 " --> pdb=" O GLN D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR D 784 " --> pdb=" O GLN D 780 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 817 removed outlier: 3.525A pdb=" N LEU D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 822 Processing helix chain 'D' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 891 through 904 removed outlier: 3.816A pdb=" N GLU D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 927 through 944 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'E' and resid 28 through 41 Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 150 removed outlier: 4.003A pdb=" N TRP E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR E 184 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.509A pdb=" N LEU E 227 " --> pdb=" O HIS E 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 331 removed outlier: 3.543A pdb=" N CYS E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 370 removed outlier: 3.783A pdb=" N THR E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 420 Proline residue: E 412 - end of helix Processing helix chain 'E' and resid 430 through 445 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.647A pdb=" N ASP E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 474 removed outlier: 3.798A pdb=" N LEU E 466 " --> pdb=" O TYR E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN E 482 " --> pdb=" O PRO E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 4.372A pdb=" N LEU E 515 " --> pdb=" O PRO E 511 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 518 " --> pdb=" O PRO E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 523 removed outlier: 3.545A pdb=" N ASP E 523 " --> pdb=" O ILE E 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 520 through 523' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'E' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN E 553 " --> pdb=" O GLN E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 587 Processing helix chain 'E' and resid 620 through 628 removed outlier: 4.119A pdb=" N ALA E 624 " --> pdb=" O PRO E 620 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN E 625 " --> pdb=" O PRO E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 709 Processing helix chain 'E' and resid 736 through 746 Processing helix chain 'E' and resid 748 through 771 Processing helix chain 'E' and resid 772 through 773 No H-bonds generated for 'chain 'E' and resid 772 through 773' Processing helix chain 'E' and resid 774 through 780 removed outlier: 3.539A pdb=" N HIS E 777 " --> pdb=" O ARG E 774 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS E 779 " --> pdb=" O ALA E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 796 removed outlier: 3.635A pdb=" N LEU E 785 " --> pdb=" O LEU E 781 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 796 " --> pdb=" O GLN E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 817 removed outlier: 4.509A pdb=" N ASN E 805 " --> pdb=" O ARG E 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY E 806 " --> pdb=" O SER E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 828 removed outlier: 3.737A pdb=" N HIS E 828 " --> pdb=" O GLU E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 864 removed outlier: 3.699A pdb=" N VAL E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU E 844 " --> pdb=" O PRO E 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 845 " --> pdb=" O PHE E 841 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR E 850 " --> pdb=" O SER E 846 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 851 " --> pdb=" O LEU E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 887 Processing helix chain 'E' and resid 896 through 904 Processing helix chain 'E' and resid 927 through 944 Processing helix chain 'E' and resid 951 through 968 removed outlier: 4.032A pdb=" N GLN E 957 " --> pdb=" O GLN E 953 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 709 Processing helix chain 'F' and resid 728 through 733 Processing helix chain 'F' and resid 739 through 746 Processing helix chain 'F' and resid 748 through 773 removed outlier: 3.710A pdb=" N VAL F 760 " --> pdb=" O ALA F 756 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU F 771 " --> pdb=" O GLN F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN F 783 " --> pdb=" O LYS F 779 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR F 784 " --> pdb=" O GLN F 780 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 800 through 817 removed outlier: 3.524A pdb=" N LEU F 804 " --> pdb=" O LYS F 800 " (cutoff:3.500A) Processing helix chain 'F' and resid 818 through 822 Processing helix chain 'F' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 863 " --> pdb=" O ILE F 859 " (cutoff:3.500A) Processing helix chain 'F' and resid 880 through 887 Processing helix chain 'F' and resid 891 through 904 removed outlier: 3.814A pdb=" N GLU F 895 " --> pdb=" O ARG F 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 908 through 910 No H-bonds generated for 'chain 'F' and resid 908 through 910' Processing helix chain 'F' and resid 927 through 944 Processing helix chain 'F' and resid 950 through 969 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.486A pdb=" N ARG A 29 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU A 36 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 31 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 34 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 68 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 80 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.560A pdb=" N HIS A 80 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS B 3 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA4, first strand: chain 'C' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE C 236 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 268 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS C 238 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY C 263 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 161 " --> pdb=" O LYS C 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.508A pdb=" N HIS C 492 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 580 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 533 through 538 removed outlier: 4.111A pdb=" N ILE C 544 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 652 through 656 removed outlier: 6.986A pdb=" N THR C 652 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL C 690 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU C 654 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 692 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU C 656 " --> pdb=" O LEU C 692 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 713 " --> pdb=" O VAL C 726 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 724 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 724 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N HIS F 714 " --> pdb=" O HIS F 688 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 690 " --> pdb=" O HIS F 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA F 716 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU F 692 " --> pdb=" O ALA F 716 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR F 652 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA F 689 " --> pdb=" O THR F 652 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL C 672 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS C 681 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU C 670 " --> pdb=" O LYS C 681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 912 through 916 Processing sheet with id=AB1, first strand: chain 'D' and resid 652 through 656 removed outlier: 5.724A pdb=" N THR D 652 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 689 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N HIS D 714 " --> pdb=" O HIS D 688 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 690 " --> pdb=" O HIS D 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA D 716 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 692 " --> pdb=" O ALA D 716 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 724 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 724 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 713 " --> pdb=" O VAL E 726 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR E 652 " --> pdb=" O HIS E 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL E 690 " --> pdb=" O THR E 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 654 " --> pdb=" O VAL E 690 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU E 692 " --> pdb=" O LEU E 654 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU E 656 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 674 " --> pdb=" O ILE D 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 912 through 916 Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 53 Processing sheet with id=AB5, first strand: chain 'E' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE E 236 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER E 268 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS E 238 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY E 263 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN E 161 " --> pdb=" O LYS E 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 391 through 394 removed outlier: 3.508A pdb=" N HIS E 492 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 580 " --> pdb=" O GLU E 499 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 533 through 538 removed outlier: 4.111A pdb=" N ILE E 544 " --> pdb=" O TYR E 450 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL E 672 " --> pdb=" O THR E 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 681 " --> pdb=" O LEU E 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU E 670 " --> pdb=" O LYS E 681 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 912 through 916 Processing sheet with id=AC1, first strand: chain 'F' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE F 678 " --> pdb=" O LYS F 674 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS F 674 " --> pdb=" O ILE F 678 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 912 through 916 1021 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6774 1.34 - 1.45: 3211 1.45 - 1.57: 12265 1.57 - 1.69: 2 1.69 - 1.81: 80 Bond restraints: 22332 Sorted by residual: bond pdb=" N GLN A 89 " pdb=" CA GLN A 89 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.23e-02 6.61e+03 6.07e+00 bond pdb=" CB VAL C 713 " pdb=" CG1 VAL C 713 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 bond pdb=" CB VAL E 713 " pdb=" CG1 VAL E 713 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.12e+00 bond pdb=" CB VAL E 690 " pdb=" CG1 VAL E 690 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB LYS C 346 " pdb=" CG LYS C 346 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.35e+00 ... (remaining 22327 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.43: 346 105.43 - 112.60: 11681 112.60 - 119.77: 7413 119.77 - 126.94: 10390 126.94 - 134.11: 344 Bond angle restraints: 30174 Sorted by residual: angle pdb=" C GLU C 979 " pdb=" N LEU C 980 " pdb=" CA LEU C 980 " ideal model delta sigma weight residual 120.82 126.61 -5.79 1.47e+00 4.63e-01 1.55e+01 angle pdb=" C GLU E 979 " pdb=" N LEU E 980 " pdb=" CA LEU E 980 " ideal model delta sigma weight residual 120.82 126.57 -5.75 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C ASP D 666 " pdb=" N ASN D 667 " pdb=" CA ASN D 667 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C ASP F 666 " pdb=" N ASN F 667 " pdb=" CA ASN F 667 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N LEU C 919 " pdb=" CA LEU C 919 " pdb=" C LEU C 919 " ideal model delta sigma weight residual 114.75 109.96 4.79 1.26e+00 6.30e-01 1.45e+01 ... (remaining 30169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 12009 17.86 - 35.72: 1199 35.72 - 53.59: 195 53.59 - 71.45: 41 71.45 - 89.31: 10 Dihedral angle restraints: 13454 sinusoidal: 5606 harmonic: 7848 Sorted by residual: dihedral pdb=" CA ARG C 891 " pdb=" C ARG C 891 " pdb=" N HIS C 892 " pdb=" CA HIS C 892 " ideal model delta harmonic sigma weight residual 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG E 891 " pdb=" C ARG E 891 " pdb=" N HIS E 892 " pdb=" CA HIS E 892 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG D 835 " pdb=" C ARG D 835 " pdb=" N PRO D 836 " pdb=" CA PRO D 836 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2734 0.064 - 0.129: 517 0.129 - 0.193: 58 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CB ILE A 66 " pdb=" CA ILE A 66 " pdb=" CG1 ILE A 66 " pdb=" CG2 ILE A 66 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CG LEU C 36 " pdb=" CB LEU C 36 " pdb=" CD1 LEU C 36 " pdb=" CD2 LEU C 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU E 36 " pdb=" CB LEU E 36 " pdb=" CD1 LEU E 36 " pdb=" CD2 LEU E 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3309 not shown) Planarity restraints: 3870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 41 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO A 42 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 42 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 42 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 477 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.67e+00 pdb=" N PRO C 478 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 477 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO E 478 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 478 " -0.036 5.00e-02 4.00e+02 ... (remaining 3867 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 6 2.22 - 2.89: 7834 2.89 - 3.56: 28885 3.56 - 4.23: 45548 4.23 - 4.90: 82294 Nonbonded interactions: 164567 Sorted by model distance: nonbonded pdb=" CE1 TYR A 50 " pdb=" CG GLN E 554 " model vdw 1.548 3.740 nonbonded pdb=" CD1 TYR A 50 " pdb=" CG GLN E 554 " model vdw 1.892 3.740 nonbonded pdb=" NZ LYS A 25 " pdb=" OE1 GLN C 668 " model vdw 1.909 2.520 nonbonded pdb=" O LEU D 723 " pdb=" OG SER E 728 " model vdw 2.124 2.440 nonbonded pdb=" OD1 ASN A 65 " pdb=" NE2 GLN B 31 " model vdw 2.185 2.520 ... (remaining 164562 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 46 5.16 5 C 13912 2.51 5 N 3988 2.21 5 O 3902 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 group one per residue 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: 7.060 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: 15.230 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.200 Process input model: 55.930 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 : 0.006 0.076 22332 Z= 0.364 Angle : 0.829 8.962 30174 Z= 0.471 Chirality : 0.050 0.322 3312 Planarity : 0.006 0.068 3870 Dihedral : 14.440 89.310 8362 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % 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: -1.04 (0.15), residues: 2638 helix: 0.28 (0.15), residues: 1192 sheet: -0.22 (0.31), residues: 280 loop : -1.86 (0.16), residues: 1166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.4065 time to fit residues: 299.0638 Evaluate side-chains 201 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.6980 chunk 200 optimal weight: 0.0060 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 0.0050 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 83 ASN A 89 GLN B 54 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 447 HIS C 653 HIS C 730 GLN C 734 ASN C 767 GLN C 817 GLN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 554 GLN E 973 GLN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 767 GLN ** F 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 969 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 22332 Z= 0.206 Angle : 0.628 8.283 30174 Z= 0.329 Chirality : 0.044 0.215 3312 Planarity : 0.006 0.114 3870 Dihedral : 4.881 21.179 2910 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 1.99 % 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: -0.21 (0.16), residues: 2638 helix: 1.07 (0.15), residues: 1202 sheet: 0.01 (0.32), residues: 274 loop : -1.50 (0.17), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 33 residues processed: 256 average time/residue: 0.4018 time to fit residues: 161.8370 Evaluate side-chains 208 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2339 time to fit residues: 17.2340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 89 GLN B 12 HIS C 91 HIS C 576 HIS C 667 ASN C 855 HIS C 953 GLN C 973 GLN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 668 GLN E 334 HIS E 518 ASN E 842 ASN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 921 GLN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 714 HIS F 817 GLN F 952 HIS ** F 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 22332 Z= 0.389 Angle : 0.708 12.433 30174 Z= 0.376 Chirality : 0.048 0.220 3312 Planarity : 0.005 0.084 3870 Dihedral : 5.088 20.961 2910 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 1.61 % 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: -0.23 (0.16), residues: 2638 helix: 1.07 (0.15), residues: 1192 sheet: 0.09 (0.31), residues: 300 loop : -1.56 (0.17), residues: 1146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 220 average time/residue: 0.3454 time to fit residues: 119.9879 Evaluate side-chains 189 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 2.840 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2000 time to fit residues: 10.0601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 228 optimal weight: 0.0970 chunk 68 optimal weight: 0.7980 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 54 GLN C 334 HIS C 632 GLN C 667 ASN C 730 GLN C 734 ASN ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 22332 Z= 0.180 Angle : 0.593 10.845 30174 Z= 0.307 Chirality : 0.043 0.212 3312 Planarity : 0.005 0.105 3870 Dihedral : 4.664 20.620 2910 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.36 % 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 (0.17), residues: 2638 helix: 1.54 (0.16), residues: 1192 sheet: -0.00 (0.30), residues: 308 loop : -1.40 (0.18), residues: 1138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 227 average time/residue: 0.3365 time to fit residues: 120.9943 Evaluate side-chains 186 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 2.771 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2106 time to fit residues: 10.0488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 217 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 229 optimal weight: 0.5980 chunk 64 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 54 GLN C 86 HIS C 561 GLN C 953 GLN ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** E 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.134 22332 Z= 0.182 Angle : 0.566 9.373 30174 Z= 0.296 Chirality : 0.042 0.187 3312 Planarity : 0.005 0.112 3870 Dihedral : 4.496 22.169 2910 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 1.53 % 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: 0.36 (0.17), residues: 2638 helix: 1.68 (0.16), residues: 1188 sheet: -0.02 (0.30), residues: 310 loop : -1.28 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 222 average time/residue: 0.3377 time to fit residues: 119.7345 Evaluate side-chains 181 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2019 time to fit residues: 9.0237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 134 optimal weight: 0.5980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 HIS C 961 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.207 22332 Z= 0.211 Angle : 0.575 12.815 30174 Z= 0.303 Chirality : 0.042 0.221 3312 Planarity : 0.005 0.112 3870 Dihedral : 4.410 20.837 2910 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.06 % 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: 0.43 (0.17), residues: 2638 helix: 1.76 (0.16), residues: 1188 sheet: -0.04 (0.30), residues: 310 loop : -1.25 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 196 average time/residue: 0.3456 time to fit residues: 107.6235 Evaluate side-chains 168 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 2.723 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2131 time to fit residues: 7.9944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 145 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN C 86 HIS C 667 ASN C 953 GLN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 873 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.317 22332 Z= 0.242 Angle : 0.596 19.578 30174 Z= 0.317 Chirality : 0.043 0.289 3312 Planarity : 0.004 0.089 3870 Dihedral : 4.433 21.435 2910 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.06 % 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: 0.40 (0.17), residues: 2638 helix: 1.74 (0.16), residues: 1188 sheet: -0.12 (0.31), residues: 310 loop : -1.25 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 181 average time/residue: 0.3586 time to fit residues: 103.1737 Evaluate side-chains 169 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2550 time to fit residues: 8.3127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.161 22332 Z= 0.595 Angle : 0.868 106.100 30174 Z= 0.379 Chirality : 0.043 0.277 3312 Planarity : 0.005 0.087 3870 Dihedral : 4.436 21.495 2910 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.04 % 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: 0.36 (0.17), residues: 2638 helix: 1.70 (0.15), residues: 1188 sheet: -0.15 (0.31), residues: 310 loop : -1.25 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 167 average time/residue: 0.3524 time to fit residues: 94.4578 Evaluate side-chains 157 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3484 time to fit residues: 5.4197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 89 GLN C 86 HIS C 953 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.032 22332 Z= 0.554 Angle : 0.862 102.189 30174 Z= 0.384 Chirality : 0.044 0.294 3312 Planarity : 0.004 0.080 3870 Dihedral : 4.517 21.464 2910 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.04 % 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: 0.30 (0.17), residues: 2638 helix: 1.65 (0.16), residues: 1188 sheet: -0.20 (0.31), residues: 310 loop : -1.28 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 172 average time/residue: 0.3450 time to fit residues: 94.8241 Evaluate side-chains 162 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 2.949 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2783 time to fit residues: 7.9886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.0970 chunk 153 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 242 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.026 22332 Z= 0.553 Angle : 0.882 106.071 30174 Z= 0.397 Chirality : 0.044 0.444 3312 Planarity : 0.005 0.123 3870 Dihedral : 4.519 21.324 2910 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.04 % 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: 0.30 (0.17), residues: 2638 helix: 1.65 (0.16), residues: 1188 sheet: -0.20 (0.31), residues: 310 loop : -1.29 (0.18), residues: 1140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 156 average time/residue: 0.4239 time to fit residues: 106.6832 Evaluate side-chains 153 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2237 time to fit residues: 4.5785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 193 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.156052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123385 restraints weight = 53277.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.119923 restraints weight = 48231.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119359 restraints weight = 44184.089| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.026 22332 Z= 0.553 Angle : 0.882 106.099 30174 Z= 0.397 Chirality : 0.044 0.445 3312 Planarity : 0.005 0.122 3870 Dihedral : 4.519 21.325 2910 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % 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: 0.30 (0.17), residues: 2638 helix: 1.65 (0.16), residues: 1188 sheet: -0.20 (0.31), residues: 310 loop : -1.29 (0.18), residues: 1140 =============================================================================== Job complete usr+sys time: 3760.41 seconds wall clock time: 70 minutes 30.18 seconds (4230.18 seconds total)