Starting phenix.real_space_refine (version: dev) on Tue May 17 11:31:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/05_2022/6tqh_10551_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/05_2022/6tqh_10551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/05_2022/6tqh_10551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/05_2022/6tqh_10551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/05_2022/6tqh_10551_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/05_2022/6tqh_10551_trim_updated.pdb" } resolution = 3.4 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= 0.002 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 PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 39677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "F" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6486 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "C" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6487 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "B" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' FE': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' FE': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 18.04, per 1000 atoms: 0.45 Number of scatterers: 39677 At special positions: 0 Unit cell: (120.91, 116.39, 142.38, 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) Fe 2 26.01 S 92 16.00 P 8 15.00 O 3778 8.00 N 3384 7.00 C 12620 6.00 H 19793 1.00 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: 34.34 Conformation dependent library (CDL) restraints added in 3.7 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 8 sheets defined 43.6% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 6 through 23 removed outlier: 3.934A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 43 removed outlier: 4.255A pdb=" N ILE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.690A pdb=" N ALA A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 80 removed outlier: 4.078A pdb=" N ILE A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.512A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 removed outlier: 3.644A pdb=" N LYS A 143 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 147 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 149 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP A 151 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 154 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN A 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 158 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.034A pdb=" N SER A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 256 through 268 removed outlier: 5.715A pdb=" N ASP A 260 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.585A pdb=" N VAL A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.559A pdb=" N GLU A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 349 through 363 removed outlier: 3.675A pdb=" N LYS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.944A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 503 removed outlier: 4.837A pdb=" N VAL A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.535A pdb=" N LEU A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 4.254A pdb=" N LYS A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 560 " --> pdb=" O TRP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 644 through 662 removed outlier: 3.864A pdb=" N THR A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 661 " --> pdb=" O HIS A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 679 removed outlier: 3.608A pdb=" N LEU A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 693 through 714 Proline residue: A 697 - end of helix removed outlier: 3.717A pdb=" N GLU A 701 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 703 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 707 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 710 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 729 removed outlier: 4.394A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 745 through 752 removed outlier: 5.427A pdb=" N ARG A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 774 No H-bonds generated for 'chain 'A' and resid 771 through 774' Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 793 through 807 Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 822 through 825 No H-bonds generated for 'chain 'A' and resid 822 through 825' Processing helix chain 'A' and resid 830 through 837 removed outlier: 3.569A pdb=" N GLU A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 851 through 854 No H-bonds generated for 'chain 'A' and resid 851 through 854' Processing helix chain 'A' and resid 856 through 862 removed outlier: 4.226A pdb=" N THR A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 471 No H-bonds generated for 'chain 'F' and resid 468 through 471' Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 500 through 504 Processing helix chain 'F' and resid 522 through 535 Processing helix chain 'F' and resid 549 through 560 removed outlier: 4.515A pdb=" N ILE F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 568 No H-bonds generated for 'chain 'F' and resid 566 through 568' Processing helix chain 'F' and resid 625 through 627 No H-bonds generated for 'chain 'F' and resid 625 through 627' Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 644 through 659 removed outlier: 3.859A pdb=" N PHE F 649 " --> pdb=" O SER F 645 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL F 655 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 656 " --> pdb=" O LEU F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 671 No H-bonds generated for 'chain 'F' and resid 669 through 671' Processing helix chain 'F' and resid 673 through 680 Processing helix chain 'F' and resid 686 through 691 Processing helix chain 'F' and resid 693 through 714 Proline residue: F 697 - end of helix removed outlier: 4.725A pdb=" N VAL F 703 " --> pdb=" O ARG F 700 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA F 707 " --> pdb=" O HIS F 704 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA F 710 " --> pdb=" O ALA F 707 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE F 714 " --> pdb=" O GLY F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 731 Processing helix chain 'F' and resid 737 through 752 removed outlier: 3.604A pdb=" N LEU F 743 " --> pdb=" O LEU F 739 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F 744 " --> pdb=" O ALA F 740 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS F 746 " --> pdb=" O ALA F 742 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN F 747 " --> pdb=" O LEU F 743 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG F 750 " --> pdb=" O CYS F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 782 removed outlier: 4.190A pdb=" N ALA F 776 " --> pdb=" O ARG F 772 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 779 " --> pdb=" O TYR F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 806 Processing helix chain 'F' and resid 816 through 818 No H-bonds generated for 'chain 'F' and resid 816 through 818' Processing helix chain 'F' and resid 822 through 826 Processing helix chain 'F' and resid 829 through 836 Processing helix chain 'F' and resid 840 through 844 Processing helix chain 'F' and resid 851 through 862 removed outlier: 3.693A pdb=" N LYS F 855 " --> pdb=" O ILE F 851 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE F 857 " --> pdb=" O GLU F 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 471 No H-bonds generated for 'chain 'C' and resid 468 through 471' Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 500 through 504 Processing helix chain 'C' and resid 522 through 535 Processing helix chain 'C' and resid 549 through 560 removed outlier: 4.515A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 625 through 627 No H-bonds generated for 'chain 'C' and resid 625 through 627' Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 644 through 659 removed outlier: 3.859A pdb=" N PHE C 649 " --> pdb=" O SER C 645 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 671 No H-bonds generated for 'chain 'C' and resid 669 through 671' Processing helix chain 'C' and resid 673 through 680 Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 693 through 714 Proline residue: C 697 - end of helix removed outlier: 4.725A pdb=" N VAL C 703 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA C 707 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 710 " --> pdb=" O ALA C 707 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 714 " --> pdb=" O GLY C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 731 Processing helix chain 'C' and resid 737 through 752 removed outlier: 3.604A pdb=" N LEU C 743 " --> pdb=" O LEU C 739 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS C 746 " --> pdb=" O ALA C 742 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG C 750 " --> pdb=" O CYS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 782 removed outlier: 4.189A pdb=" N ALA C 776 " --> pdb=" O ARG C 772 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 779 " --> pdb=" O TYR C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 806 Processing helix chain 'C' and resid 816 through 818 No H-bonds generated for 'chain 'C' and resid 816 through 818' Processing helix chain 'C' and resid 822 through 826 Processing helix chain 'C' and resid 829 through 836 Processing helix chain 'C' and resid 840 through 844 Processing helix chain 'C' and resid 851 through 862 removed outlier: 3.693A pdb=" N LYS C 855 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 23 removed outlier: 3.934A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 43 removed outlier: 4.254A pdb=" N ILE B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.689A pdb=" N ALA B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 80 removed outlier: 4.079A pdb=" N ILE B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.511A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.644A pdb=" N LYS B 143 " --> pdb=" O PRO B 140 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 146 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 147 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 149 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP B 151 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 154 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN B 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE B 158 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 159 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 199 through 205 removed outlier: 4.034A pdb=" N SER B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 256 through 268 removed outlier: 5.716A pdb=" N ASP B 260 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 266 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 268 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.586A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.559A pdb=" N GLU B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.676A pdb=" N LYS B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.945A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 503 removed outlier: 4.837A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.535A pdb=" N LEU B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 4.253A pdb=" N LYS B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 560 " --> pdb=" O TRP B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 569 No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 644 through 662 removed outlier: 3.864A pdb=" N THR B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 661 " --> pdb=" O HIS B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 679 removed outlier: 3.608A pdb=" N LEU B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 693 through 714 Proline residue: B 697 - end of helix removed outlier: 3.718A pdb=" N GLU B 701 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 703 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 707 " --> pdb=" O HIS B 704 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 710 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 729 removed outlier: 4.395A pdb=" N LYS B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 745 through 752 removed outlier: 5.427A pdb=" N ARG B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 774 No H-bonds generated for 'chain 'B' and resid 771 through 774' Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 793 through 807 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 822 through 825 No H-bonds generated for 'chain 'B' and resid 822 through 825' Processing helix chain 'B' and resid 830 through 837 removed outlier: 3.568A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 851 through 854 No H-bonds generated for 'chain 'B' and resid 851 through 854' Processing helix chain 'B' and resid 856 through 862 removed outlier: 4.227A pdb=" N THR B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 97 through 99 removed outlier: 3.521A pdb=" N ILE A 98 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.346A pdb=" N ILE A 135 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 394 through 396 removed outlier: 6.826A pdb=" N SER A 369 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 251 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 221 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 253 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL A 252 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA A 342 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 254 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR A 344 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 319 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET A 343 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY A 321 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ARG A 345 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 509 through 513 removed outlier: 6.452A pdb=" N VAL F 539 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL F 485 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE F 541 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS F 591 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA F 542 " --> pdb=" O LYS F 591 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 593 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET F 631 " --> pdb=" O ALA F 594 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 509 through 513 removed outlier: 6.453A pdb=" N VAL C 539 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL C 485 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 541 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 591 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 542 " --> pdb=" O LYS C 591 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 593 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET C 631 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.522A pdb=" N ILE B 98 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.345A pdb=" N ILE B 135 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 394 through 396 removed outlier: 6.826A pdb=" N SER B 369 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER B 251 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE B 221 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 253 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL B 252 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 342 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 254 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR B 344 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 319 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET B 343 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B 321 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG B 345 " --> pdb=" O GLY B 321 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1278 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: 15.11 Time building geometry restraints manager: 35.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 19767 1.02 - 1.21: 30 1.21 - 1.41: 8227 1.41 - 1.61: 11899 1.61 - 1.81: 166 Bond restraints: 40089 Sorted by residual: bond pdb=" C ARG B 865 " pdb=" N ASP B 866 " ideal model delta sigma weight residual 1.331 1.554 -0.223 1.38e-02 5.25e+03 2.60e+02 bond pdb=" C ARG A 865 " pdb=" N ASP A 866 " ideal model delta sigma weight residual 1.331 1.553 -0.222 1.38e-02 5.25e+03 2.59e+02 bond pdb=" O5D NAD B 901 " pdb=" PN NAD B 901 " ideal model delta sigma weight residual 1.637 1.777 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O5D NAD A 902 " pdb=" PN NAD A 902 " ideal model delta sigma weight residual 1.637 1.776 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O5D NAD A 901 " pdb=" PN NAD A 901 " ideal model delta sigma weight residual 1.637 1.772 -0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 40084 not shown) Histogram of bond angle deviations from ideal: 72.24 - 84.84: 18 84.84 - 97.44: 13 97.44 - 110.04: 34138 110.04 - 122.64: 33168 122.64 - 135.24: 5311 Bond angle restraints: 72648 Sorted by residual: angle pdb=" CG2 THR B 27 " pdb=" CB THR B 27 " pdb=" HB THR B 27 " ideal model delta sigma weight residual 108.00 72.24 35.76 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CG2 THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 108.00 73.55 34.45 3.00e+00 1.11e-01 1.32e+02 angle pdb=" OG1 THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 109.00 75.81 33.19 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CA THR B 27 " pdb=" CB THR B 27 " pdb=" HB THR B 27 " ideal model delta sigma weight residual 109.00 77.12 31.88 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CA THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 109.00 77.61 31.39 3.00e+00 1.11e-01 1.10e+02 ... (remaining 72643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14355 17.98 - 35.96: 1304 35.96 - 53.94: 197 53.94 - 71.92: 63 71.92 - 89.90: 8 Dihedral angle restraints: 15927 sinusoidal: 7332 harmonic: 8595 Sorted by residual: dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N LEU A 417 " pdb=" CA LEU A 417 " ideal model delta harmonic sigma weight residual 180.00 147.04 32.96 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA SER B 416 " pdb=" C SER B 416 " pdb=" N LEU B 417 " pdb=" CA LEU B 417 " ideal model delta harmonic sigma weight residual 180.00 147.10 32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ILE A 405 " pdb=" C ILE A 405 " pdb=" N GLY A 406 " pdb=" CA GLY A 406 " ideal model delta harmonic sigma weight residual 180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 15924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3023 0.109 - 0.217: 109 0.217 - 0.326: 10 0.326 - 0.435: 0 0.435 - 0.544: 4 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CB THR A 27 " pdb=" CA THR A 27 " pdb=" OG1 THR A 27 " pdb=" CG2 THR A 27 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CB THR B 27 " pdb=" CA THR B 27 " pdb=" OG1 THR B 27 " pdb=" CG2 THR B 27 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CB THR B 616 " pdb=" CA THR B 616 " pdb=" OG1 THR B 616 " pdb=" CG2 THR B 616 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.32e+00 ... (remaining 3143 not shown) Planarity restraints: 5992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 628 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 629 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 629 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 629 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 628 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 629 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 629 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 629 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.038 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 112 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.031 5.00e-02 4.00e+02 ... (remaining 5989 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 214 1.83 - 2.52: 37628 2.52 - 3.21: 125395 3.21 - 3.91: 164041 3.91 - 4.60: 272436 Nonbonded interactions: 599714 Sorted by model distance: nonbonded pdb=" HE1 HIS A 737 " pdb="FE FE A 903 " model vdw 1.137 1.790 nonbonded pdb=" HE1 HIS B 737 " pdb="FE FE B 903 " model vdw 1.140 1.790 nonbonded pdb="HH12 ARG A 579 " pdb=" O TYR A 581 " model vdw 1.465 1.850 nonbonded pdb="HH12 ARG B 579 " pdb=" O TYR B 581 " model vdw 1.466 1.850 nonbonded pdb=" O GLU A 63 " pdb=" HH TYR B 848 " model vdw 1.509 1.850 ... (remaining 599709 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 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 71 through 869 or resid 901 through 903)) selection = (chain 'B' and (resid 1 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name HA2 or name HA3)) or resid 435 through 869 or resid 901 thr \ ough 903)) } ncs_group { reference = (chain 'C' and (resid 451 through 715 or (resid 716 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name \ HB2 or name HB3 or name HD21 or name HD22)) or resid 717 through 869)) 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 8 5.49 5 S 92 5.16 5 C 12620 2.51 5 N 3384 2.21 5 O 3778 1.98 5 H 19793 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.070 Extract box with map and model: 7.530 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.340 Process input model: 119.730 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.223 20296 Z= 0.850 Angle : 0.924 15.110 27558 Z= 0.455 Chirality : 0.057 0.544 3146 Planarity : 0.005 0.065 3542 Dihedral : 13.906 89.897 7380 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.51 (0.11), residues: 2568 helix: -4.81 (0.06), residues: 1254 sheet: -3.96 (0.21), residues: 332 loop : -3.39 (0.16), residues: 982 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 320 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 344 average time/residue: 0.8012 time to fit residues: 409.9196 Evaluate side-chains 181 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 3.226 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4185 time to fit residues: 11.7460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 155 GLN A 677 GLN A 754 ASN ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 479 HIS B 752 ASN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 20296 Z= 0.176 Angle : 0.591 10.966 27558 Z= 0.304 Chirality : 0.054 1.424 3146 Planarity : 0.005 0.064 3542 Dihedral : 6.232 73.731 2782 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.68 % 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: -4.95 (0.13), residues: 2568 helix: -3.58 (0.09), residues: 1280 sheet: -3.49 (0.23), residues: 320 loop : -2.40 (0.19), residues: 968 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 202 average time/residue: 0.7431 time to fit residues: 239.9509 Evaluate side-chains 169 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5093 time to fit residues: 11.4629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 716 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 ASN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 20296 Z= 0.314 Angle : 0.610 11.013 27558 Z= 0.317 Chirality : 0.054 1.396 3146 Planarity : 0.004 0.068 3542 Dihedral : 5.833 77.041 2782 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.34 % 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: -3.58 (0.15), residues: 2568 helix: -2.33 (0.12), residues: 1280 sheet: -3.17 (0.25), residues: 330 loop : -1.78 (0.21), residues: 958 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 163 average time/residue: 0.7090 time to fit residues: 182.6524 Evaluate side-chains 152 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 3.327 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5012 time to fit residues: 8.5467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 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 716 ASN ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20296 Z= 0.222 Angle : 0.544 11.064 27558 Z= 0.279 Chirality : 0.054 1.426 3146 Planarity : 0.004 0.051 3542 Dihedral : 5.621 74.144 2782 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.63 % 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: -2.82 (0.16), residues: 2568 helix: -1.64 (0.13), residues: 1272 sheet: -3.01 (0.26), residues: 334 loop : -1.42 (0.22), residues: 962 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 166 average time/residue: 0.7223 time to fit residues: 188.6407 Evaluate side-chains 144 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 3.188 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4801 time to fit residues: 10.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 20296 Z= 0.289 Angle : 0.570 11.034 27558 Z= 0.294 Chirality : 0.054 1.412 3146 Planarity : 0.004 0.056 3542 Dihedral : 5.556 76.627 2782 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.87 % 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: -2.34 (0.17), residues: 2568 helix: -1.22 (0.14), residues: 1278 sheet: -2.94 (0.26), residues: 334 loop : -1.16 (0.22), residues: 956 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.6854 time to fit residues: 164.9454 Evaluate side-chains 138 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 3.201 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.4805 time to fit residues: 12.6712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 144 optimal weight: 0.0060 chunk 60 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 0.0370 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 129 optimal weight: 0.9980 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN F 618 GLN ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 20296 Z= 0.128 Angle : 0.502 11.063 27558 Z= 0.255 Chirality : 0.053 1.425 3146 Planarity : 0.004 0.050 3542 Dihedral : 5.268 77.615 2782 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.39 % 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: -1.81 (0.17), residues: 2568 helix: -0.78 (0.15), residues: 1280 sheet: -2.77 (0.27), residues: 338 loop : -0.86 (0.23), residues: 950 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 153 average time/residue: 0.7072 time to fit residues: 172.7629 Evaluate side-chains 131 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 3.118 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.7334 time to fit residues: 9.5448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 20296 Z= 0.282 Angle : 0.554 11.083 27558 Z= 0.286 Chirality : 0.054 1.416 3146 Planarity : 0.004 0.047 3542 Dihedral : 5.317 77.108 2782 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.39 % 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: -1.71 (0.17), residues: 2568 helix: -0.66 (0.15), residues: 1278 sheet: -2.80 (0.26), residues: 340 loop : -0.84 (0.23), residues: 950 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 136 average time/residue: 0.6990 time to fit residues: 153.1245 Evaluate side-chains 127 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 3.135 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.4919 time to fit residues: 8.2490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 20296 Z= 0.188 Angle : 0.516 11.108 27558 Z= 0.263 Chirality : 0.053 1.429 3146 Planarity : 0.004 0.046 3542 Dihedral : 5.194 78.219 2782 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 0.34 % 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: -1.49 (0.17), residues: 2568 helix: -0.48 (0.15), residues: 1290 sheet: -2.72 (0.27), residues: 340 loop : -0.73 (0.23), residues: 938 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 137 average time/residue: 0.6833 time to fit residues: 152.1521 Evaluate side-chains 122 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 3.084 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4931 time to fit residues: 5.5672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 20296 Z= 0.144 Angle : 0.503 11.121 27558 Z= 0.255 Chirality : 0.053 1.430 3146 Planarity : 0.004 0.069 3542 Dihedral : 5.026 77.917 2782 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.14 % 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: -1.18 (0.18), residues: 2568 helix: -0.22 (0.15), residues: 1288 sheet: -2.61 (0.27), residues: 340 loop : -0.58 (0.23), residues: 940 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 133 average time/residue: 0.6960 time to fit residues: 149.5562 Evaluate side-chains 126 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 3.112 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.4627 time to fit residues: 6.4769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 20296 Z= 0.235 Angle : 0.532 11.151 27558 Z= 0.273 Chirality : 0.054 1.426 3146 Planarity : 0.004 0.043 3542 Dihedral : 5.066 79.053 2782 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.19 (0.18), residues: 2568 helix: -0.21 (0.15), residues: 1288 sheet: -2.67 (0.27), residues: 348 loop : -0.54 (0.23), residues: 932 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.6831 time to fit residues: 141.4181 Evaluate side-chains 121 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 3.026 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4386 time to fit residues: 4.5869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 185 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.068588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059387 restraints weight = 152876.842| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.89 r_work: 0.2831 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work: 0.2803 rms_B_bonded: 2.67 restraints_weight: 0.1250 r_work: 0.2788 rms_B_bonded: 2.77 restraints_weight: 0.0625 r_work: 0.2772 rms_B_bonded: 2.93 restraints_weight: 0.0312 r_work: 0.2755 rms_B_bonded: 3.13 restraints_weight: 0.0156 r_work: 0.2737 rms_B_bonded: 3.38 restraints_weight: 0.0078 r_work: 0.2718 rms_B_bonded: 3.67 restraints_weight: 0.0039 r_work: 0.2696 rms_B_bonded: 4.02 restraints_weight: 0.0020 r_work: 0.2673 rms_B_bonded: 4.43 restraints_weight: 0.0010 r_work: 0.2648 rms_B_bonded: 4.91 restraints_weight: 0.0005 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 20296 Z= 0.145 Angle : 0.506 11.106 27558 Z= 0.256 Chirality : 0.053 1.433 3146 Planarity : 0.004 0.046 3542 Dihedral : 4.960 79.739 2782 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.94 (0.18), residues: 2568 helix: 0.01 (0.15), residues: 1270 sheet: -2.59 (0.27), residues: 348 loop : -0.44 (0.23), residues: 950 =============================================================================== Job complete usr+sys time: 6460.13 seconds wall clock time: 116 minutes 33.50 seconds (6993.50 seconds total)