Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 08:05:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v99_31811/04_2023/7v99_31811.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v99_31811/04_2023/7v99_31811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v99_31811/04_2023/7v99_31811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v99_31811/04_2023/7v99_31811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v99_31811/04_2023/7v99_31811.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v99_31811/04_2023/7v99_31811.pdb" } resolution = 3.54 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= 0.008 sd= 0.242 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 249 5.49 5 S 39 5.16 5 C 8291 2.51 5 N 2662 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A ARG 522": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ASP 637": "OD1" <-> "OD2" Residue "A TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 1034": "NH1" <-> "NH2" Residue "A ASP 1038": "OD1" <-> "OD2" Residue "A ARG 1084": "NH1" <-> "NH2" Residue "A PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 113": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14582 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7898 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 62, 'TRANS': 928} Chain breaks: 1 Chain: "K" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 668 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "L" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "R" Number of atoms: 5156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 5156 Classifications: {'RNA': 243} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 105, 'rna3p_pyr': 123} Link IDs: {'rna2p': 15, 'rna3p': 227} Chain breaks: 2 Chain: "S" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 8.21, per 1000 atoms: 0.56 Number of scatterers: 14582 At special positions: 0 Unit cell: (148.5, 125.4, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 249 15.00 O 3341 8.00 N 2662 7.00 C 8291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 896 " distance=2.05 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1043 " distance=2.05 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: 6.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 57.2% alpha, 9.1% beta 53 base pairs and 118 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.783A pdb=" N LEU A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 31 through 42 removed outlier: 3.587A pdb=" N ARG A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.649A pdb=" N ALA A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 132 through 140 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.653A pdb=" N MET A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.624A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 397 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.607A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Proline residue: A 421 - end of helix removed outlier: 3.875A pdb=" N LYS A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 4.258A pdb=" N ASP A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 3.503A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.837A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.781A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 479' Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.624A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.537A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.960A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.843A pdb=" N VAL A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 672 removed outlier: 3.535A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 699 removed outlier: 3.858A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 737 removed outlier: 4.192A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.924A pdb=" N THR A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 removed outlier: 4.650A pdb=" N ASP A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.704A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 887 " --> pdb=" O PHE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.848A pdb=" N SER A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 removed outlier: 4.014A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1018 removed outlier: 3.511A pdb=" N TYR A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 4.418A pdb=" N ALA A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 4.046A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1107 removed outlier: 4.052A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.655A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 22 Processing helix chain 'K' and resid 27 through 37 Processing helix chain 'K' and resid 46 through 72 removed outlier: 3.730A pdb=" N TYR K 50 " --> pdb=" O GLY K 46 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU K 65 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.649A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 Processing helix chain 'L' and resid 37 through 49 removed outlier: 3.776A pdb=" N VAL L 44 " --> pdb=" O TYR L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 83 removed outlier: 3.725A pdb=" N ILE L 61 " --> pdb=" O LYS L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.844A pdb=" N LEU L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 124 removed outlier: 3.815A pdb=" N HIS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.542A pdb=" N VAL A 119 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.981A pdb=" N ARG A 108 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A 113 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 removed outlier: 3.638A pdb=" N THR A 564 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600 removed outlier: 4.313A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 618 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.542A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 874 " --> pdb=" O TYR A 707 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 707 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 712 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 904 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 765 removed outlier: 3.999A pdb=" N ARG A 756 " --> pdb=" O LYS A 749 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 749 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 758 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS A 740 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 799 " --> pdb=" O CYS A 740 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 744 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER A 795 " --> pdb=" O TYR A 744 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 746 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU A 793 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN A 748 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 791 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ALA A 750 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA A 789 " --> pdb=" O ALA A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 928 through 929 Processing sheet with id=AB1, first strand: chain 'K' and resid 42 through 43 removed outlier: 6.581A pdb=" N ARG K 42 " --> pdb=" O ILE L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 77 through 78 468 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 118 stacking parallelities Total time for adding SS restraints: 7.63 Time building geometry restraints manager: 6.89 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: 3841 1.34 - 1.46: 4715 1.46 - 1.58: 6300 1.58 - 1.70: 494 1.70 - 1.82: 52 Bond restraints: 15402 Sorted by residual: bond pdb=" C PRO A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.12e-02 7.97e+03 8.17e+00 bond pdb=" C ASN A1120 " pdb=" N PRO A1121 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.12e-02 7.97e+03 3.34e+00 bond pdb=" C ALA K 47 " pdb=" N PRO K 48 " ideal model delta sigma weight residual 1.336 1.356 -0.021 1.23e-02 6.61e+03 2.78e+00 bond pdb=" C LYS A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.30e-02 5.92e+03 2.42e+00 bond pdb=" CA ASN A 799 " pdb=" CB ASN A 799 " ideal model delta sigma weight residual 1.527 1.562 -0.035 2.48e-02 1.63e+03 2.00e+00 ... (remaining 15397 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.14: 1700 107.14 - 113.85: 9114 113.85 - 120.56: 6004 120.56 - 127.27: 4717 127.27 - 133.98: 518 Bond angle restraints: 22053 Sorted by residual: angle pdb=" N GLN A 569 " pdb=" CA GLN A 569 " pdb=" C GLN A 569 " ideal model delta sigma weight residual 110.44 106.41 4.03 1.20e+00 6.94e-01 1.13e+01 angle pdb=" N ALA A 918 " pdb=" CA ALA A 918 " pdb=" C ALA A 918 " ideal model delta sigma weight residual 114.56 110.75 3.81 1.27e+00 6.20e-01 9.00e+00 angle pdb=" C VAL A 162 " pdb=" N ALA A 163 " pdb=" CA ALA A 163 " ideal model delta sigma weight residual 122.85 119.74 3.11 1.10e+00 8.26e-01 7.97e+00 angle pdb=" C LEU A1042 " pdb=" N CYS A1043 " pdb=" CA CYS A1043 " ideal model delta sigma weight residual 121.58 116.08 5.50 1.95e+00 2.63e-01 7.95e+00 angle pdb=" N VAL A1087 " pdb=" CA VAL A1087 " pdb=" C VAL A1087 " ideal model delta sigma weight residual 112.12 109.77 2.35 8.40e-01 1.42e+00 7.84e+00 ... (remaining 22048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8530 35.43 - 70.86: 198 70.86 - 106.29: 18 106.29 - 141.72: 1 141.72 - 177.14: 4 Dihedral angle restraints: 8751 sinusoidal: 5349 harmonic: 3402 Sorted by residual: dihedral pdb=" CB CYS A 982 " pdb=" SG CYS A 982 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 45.52 47.48 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA GLN A 569 " pdb=" C GLN A 569 " pdb=" N LYS A 570 " pdb=" CA LYS A 570 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C4' G R 76 " pdb=" C3' G R 76 " pdb=" O3' G R 76 " pdb=" P U R 77 " ideal model delta sinusoidal sigma weight residual -140.00 37.14 -177.14 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2105 0.028 - 0.057: 414 0.057 - 0.085: 106 0.085 - 0.113: 51 0.113 - 0.142: 12 Chirality restraints: 2688 Sorted by residual: chirality pdb=" C3' C R 72 " pdb=" C4' C R 72 " pdb=" O3' C R 72 " pdb=" C2' C R 72 " both_signs ideal model delta sigma weight residual False -2.48 -2.34 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" C1' A R 174 " pdb=" O4' A R 174 " pdb=" C2' A R 174 " pdb=" N9 A R 174 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CB THR A 375 " pdb=" CA THR A 375 " pdb=" OG1 THR A 375 " pdb=" CG2 THR A 375 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 2685 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 68 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO A 69 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 79 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO K 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO K 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1043 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C CYS A1043 " -0.025 2.00e-02 2.50e+03 pdb=" O CYS A1043 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A1044 " 0.008 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3114 2.79 - 3.31: 12557 3.31 - 3.84: 24599 3.84 - 4.37: 27023 4.37 - 4.90: 42288 Nonbonded interactions: 109581 Sorted by model distance: nonbonded pdb=" O2' G R 76 " pdb=" OP1 U R 77 " model vdw 2.258 2.440 nonbonded pdb=" O2' C R 72 " pdb=" O5' G R 73 " model vdw 2.273 2.440 nonbonded pdb=" NH2 ARG A 390 " pdb=" OP2 C R 290 " model vdw 2.292 2.520 nonbonded pdb=" O ARG A 696 " pdb=" NE2 GLN A 700 " model vdw 2.314 2.520 nonbonded pdb=" OG SER A 619 " pdb=" O ALA A 817 " model vdw 2.324 2.440 ... (remaining 109576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 4.690 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: 15.980 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 45.270 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 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 : 0.002 0.035 15402 Z= 0.138 Angle : 0.530 7.050 22053 Z= 0.320 Chirality : 0.028 0.142 2688 Planarity : 0.004 0.061 1895 Dihedral : 14.511 177.144 6545 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer Outliers : 0.10 % 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: -3.21 (0.21), residues: 1162 helix: -1.05 (0.19), residues: 615 sheet: -1.52 (0.50), residues: 77 loop : -3.76 (0.22), residues: 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.408 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: 0 residues processed: 181 average time/residue: 0.4383 time to fit residues: 102.4561 Evaluate side-chains 97 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 71 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 95 ASN A 490 ASN A 506 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 906 ASN A 921 GLN A1022 HIS A1023 GLN K 31 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 15402 Z= 0.191 Angle : 0.566 9.059 22053 Z= 0.279 Chirality : 0.033 0.194 2688 Planarity : 0.004 0.049 1895 Dihedral : 13.087 177.448 4286 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer Outliers : 1.50 % 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 (0.23), residues: 1162 helix: 0.35 (0.21), residues: 617 sheet: -1.15 (0.51), residues: 77 loop : -3.30 (0.23), residues: 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.3536 time to fit residues: 51.4685 Evaluate side-chains 88 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1943 time to fit residues: 4.6834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN L 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 15402 Z= 0.160 Angle : 0.533 12.457 22053 Z= 0.261 Chirality : 0.033 0.219 2688 Planarity : 0.004 0.044 1895 Dihedral : 13.131 175.270 4286 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.55 % Rotamer Outliers : 1.71 % 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: -0.99 (0.25), residues: 1162 helix: 0.95 (0.22), residues: 623 sheet: -0.74 (0.50), residues: 88 loop : -3.10 (0.24), residues: 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 96 average time/residue: 0.2842 time to fit residues: 40.1803 Evaluate side-chains 83 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1409 time to fit residues: 3.0450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 737 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS A1023 GLN L 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 15402 Z= 0.203 Angle : 0.570 11.636 22053 Z= 0.283 Chirality : 0.034 0.225 2688 Planarity : 0.005 0.060 1895 Dihedral : 13.284 177.849 4286 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.72 % Rotamer Outliers : 2.01 % 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: -0.71 (0.25), residues: 1162 helix: 1.12 (0.22), residues: 628 sheet: -0.61 (0.49), residues: 98 loop : -2.95 (0.25), residues: 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 0.3087 time to fit residues: 44.5600 Evaluate side-chains 86 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1441 time to fit residues: 4.3710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.074 15402 Z= 0.153 Angle : 0.528 11.880 22053 Z= 0.255 Chirality : 0.033 0.184 2688 Planarity : 0.004 0.044 1895 Dihedral : 13.186 176.898 4286 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.89 % Rotamer Outliers : 1.10 % 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: -0.53 (0.25), residues: 1162 helix: 1.28 (0.22), residues: 633 sheet: -0.32 (0.50), residues: 97 loop : -3.00 (0.26), residues: 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 85 average time/residue: 0.2428 time to fit residues: 33.2060 Evaluate side-chains 77 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1376 time to fit residues: 2.6955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 0.0070 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.0470 chunk 130 optimal weight: 10.0000 overall best weight: 0.7716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 15402 Z= 0.157 Angle : 0.522 12.285 22053 Z= 0.253 Chirality : 0.032 0.176 2688 Planarity : 0.004 0.042 1895 Dihedral : 13.162 177.684 4286 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.98 % Rotamer Outliers : 1.10 % 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: -0.39 (0.25), residues: 1162 helix: 1.40 (0.22), residues: 628 sheet: -0.54 (0.49), residues: 107 loop : -2.87 (0.27), residues: 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.2655 time to fit residues: 34.1281 Evaluate side-chains 77 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1375 time to fit residues: 3.3531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15402 Z= 0.134 Angle : 0.508 13.187 22053 Z= 0.243 Chirality : 0.032 0.263 2688 Planarity : 0.004 0.044 1895 Dihedral : 13.098 176.979 4286 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer Outliers : 1.40 % 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 (0.26), residues: 1162 helix: 1.56 (0.22), residues: 630 sheet: -0.43 (0.50), residues: 107 loop : -2.81 (0.27), residues: 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 88 average time/residue: 0.2543 time to fit residues: 34.8400 Evaluate side-chains 76 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1300 time to fit residues: 3.1057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 15402 Z= 0.174 Angle : 0.547 13.466 22053 Z= 0.263 Chirality : 0.033 0.227 2688 Planarity : 0.004 0.045 1895 Dihedral : 13.191 178.749 4286 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.89 % Rotamer Outliers : 1.10 % 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: -0.18 (0.26), residues: 1162 helix: 1.51 (0.22), residues: 630 sheet: -0.17 (0.51), residues: 97 loop : -2.71 (0.28), residues: 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.2681 time to fit residues: 32.0304 Evaluate side-chains 72 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1467 time to fit residues: 3.0589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.0060 chunk 38 optimal weight: 0.0370 chunk 113 optimal weight: 0.0020 chunk 118 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15402 Z= 0.130 Angle : 0.520 13.571 22053 Z= 0.247 Chirality : 0.031 0.207 2688 Planarity : 0.004 0.046 1895 Dihedral : 13.079 177.300 4286 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % 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: -0.09 (0.26), residues: 1162 helix: 1.60 (0.22), residues: 632 sheet: -0.23 (0.52), residues: 91 loop : -2.67 (0.28), residues: 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2506 time to fit residues: 28.9975 Evaluate side-chains 68 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 HIS A 737 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15402 Z= 0.150 Angle : 0.536 13.472 22053 Z= 0.254 Chirality : 0.032 0.191 2688 Planarity : 0.004 0.048 1895 Dihedral : 13.092 177.491 4286 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.41 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1162 helix: 1.65 (0.22), residues: 629 sheet: -0.14 (0.53), residues: 89 loop : -2.59 (0.28), residues: 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.2611 time to fit residues: 29.7232 Evaluate side-chains 67 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1433 time to fit residues: 2.1631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 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 = 0.4406 r_free = 0.4406 target = 0.103372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.074051 restraints weight = 83429.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.075812 restraints weight = 45231.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.076902 restraints weight = 33545.868| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15402 Z= 0.163 Angle : 0.554 13.806 22053 Z= 0.263 Chirality : 0.033 0.184 2688 Planarity : 0.004 0.048 1895 Dihedral : 13.181 176.846 4286 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer Outliers : 0.30 % 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: -0.03 (0.26), residues: 1162 helix: 1.64 (0.22), residues: 632 sheet: -0.11 (0.53), residues: 89 loop : -2.63 (0.28), residues: 441 =============================================================================== Job complete usr+sys time: 2542.27 seconds wall clock time: 47 minutes 19.94 seconds (2839.94 seconds total)