Starting phenix.real_space_refine on Sun Mar 17 13:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeb_18350/03_2024/8qeb_18350_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeb_18350/03_2024/8qeb_18350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeb_18350/03_2024/8qeb_18350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeb_18350/03_2024/8qeb_18350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeb_18350/03_2024/8qeb_18350_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeb_18350/03_2024/8qeb_18350_trim.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.039 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 S 57 5.16 5 C 5863 2.51 5 N 1400 2.21 5 O 1651 1.98 5 H 8700 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17671 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 17485 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 47, 'TRANS': 1050} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'ERG': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 8.67, per 1000 atoms: 0.49 Number of scatterers: 17671 At special positions: 0 Unit cell: (84.11, 102.226, 161.75, 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 57 16.00 O 1651 8.00 N 1400 7.00 C 5863 6.00 H 8700 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 41 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 868 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 869 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 879 " - pdb=" SG CYS A 888 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 1 " - " ASN A 940 " " NAG C 1 " - " ASN A 900 " " NAG D 1 " - " ASN A 401 " Time building additional restraints: 14.84 Conformation dependent library (CDL) restraints added in 1.9 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 61.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.759A pdb=" N ALA A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.823A pdb=" N PHE A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.739A pdb=" N PHE A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 121' Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.613A pdb=" N LEU A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 4.109A pdb=" N GLY A 194 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.639A pdb=" N GLU A 210 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 318 through 337 removed outlier: 4.074A pdb=" N ALA A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.876A pdb=" N THR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 408 through 423 removed outlier: 3.520A pdb=" N ASP A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.642A pdb=" N LEU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 4.686A pdb=" N PHE A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.567A pdb=" N LEU A 481 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.705A pdb=" N LEU A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 532 removed outlier: 3.725A pdb=" N ARG A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 4.183A pdb=" N LEU A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 removed outlier: 7.449A pdb=" N ASN A 556 " --> pdb=" O ASN A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 557 through 576 removed outlier: 3.581A pdb=" N TRP A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 608 removed outlier: 3.764A pdb=" N ILE A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 645 removed outlier: 3.602A pdb=" N ILE A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Proline residue: A 622 - end of helix removed outlier: 3.782A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 632 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 682 removed outlier: 3.553A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Proline residue: A 665 - end of helix removed outlier: 3.688A pdb=" N ALA A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.675A pdb=" N THR A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 701 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.018A pdb=" N THR A 747 " --> pdb=" O LYS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.515A pdb=" N ILE A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 770 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.893A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 786 through 794 removed outlier: 3.924A pdb=" N ASP A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 908 through 919 removed outlier: 4.259A pdb=" N ILE A 916 " --> pdb=" O GLU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 976 removed outlier: 3.862A pdb=" N PHE A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 995 removed outlier: 4.358A pdb=" N GLN A 993 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 994 " --> pdb=" O PHE A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1021 removed outlier: 3.580A pdb=" N LEU A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1047 removed outlier: 3.523A pdb=" N ILE A1037 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A1045 " --> pdb=" O GLY A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1079 removed outlier: 3.568A pdb=" N ASN A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1100 Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1106 through 1119 removed outlier: 3.710A pdb=" N VAL A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1130 Processing helix chain 'A' and resid 1136 through 1147 removed outlier: 3.525A pdb=" N ALA A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1155 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 4.214A pdb=" N CYS A 41 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 6.689A pdb=" N GLU A 139 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 127 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 137 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS A 129 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASP A 135 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 199 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.604A pdb=" N VAL A 252 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 255 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AA6, first strand: chain 'A' and resid 937 through 939 removed outlier: 4.304A pdb=" N ASP A 980 " --> pdb=" O LYS A 808 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1242 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: 6.51 Time building geometry restraints manager: 15.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8690 1.03 - 1.23: 43 1.23 - 1.43: 3849 1.43 - 1.62: 5240 1.62 - 1.82: 76 Bond restraints: 17898 Sorted by residual: bond pdb=" N ALA A 21 " pdb=" CA ALA A 21 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C6 ERG A1201 " pdb=" C7 ERG A1201 " ideal model delta sigma weight residual 1.452 1.419 0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" N ALA A 21 " pdb=" H ALA A 21 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 17893 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.98: 181 105.98 - 113.02: 20631 113.02 - 120.05: 5752 120.05 - 127.08: 5620 127.08 - 134.11: 93 Bond angle restraints: 32277 Sorted by residual: angle pdb=" N VAL A 335 " pdb=" CA VAL A 335 " pdb=" C VAL A 335 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" CB ARG A 886 " pdb=" CG ARG A 886 " pdb=" CD ARG A 886 " ideal model delta sigma weight residual 111.30 116.52 -5.22 2.30e+00 1.89e-01 5.16e+00 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" C PRO A 955 " ideal model delta sigma weight residual 112.47 116.93 -4.46 2.06e+00 2.36e-01 4.70e+00 angle pdb=" CA VAL A 335 " pdb=" C VAL A 335 " pdb=" N GLU A 336 " ideal model delta sigma weight residual 118.65 116.67 1.98 1.07e+00 8.73e-01 3.42e+00 angle pdb=" C HIS A 954 " pdb=" CA HIS A 954 " pdb=" CB HIS A 954 " ideal model delta sigma weight residual 109.96 112.73 -2.77 1.50e+00 4.44e-01 3.41e+00 ... (remaining 32272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 8127 23.57 - 47.14: 507 47.14 - 70.70: 111 70.70 - 94.27: 25 94.27 - 117.84: 6 Dihedral angle restraints: 8776 sinusoidal: 4793 harmonic: 3983 Sorted by residual: dihedral pdb=" CB CYS A 869 " pdb=" SG CYS A 869 " pdb=" SG CYS A 891 " pdb=" CB CYS A 891 " ideal model delta sinusoidal sigma weight residual 93.00 143.15 -50.15 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS A 822 " pdb=" SG CYS A 822 " pdb=" SG CYS A 828 " pdb=" CB CYS A 828 " ideal model delta sinusoidal sigma weight residual -86.00 -40.98 -45.02 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS A 223 " pdb=" SG CYS A 223 " pdb=" SG CYS A 235 " pdb=" CB CYS A 235 " ideal model delta sinusoidal sigma weight residual 93.00 49.27 43.73 1 1.00e+01 1.00e-02 2.66e+01 ... (remaining 8773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1179 0.047 - 0.094: 203 0.094 - 0.141: 46 0.141 - 0.187: 3 0.187 - 0.234: 2 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 940 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 900 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PRO A 955 " pdb=" N PRO A 955 " pdb=" C PRO A 955 " pdb=" CB PRO A 955 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1430 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 886 " 0.090 9.50e-02 1.11e+02 3.04e-02 1.25e+00 pdb=" NE ARG A 886 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 886 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 886 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 886 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 886 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 886 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 886 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 886 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 43 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 44 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 39 " 0.016 5.00e-02 4.00e+02 2.48e-02 9.87e-01 pdb=" N PRO A 40 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 40 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 40 " 0.014 5.00e-02 4.00e+02 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1516 2.22 - 2.82: 38461 2.82 - 3.41: 47331 3.41 - 4.01: 63495 4.01 - 4.60: 97283 Nonbonded interactions: 248086 Sorted by model distance: nonbonded pdb=" O LEU A 493 " pdb=" H VAL A 506 " model vdw 1.629 1.850 nonbonded pdb=" O GLY A 969 " pdb=" HG SER A 973 " model vdw 1.637 1.850 nonbonded pdb=" HG SER A 547 " pdb=" OH TYR A 785 " model vdw 1.643 1.850 nonbonded pdb=" OD1 ASP A 154 " pdb=" HZ1 LYS A 157 " model vdw 1.664 1.850 nonbonded pdb=" O ALA A 83 " pdb="HD22 ASN A 87 " model vdw 1.681 1.850 ... (remaining 248081 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 'B' selection = chain 'C' selection = chain 'D' } 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 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: 0.500 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: 0.260 Extract box with map and model: 3.480 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 59.660 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.003 0.033 9198 Z= 0.204 Angle : 0.487 5.224 12503 Z= 0.245 Chirality : 0.038 0.234 1433 Planarity : 0.003 0.040 1558 Dihedral : 17.617 117.838 3575 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.41 % Allowed : 15.03 % Favored : 84.57 % 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: 1092 helix: 0.35 (0.23), residues: 570 sheet: -0.87 (0.67), residues: 68 loop : -0.46 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.005 0.001 HIS A 954 PHE 0.017 0.001 PHE A 265 TYR 0.006 0.001 TYR A 711 ARG 0.009 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 1.341 Fit side-chains REVERT: A 805 MET cc_start: 0.9368 (mmt) cc_final: 0.9019 (mmm) outliers start: 4 outliers final: 3 residues processed: 89 average time/residue: 0.4612 time to fit residues: 58.3564 Evaluate side-chains 89 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9198 Z= 0.238 Angle : 0.563 8.885 12503 Z= 0.303 Chirality : 0.040 0.187 1433 Planarity : 0.004 0.031 1558 Dihedral : 9.178 99.606 1512 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 1.52 % Allowed : 14.21 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1092 helix: 0.21 (0.21), residues: 602 sheet: -0.98 (0.68), residues: 65 loop : -0.69 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 466 HIS 0.005 0.001 HIS A 954 PHE 0.019 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.002 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.6871 (tmm) cc_final: 0.6344 (tmm) REVERT: A 47 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.4446 (p90) REVERT: A 92 GLN cc_start: 0.7153 (tt0) cc_final: 0.6657 (tt0) REVERT: A 457 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7327 (mm-40) REVERT: A 522 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 589 ILE cc_start: 0.7635 (mm) cc_final: 0.7184 (mt) REVERT: A 805 MET cc_start: 0.9377 (mmt) cc_final: 0.9032 (mmm) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.4223 time to fit residues: 66.3014 Evaluate side-chains 103 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9198 Z= 0.261 Angle : 0.540 8.578 12503 Z= 0.283 Chirality : 0.039 0.185 1433 Planarity : 0.004 0.040 1558 Dihedral : 8.012 83.228 1510 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 2.03 % Allowed : 14.82 % Favored : 83.15 % 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: -0.54 (0.25), residues: 1092 helix: 0.17 (0.21), residues: 603 sheet: -1.23 (0.67), residues: 66 loop : -0.83 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.006 0.001 HIS A 954 PHE 0.018 0.001 PHE A 569 TYR 0.011 0.001 TYR A 857 ARG 0.004 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6873 (tmm) cc_final: 0.6386 (tmm) REVERT: A 47 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4500 (p90) REVERT: A 92 GLN cc_start: 0.7108 (tt0) cc_final: 0.6559 (tt0) REVERT: A 457 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7455 (mm-40) REVERT: A 580 ASP cc_start: 0.7911 (t70) cc_final: 0.7661 (t70) REVERT: A 589 ILE cc_start: 0.7648 (mm) cc_final: 0.7240 (mt) REVERT: A 805 MET cc_start: 0.9385 (mmt) cc_final: 0.9000 (mmm) REVERT: A 859 MET cc_start: 0.8570 (mmp) cc_final: 0.8041 (mmp) outliers start: 20 outliers final: 16 residues processed: 111 average time/residue: 0.4458 time to fit residues: 71.4153 Evaluate side-chains 106 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9198 Z= 0.183 Angle : 0.500 7.247 12503 Z= 0.261 Chirality : 0.038 0.181 1433 Planarity : 0.003 0.036 1558 Dihedral : 7.414 67.815 1510 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.24 % Rotamer: Outliers : 2.34 % Allowed : 14.62 % Favored : 83.05 % 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: -0.44 (0.25), residues: 1092 helix: 0.27 (0.21), residues: 606 sheet: -1.25 (0.67), residues: 66 loop : -0.81 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.005 0.001 HIS A 954 PHE 0.020 0.001 PHE A 569 TYR 0.010 0.001 TYR A 711 ARG 0.001 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6880 (tmm) cc_final: 0.6330 (tmm) REVERT: A 47 PHE cc_start: 0.5034 (OUTLIER) cc_final: 0.4525 (p90) REVERT: A 92 GLN cc_start: 0.7148 (tt0) cc_final: 0.6588 (tt0) REVERT: A 580 ASP cc_start: 0.7939 (t70) cc_final: 0.7701 (t70) REVERT: A 589 ILE cc_start: 0.7628 (mm) cc_final: 0.7214 (mt) REVERT: A 805 MET cc_start: 0.9418 (mmt) cc_final: 0.9039 (mmm) REVERT: A 859 MET cc_start: 0.8546 (mmp) cc_final: 0.8013 (mmp) outliers start: 23 outliers final: 20 residues processed: 114 average time/residue: 0.4594 time to fit residues: 75.0960 Evaluate side-chains 115 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9198 Z= 0.278 Angle : 0.532 6.438 12503 Z= 0.279 Chirality : 0.039 0.184 1433 Planarity : 0.004 0.039 1558 Dihedral : 7.185 55.842 1510 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 2.94 % Allowed : 14.42 % Favored : 82.64 % 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: -0.59 (0.25), residues: 1092 helix: 0.17 (0.21), residues: 607 sheet: -1.43 (0.66), residues: 66 loop : -0.89 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.020 0.001 PHE A 569 TYR 0.015 0.001 TYR A 857 ARG 0.002 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6830 (tmm) cc_final: 0.6397 (tmm) REVERT: A 47 PHE cc_start: 0.5076 (OUTLIER) cc_final: 0.4508 (p90) REVERT: A 580 ASP cc_start: 0.7914 (t70) cc_final: 0.7676 (t70) REVERT: A 589 ILE cc_start: 0.7651 (mm) cc_final: 0.7233 (mt) REVERT: A 778 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6792 (pp) REVERT: A 805 MET cc_start: 0.9417 (mmt) cc_final: 0.9047 (mmm) outliers start: 29 outliers final: 22 residues processed: 117 average time/residue: 0.4549 time to fit residues: 77.4708 Evaluate side-chains 113 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9198 Z= 0.165 Angle : 0.486 5.579 12503 Z= 0.254 Chirality : 0.038 0.176 1433 Planarity : 0.003 0.038 1558 Dihedral : 6.907 56.564 1510 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 2.34 % Allowed : 15.43 % Favored : 82.23 % 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: -0.33 (0.26), residues: 1092 helix: 0.38 (0.22), residues: 606 sheet: -1.35 (0.66), residues: 66 loop : -0.76 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.005 0.001 HIS A 954 PHE 0.020 0.001 PHE A 569 TYR 0.011 0.001 TYR A 711 ARG 0.001 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6853 (tmm) cc_final: 0.6351 (tmm) REVERT: A 39 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 47 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.4517 (p90) REVERT: A 89 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7783 (mm-40) REVERT: A 421 PHE cc_start: 0.8111 (t80) cc_final: 0.7773 (t80) REVERT: A 580 ASP cc_start: 0.7884 (t70) cc_final: 0.7633 (t70) REVERT: A 589 ILE cc_start: 0.7626 (mm) cc_final: 0.7218 (mt) REVERT: A 778 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6744 (pp) REVERT: A 805 MET cc_start: 0.9416 (mmt) cc_final: 0.9036 (mmm) REVERT: A 859 MET cc_start: 0.8522 (mmp) cc_final: 0.8182 (mmp) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.4184 time to fit residues: 68.4802 Evaluate side-chains 112 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9198 Z= 0.207 Angle : 0.494 5.521 12503 Z= 0.259 Chirality : 0.038 0.184 1433 Planarity : 0.003 0.039 1558 Dihedral : 6.956 59.924 1510 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 2.44 % Allowed : 15.33 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1092 helix: 0.41 (0.21), residues: 606 sheet: -1.38 (0.66), residues: 66 loop : -0.77 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.023 0.001 PHE A 569 TYR 0.011 0.001 TYR A 711 ARG 0.001 0.000 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6678 (tmm) cc_final: 0.6238 (tmm) REVERT: A 39 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8316 (tt) REVERT: A 47 PHE cc_start: 0.5110 (OUTLIER) cc_final: 0.4547 (p90) REVERT: A 89 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7804 (mm-40) REVERT: A 421 PHE cc_start: 0.8078 (t80) cc_final: 0.7749 (t80) REVERT: A 580 ASP cc_start: 0.7902 (t70) cc_final: 0.7657 (t70) REVERT: A 589 ILE cc_start: 0.7636 (mm) cc_final: 0.7224 (mt) REVERT: A 778 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6763 (pp) REVERT: A 805 MET cc_start: 0.9423 (mmt) cc_final: 0.9048 (mmm) outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 0.4261 time to fit residues: 68.9869 Evaluate side-chains 114 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 9198 Z= 0.230 Angle : 0.507 7.093 12503 Z= 0.268 Chirality : 0.038 0.179 1433 Planarity : 0.003 0.040 1558 Dihedral : 6.941 57.012 1509 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 2.34 % Allowed : 15.53 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1092 helix: 0.43 (0.21), residues: 606 sheet: -1.42 (0.66), residues: 66 loop : -0.79 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.020 0.001 PHE A 569 TYR 0.011 0.001 TYR A 711 ARG 0.001 0.000 ARG A 721 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6671 (tmm) cc_final: 0.6347 (tmm) REVERT: A 39 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 47 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4486 (p90) REVERT: A 89 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7781 (mm-40) REVERT: A 421 PHE cc_start: 0.8082 (t80) cc_final: 0.7727 (t80) REVERT: A 580 ASP cc_start: 0.7917 (t70) cc_final: 0.7671 (t70) REVERT: A 589 ILE cc_start: 0.7638 (mm) cc_final: 0.7226 (mt) REVERT: A 778 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6760 (pp) outliers start: 23 outliers final: 18 residues processed: 113 average time/residue: 0.4306 time to fit residues: 69.7922 Evaluate side-chains 115 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9198 Z= 0.181 Angle : 0.485 5.229 12503 Z= 0.255 Chirality : 0.038 0.177 1433 Planarity : 0.003 0.039 1558 Dihedral : 6.780 57.686 1509 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.40 % Favored : 94.51 % Rotamer: Outliers : 2.23 % Allowed : 15.84 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1092 helix: 0.54 (0.22), residues: 600 sheet: -1.36 (0.66), residues: 66 loop : -0.79 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.023 0.001 PHE A 569 TYR 0.011 0.001 TYR A 711 ARG 0.001 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6668 (tmm) cc_final: 0.6377 (tmm) REVERT: A 47 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4513 (p90) REVERT: A 89 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7805 (mm-40) REVERT: A 421 PHE cc_start: 0.8214 (t80) cc_final: 0.7841 (t80) REVERT: A 580 ASP cc_start: 0.7907 (t70) cc_final: 0.7662 (t70) REVERT: A 589 ILE cc_start: 0.7631 (mm) cc_final: 0.7212 (mt) REVERT: A 778 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6759 (pp) REVERT: A 859 MET cc_start: 0.8451 (mmp) cc_final: 0.8108 (mmp) REVERT: A 968 ASP cc_start: 0.8550 (m-30) cc_final: 0.8257 (m-30) outliers start: 22 outliers final: 16 residues processed: 115 average time/residue: 0.4195 time to fit residues: 70.2921 Evaluate side-chains 116 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 9198 Z= 0.162 Angle : 0.483 5.545 12503 Z= 0.254 Chirality : 0.037 0.172 1433 Planarity : 0.003 0.040 1558 Dihedral : 6.725 57.080 1509 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.83 % Allowed : 16.35 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.11 (0.26), residues: 1092 helix: 0.64 (0.22), residues: 600 sheet: -1.39 (0.66), residues: 66 loop : -0.76 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 148 HIS 0.005 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.010 0.001 TYR A 711 ARG 0.001 0.000 ARG A 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.6612 (tmm) cc_final: 0.6359 (tmm) REVERT: A 47 PHE cc_start: 0.5077 (OUTLIER) cc_final: 0.4526 (p90) REVERT: A 89 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7806 (mm-40) REVERT: A 421 PHE cc_start: 0.8097 (t80) cc_final: 0.7726 (t80) REVERT: A 450 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 580 ASP cc_start: 0.7903 (t70) cc_final: 0.7660 (t70) REVERT: A 589 ILE cc_start: 0.7618 (mm) cc_final: 0.7212 (mt) REVERT: A 778 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6743 (pp) REVERT: A 859 MET cc_start: 0.8456 (mmp) cc_final: 0.8105 (mmp) REVERT: A 968 ASP cc_start: 0.8528 (m-30) cc_final: 0.8241 (m-30) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.4132 time to fit residues: 67.7136 Evaluate side-chains 114 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 ASN ** 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 = 0.3997 r_free = 0.3997 target = 0.179502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136220 restraints weight = 30041.780| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.26 r_work: 0.3286 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9198 Z= 0.299 Angle : 0.537 5.477 12503 Z= 0.281 Chirality : 0.040 0.187 1433 Planarity : 0.004 0.042 1558 Dihedral : 6.911 57.578 1509 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 2.23 % Allowed : 15.94 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1092 helix: 0.41 (0.21), residues: 607 sheet: -1.58 (0.64), residues: 66 loop : -0.86 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.023 0.001 PHE A 569 TYR 0.015 0.001 TYR A 179 ARG 0.005 0.000 ARG A 886 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4030.08 seconds wall clock time: 71 minutes 47.29 seconds (4307.29 seconds total)