Starting phenix.real_space_refine (version: dev) on Tue Feb 21 07:04:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/02_2023/6tbu_10452_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/02_2023/6tbu_10452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/02_2023/6tbu_10452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/02_2023/6tbu_10452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/02_2023/6tbu_10452_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/02_2023/6tbu_10452_trim.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 49": "OD1" <-> "OD2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ARG 812": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 853": "OD1" <-> "OD2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ARG 920": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 949": "OD1" <-> "OD2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1040": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1121": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13733 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 13376 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 34, 'TRANS': 807} Chain breaks: 10 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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 chiralities: 2 Chain: "A" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 329 Unusual residues: {'NAG': 1, 'Y01': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.96, per 1000 atoms: 0.51 Number of scatterers: 13733 At special positions: 0 Unit cell: (115.02, 84.24, 98.01, 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 50 16.00 O 1237 8.00 N 1058 7.00 C 4743 6.00 H 6645 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 304 " distance=2.04 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 843 " 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-ASN " NAG A1510 " - " ASN A 319 " " NAG B 1 " - " ASN A 767 " Time building additional restraints: 13.00 Conformation dependent library (CDL) restraints added in 1.3 seconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 3 sheets defined 66.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.521A pdb=" N TRP A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 42 removed outlier: 3.943A pdb=" N VAL A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 76 removed outlier: 4.773A pdb=" N ASP A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.615A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 326 through 341 removed outlier: 4.391A pdb=" N THR A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.520A pdb=" N VAL A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 467 removed outlier: 3.988A pdb=" N TRP A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 453 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 492 removed outlier: 4.292A pdb=" N THR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 514 removed outlier: 4.004A pdb=" N LEU A 505 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.560A pdb=" N PHE A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 588 removed outlier: 5.054A pdb=" N ALA A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 629 Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 649 through 669 Processing helix chain 'A' and resid 670 through 690 Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.894A pdb=" N SER A 715 " --> pdb=" O PHE A 711 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 801 through 812 removed outlier: 4.080A pdb=" N ASN A 805 " --> pdb=" O CYS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 854 Proline residue: A 845 - end of helix removed outlier: 3.502A pdb=" N THR A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 935 removed outlier: 4.283A pdb=" N ILE A 919 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 982 removed outlier: 3.607A pdb=" N SER A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1010 removed outlier: 3.821A pdb=" N SER A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1041 removed outlier: 4.454A pdb=" N ILE A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1077 removed outlier: 5.844A pdb=" N GLY A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Proline residue: A1061 - end of helix removed outlier: 3.740A pdb=" N MET A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1114 removed outlier: 3.969A pdb=" N LEU A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 404 removed outlier: 4.329A pdb=" N SER A 254 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS A 255 " --> pdb=" O MET A 431 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET A 431 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 257 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.904A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL A 899 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 867 " --> pdb=" O VAL A 899 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 901 " --> pdb=" O LYS A 865 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.904A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 735 " --> pdb=" O SER A 908 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1263 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: 5.10 Time building geometry restraints manager: 13.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6627 1.03 - 1.23: 308 1.23 - 1.43: 2832 1.43 - 1.63: 4088 1.63 - 1.83: 89 Bond restraints: 13944 Sorted by residual: bond pdb=" CAE Y01 A1504 " pdb=" CBI Y01 A1504 " ideal model delta sigma weight residual 1.532 1.648 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" CAE Y01 A1501 " pdb=" CBI Y01 A1501 " ideal model delta sigma weight residual 1.532 1.643 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" CAE Y01 A1506 " pdb=" CBI Y01 A1506 " ideal model delta sigma weight residual 1.532 1.640 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" CAE Y01 A1502 " pdb=" CBI Y01 A1502 " ideal model delta sigma weight residual 1.532 1.640 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" CAE Y01 A1505 " pdb=" CBI Y01 A1505 " ideal model delta sigma weight residual 1.532 1.638 -0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 13939 not shown) Histogram of bond angle deviations from ideal: 80.31 - 91.09: 32 91.09 - 101.87: 66 101.87 - 112.65: 15675 112.65 - 123.43: 8015 123.43 - 134.21: 1228 Bond angle restraints: 25016 Sorted by residual: angle pdb=" CG2 VAL A 983 " pdb=" CB VAL A 983 " pdb=" HB VAL A 983 " ideal model delta sigma weight residual 108.00 80.31 27.69 3.00e+00 1.11e-01 8.52e+01 angle pdb=" CD2 LEU A1048 " pdb=" CG LEU A1048 " pdb=" HG LEU A1048 " ideal model delta sigma weight residual 108.00 83.10 24.90 3.00e+00 1.11e-01 6.89e+01 angle pdb=" CD2 LEU A1009 " pdb=" CG LEU A1009 " pdb=" HG LEU A1009 " ideal model delta sigma weight residual 108.00 83.44 24.56 3.00e+00 1.11e-01 6.70e+01 angle pdb=" CB LEU A1048 " pdb=" CG LEU A1048 " pdb=" HG LEU A1048 " ideal model delta sigma weight residual 109.00 84.52 24.48 3.00e+00 1.11e-01 6.66e+01 angle pdb=" CB LEU A 337 " pdb=" CG LEU A 337 " pdb=" HG LEU A 337 " ideal model delta sigma weight residual 109.00 84.65 24.35 3.00e+00 1.11e-01 6.59e+01 ... (remaining 25011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 5215 21.94 - 43.87: 389 43.87 - 65.81: 62 65.81 - 87.75: 10 87.75 - 109.68: 7 Dihedral angle restraints: 5683 sinusoidal: 2547 harmonic: 3136 Sorted by residual: dihedral pdb=" CA LEU A 369 " pdb=" C LEU A 369 " pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta harmonic sigma weight residual -180.00 -119.35 -60.65 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ILE A 422 " pdb=" C ILE A 422 " pdb=" N ASN A 423 " pdb=" CA ASN A 423 " ideal model delta harmonic sigma weight residual 180.00 -149.98 -30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA LEU A 326 " pdb=" C LEU A 326 " pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 5680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.372: 1137 0.372 - 0.745: 18 0.745 - 1.117: 0 1.117 - 1.490: 0 1.490 - 1.862: 10 Chirality restraints: 1165 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.63 -1.77 2.00e-02 2.50e+03 7.80e+03 chirality pdb=" CG LEU A 421 " pdb=" CB LEU A 421 " pdb=" CD1 LEU A 421 " pdb=" CD2 LEU A 421 " both_signs ideal model delta sigma weight residual False -2.59 -0.73 -1.86 2.00e-01 2.50e+01 8.67e+01 chirality pdb=" CG LEU A 338 " pdb=" CB LEU A 338 " pdb=" CD1 LEU A 338 " pdb=" CD2 LEU A 338 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 8.04e+01 ... (remaining 1162 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1082 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO A1083 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1083 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1083 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1025 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C ILE A1025 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE A1025 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY A1026 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 614 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C MET A 614 " 0.043 2.00e-02 2.50e+03 pdb=" O MET A 614 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 615 " -0.014 2.00e-02 2.50e+03 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 191 2.10 - 2.73: 22461 2.73 - 3.35: 39625 3.35 - 3.98: 48347 3.98 - 4.60: 78164 Nonbonded interactions: 188788 Sorted by model distance: nonbonded pdb=" HG2 PRO A 45 " pdb=" CAK Y01 A1501 " model vdw 1.477 2.920 nonbonded pdb=" CG PRO A 45 " pdb=" CAK Y01 A1501 " model vdw 1.526 3.400 nonbonded pdb=" HH TYR A 490 " pdb=" O PHE A 498 " model vdw 1.701 1.850 nonbonded pdb=" O ALA A 17 " pdb="HH21 ARG A 627 " model vdw 1.709 1.850 nonbonded pdb=" O GLU A 698 " pdb=" HG1 THR A 914 " model vdw 1.714 1.850 ... (remaining 188783 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 4743 2.51 5 N 1058 2.21 5 O 1237 1.98 5 H 6645 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.200 Extract box with map and model: 6.890 Check model and map are aligned: 0.200 Process input model: 47.800 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.012 0.136 7299 Z= 0.767 Angle : 1.504 18.173 9983 Z= 0.609 Chirality : 0.175 1.862 1165 Planarity : 0.005 0.070 1182 Dihedral : 15.736 109.685 2525 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.99 (0.26), residues: 820 helix: -0.61 (0.20), residues: 513 sheet: -0.82 (0.78), residues: 29 loop : -2.61 (0.36), residues: 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.123 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: 0 outliers final: 0 residues processed: 147 average time/residue: 0.5483 time to fit residues: 104.5095 Evaluate side-chains 100 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 720 GLN A 761 HIS A 931 GLN A 954 ASN A1052 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 7299 Z= 0.234 Angle : 0.726 11.026 9983 Z= 0.341 Chirality : 0.152 1.844 1165 Planarity : 0.004 0.067 1182 Dihedral : 11.935 106.558 1028 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.51 (0.28), residues: 820 helix: 0.66 (0.21), residues: 520 sheet: -0.24 (0.83), residues: 29 loop : -2.34 (0.38), residues: 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.097 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: 8 outliers final: 5 residues processed: 114 average time/residue: 0.3711 time to fit residues: 58.8702 Evaluate side-chains 98 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1713 time to fit residues: 2.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 0.0010 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7299 Z= 0.199 Angle : 0.690 11.159 9983 Z= 0.320 Chirality : 0.152 1.852 1165 Planarity : 0.004 0.062 1182 Dihedral : 11.379 105.702 1028 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.26 (0.30), residues: 820 helix: 1.29 (0.22), residues: 520 sheet: -0.74 (0.79), residues: 38 loop : -2.02 (0.40), residues: 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.125 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 outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.3836 time to fit residues: 60.1053 Evaluate side-chains 100 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.137 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1690 time to fit residues: 2.1123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7299 Z= 0.210 Angle : 0.682 11.058 9983 Z= 0.316 Chirality : 0.152 1.828 1165 Planarity : 0.003 0.060 1182 Dihedral : 11.173 105.221 1028 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.76 (0.30), residues: 820 helix: 1.64 (0.22), residues: 521 sheet: -0.34 (0.83), residues: 38 loop : -1.78 (0.40), residues: 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.050 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 outliers start: 4 outliers final: 3 residues processed: 104 average time/residue: 0.3696 time to fit residues: 53.6943 Evaluate side-chains 99 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.182 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1666 time to fit residues: 2.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 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 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS A 931 GLN A1117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7299 Z= 0.200 Angle : 0.671 11.029 9983 Z= 0.309 Chirality : 0.152 1.815 1165 Planarity : 0.003 0.057 1182 Dihedral : 10.954 105.619 1028 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.06 (0.30), residues: 820 helix: 1.87 (0.22), residues: 523 sheet: -0.23 (0.83), residues: 38 loop : -1.65 (0.41), residues: 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.028 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: 6 outliers final: 4 residues processed: 110 average time/residue: 0.3642 time to fit residues: 56.3421 Evaluate side-chains 101 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.215 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3074 time to fit residues: 3.3074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7299 Z= 0.230 Angle : 0.682 10.968 9983 Z= 0.315 Chirality : 0.152 1.805 1165 Planarity : 0.003 0.057 1182 Dihedral : 10.905 105.412 1028 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 820 helix: 1.96 (0.23), residues: 523 sheet: -0.08 (0.85), residues: 39 loop : -1.64 (0.41), residues: 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.082 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 outliers start: 3 outliers final: 2 residues processed: 104 average time/residue: 0.3637 time to fit residues: 52.9036 Evaluate side-chains 101 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.088 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1763 time to fit residues: 1.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7299 Z= 0.226 Angle : 0.686 10.994 9983 Z= 0.316 Chirality : 0.152 1.789 1165 Planarity : 0.003 0.056 1182 Dihedral : 10.858 105.331 1028 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.30 (0.31), residues: 820 helix: 2.06 (0.23), residues: 523 sheet: 0.77 (0.94), residues: 32 loop : -1.69 (0.40), residues: 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 110 average time/residue: 0.3583 time to fit residues: 55.6492 Evaluate side-chains 107 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.148 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1616 time to fit residues: 2.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 7299 Z= 0.296 Angle : 0.715 11.370 9983 Z= 0.334 Chirality : 0.153 1.795 1165 Planarity : 0.003 0.056 1182 Dihedral : 10.954 105.441 1028 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.16 (0.30), residues: 820 helix: 1.96 (0.23), residues: 524 sheet: 0.70 (0.92), residues: 32 loop : -1.77 (0.39), residues: 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 105 average time/residue: 0.3689 time to fit residues: 54.3333 Evaluate side-chains 102 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.089 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1706 time to fit residues: 2.3393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7299 Z= 0.204 Angle : 0.688 11.369 9983 Z= 0.316 Chirality : 0.152 1.785 1165 Planarity : 0.003 0.056 1182 Dihedral : 10.813 105.397 1028 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.33 (0.31), residues: 820 helix: 2.08 (0.23), residues: 524 sheet: 0.63 (0.91), residues: 32 loop : -1.66 (0.40), residues: 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.045 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 outliers start: 3 outliers final: 2 residues processed: 103 average time/residue: 0.3682 time to fit residues: 53.2473 Evaluate side-chains 103 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.130 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1546 time to fit residues: 1.9890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7299 Z= 0.196 Angle : 0.689 11.311 9983 Z= 0.314 Chirality : 0.151 1.774 1165 Planarity : 0.003 0.055 1182 Dihedral : 10.614 105.490 1028 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.39 (0.31), residues: 820 helix: 2.10 (0.23), residues: 530 sheet: 0.60 (0.91), residues: 32 loop : -1.65 (0.41), residues: 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.194 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 outliers start: 3 outliers final: 2 residues processed: 107 average time/residue: 0.3721 time to fit residues: 56.0725 Evaluate side-chains 103 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.129 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1558 time to fit residues: 2.0047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114457 restraints weight = 27288.405| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.48 r_work: 0.3385 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7299 Z= 0.229 Angle : 0.695 11.298 9983 Z= 0.319 Chirality : 0.152 1.781 1165 Planarity : 0.003 0.055 1182 Dihedral : 10.601 105.512 1028 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.36 (0.31), residues: 820 helix: 2.13 (0.23), residues: 524 sheet: 0.54 (0.90), residues: 32 loop : -1.68 (0.40), residues: 264 =============================================================================== Job complete usr+sys time: 3607.49 seconds wall clock time: 64 minutes 16.54 seconds (3856.54 seconds total)