Starting phenix.real_space_refine on Mon Apr 8 18:19:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/04_2024/6tbu_10452_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/04_2024/6tbu_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_10452/04_2024/6tbu_10452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/04_2024/6tbu_10452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/04_2024/6tbu_10452_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/04_2024/6tbu_10452_trim.pdb" } resolution = 3.16 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= 0.002 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 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. 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-5288/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.25, per 1000 atoms: 0.46 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: 11.96 Conformation dependent library (CDL) restraints added in 1.6 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: 1.02 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: 4.94 Time building geometry restraints manager: 11.89 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 - 24.53: 6652 24.53 - 49.06: 398 49.06 - 73.59: 89 73.59 - 98.12: 6 98.12 - 122.64: 17 Dihedral angle restraints: 7162 sinusoidal: 4026 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 7159 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 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: 1.840 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: 0.220 Extract box with map and model: 6.380 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.130 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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= 0.770 Angle : 1.507 18.173 9983 Z= 0.608 Chirality : 0.175 1.862 1165 Planarity : 0.005 0.070 1182 Dihedral : 16.676 122.645 3092 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 % Allowed : 3.94 % Favored : 96.06 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 617 HIS 0.011 0.001 HIS A 838 PHE 0.014 0.002 PHE A 840 TYR 0.012 0.001 TYR A 916 ARG 0.004 0.001 ARG A1057 *********************** 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 : 0.998 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: A 393 TYR cc_start: 0.7807 (t80) cc_final: 0.7501 (t80) REVERT: A 427 GLU cc_start: 0.7700 (tp30) cc_final: 0.7206 (tp30) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4902 time to fit residues: 92.2513 Evaluate side-chains 101 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7299 Z= 0.220 Angle : 0.752 11.739 9983 Z= 0.343 Chirality : 0.152 1.845 1165 Planarity : 0.004 0.065 1182 Dihedral : 11.597 81.112 1595 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.09 % Allowed : 9.65 % Favored : 89.27 % 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: -0.45 (0.29), residues: 820 helix: 0.72 (0.21), residues: 520 sheet: -0.33 (0.82), residues: 30 loop : -2.33 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.012 0.001 PHE A1119 TYR 0.011 0.001 TYR A 916 ARG 0.005 0.000 ARG A 57 *********************** 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 118 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.026 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: A 393 TYR cc_start: 0.7866 (t80) cc_final: 0.7403 (t80) REVERT: A 810 MET cc_start: 0.8538 (mmp) cc_final: 0.8298 (mmp) outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 0.3700 time to fit residues: 59.5279 Evaluate side-chains 98 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 1022 SER 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: 0.0470 chunk 63 optimal weight: 0.0970 chunk 51 optimal weight: 0.0040 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.4288 ------------------------------------------------------------------------------- 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: 0.7915 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7299 Z= 0.183 Angle : 0.695 11.026 9983 Z= 0.316 Chirality : 0.151 1.807 1165 Planarity : 0.003 0.060 1182 Dihedral : 9.277 58.758 1595 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.09 % Allowed : 10.73 % Favored : 88.18 % 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: 0.31 (0.30), residues: 820 helix: 1.34 (0.22), residues: 520 sheet: -0.83 (0.77), residues: 39 loop : -1.98 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.010 0.001 PHE A 981 TYR 0.009 0.001 TYR A 916 ARG 0.002 0.000 ARG A 57 *********************** 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 114 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.046 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: A 378 PHE cc_start: 0.6316 (m-80) cc_final: 0.6004 (m-80) REVERT: A 393 TYR cc_start: 0.7847 (t80) cc_final: 0.7437 (t80) REVERT: A 459 MET cc_start: 0.7472 (mmp) cc_final: 0.7262 (mmp) outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 0.3796 time to fit residues: 58.2905 Evaluate side-chains 106 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 736 HIS 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: 0.7980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.3125 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= 0.227 Angle : 0.705 14.752 9983 Z= 0.325 Chirality : 0.154 1.874 1165 Planarity : 0.003 0.057 1182 Dihedral : 8.545 58.249 1595 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.09 % Allowed : 11.55 % Favored : 87.36 % 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: 0.70 (0.30), residues: 820 helix: 1.61 (0.22), residues: 521 sheet: -0.36 (0.83), residues: 38 loop : -1.83 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 617 HIS 0.006 0.001 HIS A 759 PHE 0.011 0.001 PHE A 981 TYR 0.018 0.001 TYR A 842 ARG 0.004 0.000 ARG A 57 *********************** 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 117 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.963 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: A 393 TYR cc_start: 0.7956 (t80) cc_final: 0.7604 (t80) REVERT: A 459 MET cc_start: 0.7602 (mmp) cc_final: 0.7351 (mmp) outliers start: 8 outliers final: 6 residues processed: 114 average time/residue: 0.3550 time to fit residues: 56.9902 Evaluate side-chains 106 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 A1117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7299 Z= 0.256 Angle : 0.696 11.599 9983 Z= 0.324 Chirality : 0.153 1.869 1165 Planarity : 0.003 0.055 1182 Dihedral : 7.976 59.250 1595 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.17 % Allowed : 12.23 % Favored : 85.60 % 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: 0.86 (0.30), residues: 820 helix: 1.72 (0.22), residues: 523 sheet: -0.29 (0.82), residues: 39 loop : -1.75 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.011 0.001 PHE A 981 TYR 0.010 0.001 TYR A 313 ARG 0.003 0.000 ARG A 57 *********************** 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 125 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8010 (t80) cc_final: 0.7701 (t80) outliers start: 16 outliers final: 8 residues processed: 119 average time/residue: 0.3601 time to fit residues: 61.1179 Evaluate side-chains 110 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7299 Z= 0.211 Angle : 0.676 11.309 9983 Z= 0.311 Chirality : 0.152 1.788 1165 Planarity : 0.003 0.055 1182 Dihedral : 7.665 59.412 1595 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.77 % Allowed : 13.18 % Favored : 85.05 % 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: 1.14 (0.30), residues: 820 helix: 1.94 (0.23), residues: 523 sheet: 0.55 (0.92), residues: 32 loop : -1.74 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.011 0.001 PHE A 654 TYR 0.014 0.001 TYR A 313 ARG 0.002 0.000 ARG A 368 *********************** 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 118 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.067 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: A 393 TYR cc_start: 0.8011 (t80) cc_final: 0.7718 (t80) REVERT: A 459 MET cc_start: 0.7576 (mmp) cc_final: 0.7318 (mmp) outliers start: 13 outliers final: 11 residues processed: 115 average time/residue: 0.3576 time to fit residues: 58.1041 Evaluate side-chains 112 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 985 ILE 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: 0.7980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7299 Z= 0.203 Angle : 0.669 10.971 9983 Z= 0.308 Chirality : 0.151 1.786 1165 Planarity : 0.003 0.054 1182 Dihedral : 7.404 59.711 1595 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.90 % Allowed : 13.45 % Favored : 84.65 % 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: 1.27 (0.31), residues: 820 helix: 2.01 (0.23), residues: 523 sheet: 0.72 (0.96), residues: 32 loop : -1.65 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.012 0.001 PHE A 654 TYR 0.014 0.001 TYR A 313 ARG 0.001 0.000 ARG A 57 *********************** 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 118 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 PHE cc_start: 0.6250 (m-80) cc_final: 0.5978 (m-80) REVERT: A 393 TYR cc_start: 0.8002 (t80) cc_final: 0.7722 (t80) REVERT: A 1084 TYR cc_start: 0.8329 (m-10) cc_final: 0.7585 (m-10) outliers start: 14 outliers final: 11 residues processed: 115 average time/residue: 0.3745 time to fit residues: 61.8458 Evaluate side-chains 113 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1022 SER 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: 3.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7299 Z= 0.325 Angle : 0.722 10.938 9983 Z= 0.338 Chirality : 0.153 1.790 1165 Planarity : 0.004 0.054 1182 Dihedral : 7.485 56.363 1595 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.77 % Allowed : 14.40 % Favored : 83.83 % 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: 1.07 (0.30), residues: 820 helix: 1.89 (0.22), residues: 524 sheet: 0.70 (0.95), residues: 32 loop : -1.81 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 617 HIS 0.006 0.001 HIS A1038 PHE 0.011 0.001 PHE A 677 TYR 0.013 0.001 TYR A 313 ARG 0.005 0.000 ARG A 813 *********************** 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 116 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8109 (t80) cc_final: 0.7841 (t80) REVERT: A 459 MET cc_start: 0.7632 (mmp) cc_final: 0.7396 (mmp) REVERT: A 474 MET cc_start: 0.7425 (mmt) cc_final: 0.7211 (mmt) outliers start: 13 outliers final: 11 residues processed: 113 average time/residue: 0.3615 time to fit residues: 57.5787 Evaluate side-chains 111 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1022 SER 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: 0.9980 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7299 Z= 0.299 Angle : 0.715 10.966 9983 Z= 0.336 Chirality : 0.153 1.779 1165 Planarity : 0.004 0.055 1182 Dihedral : 7.457 55.820 1595 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.10 % 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: 0.95 (0.30), residues: 820 helix: 1.81 (0.22), residues: 523 sheet: 0.60 (0.93), residues: 32 loop : -1.87 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 617 HIS 0.008 0.001 HIS A 14 PHE 0.012 0.001 PHE A 654 TYR 0.016 0.001 TYR A 313 ARG 0.004 0.000 ARG A 813 *********************** 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 111 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8148 (t80) cc_final: 0.7874 (t80) REVERT: A 474 MET cc_start: 0.7500 (mmt) cc_final: 0.7062 (mmt) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.3797 time to fit residues: 57.5923 Evaluate side-chains 107 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8044 moved from start: 0.4343 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= 0.190 Angle : 0.686 11.007 9983 Z= 0.315 Chirality : 0.150 1.762 1165 Planarity : 0.003 0.055 1182 Dihedral : 7.134 54.200 1595 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.36 % Allowed : 15.08 % Favored : 83.56 % 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: 1.27 (0.31), residues: 820 helix: 2.04 (0.23), residues: 523 sheet: 0.54 (0.91), residues: 32 loop : -1.66 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.015 0.001 PHE A 654 TYR 0.013 0.001 TYR A 313 ARG 0.003 0.000 ARG A 813 ********************** 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 113 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.133 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: A 393 TYR cc_start: 0.8088 (t80) cc_final: 0.7820 (t80) REVERT: A 1084 TYR cc_start: 0.8302 (m-10) cc_final: 0.7563 (m-10) outliers start: 10 outliers final: 9 residues processed: 110 average time/residue: 0.3598 time to fit residues: 55.9052 Evaluate side-chains 108 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113931 restraints weight = 27277.814| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.48 r_work: 0.3360 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4429 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 : 0.688 10.945 9983 Z= 0.316 Chirality : 0.151 1.776 1165 Planarity : 0.004 0.054 1182 Dihedral : 7.028 54.219 1595 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.36 % Allowed : 15.08 % Favored : 83.56 % 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: 1.32 (0.31), residues: 820 helix: 2.08 (0.23), residues: 523 sheet: 0.61 (0.93), residues: 32 loop : -1.65 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.014 0.001 PHE A 654 TYR 0.009 0.001 TYR A 611 ARG 0.002 0.000 ARG A 813 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3760.72 seconds wall clock time: 70 minutes 23.67 seconds (4223.67 seconds total)