Starting phenix.real_space_refine on Fri Sep 27 00:05:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/09_2024/6tbu_10452_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/09_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_10452/09_2024/6tbu_10452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/09_2024/6tbu_10452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/09_2024/6tbu_10452_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tbu_10452/09_2024/6tbu_10452_trim.cif" } 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. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.30, per 1000 atoms: 0.53 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 - 3.00 Amino acid : True - 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=1, 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.1 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: 1.09 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: 4.65 Time building geometry restraints manager: 4.53 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: 0.00 - 5.54: 24795 5.54 - 11.08: 173 11.08 - 16.61: 17 16.61 - 22.15: 4 22.15 - 27.69: 27 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: 1.70 - 2.28: 2111 2.28 - 2.86: 29952 2.86 - 3.44: 35682 3.44 - 4.02: 47263 4.02 - 4.60: 73773 Nonbonded interactions: 188781 Sorted by model distance: nonbonded pdb=" HH TYR A 490 " pdb=" O PHE A 498 " model vdw 1.701 2.450 nonbonded pdb=" O ALA A 17 " pdb="HH21 ARG A 627 " model vdw 1.709 2.450 nonbonded pdb=" O GLU A 698 " pdb=" HG1 THR A 914 " model vdw 1.714 2.450 nonbonded pdb=" O MET A 851 " pdb=" HG1 THR A 854 " model vdw 1.739 2.450 nonbonded pdb="HH21 ARG A 260 " pdb=" O SER A 268 " model vdw 1.742 2.450 ... (remaining 188776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.970 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: 0.230 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.220 Find NCS groups from input model: 0.090 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- 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= 0.789 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 : 2.060 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 : 1.008 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: 0.4747 time to fit residues: 89.7711 Evaluate side-chains 101 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 0.8980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 A1052 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7299 Z= 0.217 Angle : 0.760 10.954 9983 Z= 0.345 Chirality : 0.151 1.830 1165 Planarity : 0.004 0.065 1182 Dihedral : 11.569 79.765 1595 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.85 % Rotamer: Outliers : 0.95 % Allowed : 8.70 % Favored : 90.35 % 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: -0.43 (0.29), residues: 820 helix: 0.72 (0.21), residues: 520 sheet: -0.34 (0.81), residues: 30 loop : -2.29 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.013 0.001 PHE A1119 TYR 0.012 0.001 TYR A 342 ARG 0.003 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 116 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.975 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: 0.7862 (t80) cc_final: 0.7590 (t80) REVERT: A 427 GLU cc_start: 0.7691 (tp30) cc_final: 0.7157 (tp30) REVERT: A 810 MET cc_start: 0.8506 (mmp) cc_final: 0.8298 (mmp) REVERT: A 842 TYR cc_start: 0.7457 (t80) cc_final: 0.6870 (t80) outliers start: 7 outliers final: 4 residues processed: 113 average time/residue: 0.3598 time to fit residues: 56.7046 Evaluate side-chains 99 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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: 0.7948 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7299 Z= 0.219 Angle : 0.719 11.011 9983 Z= 0.329 Chirality : 0.152 1.807 1165 Planarity : 0.004 0.059 1182 Dihedral : 9.386 59.080 1595 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.22 % Allowed : 10.05 % Favored : 88.72 % 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: 0.32 (0.30), residues: 820 helix: 1.33 (0.22), residues: 520 sheet: -0.64 (0.80), residues: 38 loop : -1.99 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.011 0.001 PHE A 981 TYR 0.009 0.001 TYR A 490 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 117 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.002 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: 0.7878 (t80) cc_final: 0.7455 (t80) REVERT: A 459 MET cc_start: 0.7371 (mmp) cc_final: 0.7112 (mmp) outliers start: 9 outliers final: 5 residues processed: 115 average time/residue: 0.3794 time to fit residues: 61.6309 Evaluate side-chains 104 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 736 HIS Chi-restraints excluded: chain A residue 1022 SER 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: 2.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 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 ** 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: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7299 Z= 0.237 Angle : 0.705 13.649 9983 Z= 0.326 Chirality : 0.153 1.853 1165 Planarity : 0.004 0.058 1182 Dihedral : 8.924 58.025 1595 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.95 % Allowed : 10.87 % 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: 0.63 (0.30), residues: 820 helix: 1.56 (0.22), residues: 521 sheet: -0.52 (0.81), residues: 39 loop : -1.85 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.011 0.001 PHE A 981 TYR 0.017 0.001 TYR A 842 ARG 0.003 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 114 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.069 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: 0.7915 (t80) cc_final: 0.7535 (t80) REVERT: A 474 MET cc_start: 0.7325 (mmm) cc_final: 0.7118 (mmt) outliers start: 7 outliers final: 7 residues processed: 112 average time/residue: 0.3472 time to fit residues: 54.5858 Evaluate side-chains 110 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 736 HIS Chi-restraints excluded: chain A residue 985 ILE 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: 0.6980 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.8013 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7299 Z= 0.232 Angle : 0.688 12.768 9983 Z= 0.317 Chirality : 0.152 1.831 1165 Planarity : 0.003 0.057 1182 Dihedral : 8.187 59.580 1595 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.49 % Allowed : 10.87 % Favored : 87.64 % 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: 0.85 (0.30), residues: 820 helix: 1.72 (0.22), residues: 523 sheet: -0.46 (0.81), residues: 39 loop : -1.77 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.011 0.001 PHE A 981 TYR 0.009 0.001 TYR A 490 ARG 0.001 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 124 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.131 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: 0.7966 (t80) cc_final: 0.7637 (t80) REVERT: A 708 LYS cc_start: 0.8078 (pptt) cc_final: 0.7649 (pptt) outliers start: 11 outliers final: 9 residues processed: 121 average time/residue: 0.3989 time to fit residues: 69.7593 Evaluate side-chains 113 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 736 HIS Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 985 ILE 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: 0.9980 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.3852 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= 0.245 Angle : 0.687 11.879 9983 Z= 0.320 Chirality : 0.152 1.789 1165 Planarity : 0.004 0.055 1182 Dihedral : 7.857 59.418 1595 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.49 % Allowed : 11.96 % Favored : 86.55 % 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: 1.82 (0.22), residues: 523 sheet: -0.27 (0.85), residues: 39 loop : -1.80 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.011 0.001 PHE A 654 TYR 0.009 0.001 TYR A 611 ARG 0.003 0.000 ARG A 57 *********************** 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: 11 poor density : 107 time to evaluate : 1.034 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: 0.8023 (t80) cc_final: 0.7717 (t80) REVERT: A 708 LYS cc_start: 0.8048 (pptt) cc_final: 0.7648 (pptt) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.3394 time to fit residues: 55.1050 Evaluate side-chains 109 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 371 ILE Chi-restraints excluded: chain A residue 392 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 32 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: 0.8021 moved from start: 0.3989 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= 0.194 Angle : 0.673 11.029 9983 Z= 0.310 Chirality : 0.151 1.778 1165 Planarity : 0.003 0.055 1182 Dihedral : 7.533 59.559 1595 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.36 % Allowed : 12.77 % Favored : 85.87 % 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: 1.93 (0.22), residues: 523 sheet: 0.49 (0.94), residues: 32 loop : -1.72 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 PHE 0.013 0.001 PHE A 833 TYR 0.010 0.001 TYR A 313 ARG 0.001 0.000 ARG A 368 *********************** 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 116 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.7998 (t80) cc_final: 0.7701 (t80) REVERT: A 708 LYS cc_start: 0.8050 (pptt) cc_final: 0.7654 (pptt) REVERT: A 1084 TYR cc_start: 0.8312 (m-10) cc_final: 0.7619 (m-10) outliers start: 10 outliers final: 9 residues processed: 114 average time/residue: 0.3722 time to fit residues: 60.7804 Evaluate side-chains 111 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7299 Z= 0.220 Angle : 0.686 10.976 9983 Z= 0.317 Chirality : 0.152 1.766 1165 Planarity : 0.004 0.054 1182 Dihedral : 7.379 56.233 1595 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.22 % Allowed : 13.32 % Favored : 85.46 % 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: 1.17 (0.30), residues: 820 helix: 1.97 (0.22), residues: 523 sheet: 0.45 (0.92), residues: 32 loop : -1.72 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 PHE 0.013 0.001 PHE A 654 TYR 0.012 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 112 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.936 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: 0.8015 (t80) cc_final: 0.7727 (t80) REVERT: A 708 LYS cc_start: 0.8089 (pptt) cc_final: 0.7692 (pptt) REVERT: A 1084 TYR cc_start: 0.8306 (m-10) cc_final: 0.7608 (m-10) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.3452 time to fit residues: 53.5596 Evaluate side-chains 107 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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=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: 0.5980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7299 Z= 0.284 Angle : 0.712 10.934 9983 Z= 0.334 Chirality : 0.153 1.778 1165 Planarity : 0.004 0.053 1182 Dihedral : 7.416 56.325 1595 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.36 % Allowed : 13.59 % 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: 1.06 (0.30), residues: 820 helix: 1.88 (0.22), residues: 524 sheet: 0.44 (0.92), residues: 32 loop : -1.78 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.011 0.001 PHE A 833 TYR 0.010 0.001 TYR A 611 ARG 0.003 0.000 ARG A 57 *********************** 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 113 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.947 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: 0.8112 (t80) cc_final: 0.7841 (t80) REVERT: A 708 LYS cc_start: 0.8126 (pptt) cc_final: 0.7744 (pptt) outliers start: 10 outliers final: 8 residues processed: 111 average time/residue: 0.3727 time to fit residues: 57.2828 Evaluate side-chains 103 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 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 A 931 GLN A 954 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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= 0.195 Angle : 0.682 11.017 9983 Z= 0.314 Chirality : 0.151 1.765 1165 Planarity : 0.004 0.054 1182 Dihedral : 7.147 55.114 1595 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.09 % Allowed : 14.40 % Favored : 84.51 % 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: 1.21 (0.30), residues: 820 helix: 2.00 (0.23), residues: 524 sheet: 0.31 (0.90), residues: 32 loop : -1.68 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 PHE 0.014 0.001 PHE A 654 TYR 0.012 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 106 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8044 (t80) cc_final: 0.7775 (t80) REVERT: A 708 LYS cc_start: 0.8111 (pptt) cc_final: 0.7753 (pptt) REVERT: A 1084 TYR cc_start: 0.8295 (m-10) cc_final: 0.7511 (m-10) outliers start: 8 outliers final: 8 residues processed: 106 average time/residue: 0.3477 time to fit residues: 51.9022 Evaluate side-chains 103 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.141913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114288 restraints weight = 27263.823| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.48 r_work: 0.3366 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7299 Z= 0.216 Angle : 0.693 10.975 9983 Z= 0.319 Chirality : 0.151 1.766 1165 Planarity : 0.004 0.054 1182 Dihedral : 7.041 55.009 1595 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.22 % Allowed : 14.67 % 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: 1.26 (0.30), residues: 820 helix: 2.04 (0.22), residues: 524 sheet: 0.36 (0.91), residues: 32 loop : -1.68 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.014 0.001 PHE A 654 TYR 0.009 0.001 TYR A 611 ARG 0.006 0.000 ARG A 858 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3686.95 seconds wall clock time: 64 minutes 50.84 seconds (3890.84 seconds total)