Starting phenix.real_space_refine on Fri Jan 19 00:59:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h66_0145/01_2024/6h66_0145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h66_0145/01_2024/6h66_0145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h66_0145/01_2024/6h66_0145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h66_0145/01_2024/6h66_0145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h66_0145/01_2024/6h66_0145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h66_0145/01_2024/6h66_0145.pdb" } resolution = 4.16 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= 0.001 sd= 0.011 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 30 5.49 5 S 33 5.16 5 C 3624 2.51 5 N 1034 2.21 5 O 1175 1.98 5 H 4120 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10017 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 9377 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 645} Chain breaks: 7 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "X" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7936 SG CYS A 907 79.226 42.468 38.240 1.00 94.73 S ATOM 7983 SG CYS A 910 82.212 42.289 38.218 1.00 95.46 S ATOM 8600 SG CYS A 962 80.015 43.857 41.901 1.00 95.10 S ATOM 8615 SG CYS A 964 79.715 45.327 39.850 1.00 99.85 S Time building chain proxies: 4.88, per 1000 atoms: 0.49 Number of scatterers: 10017 At special positions: 0 Unit cell: (99.84, 91.52, 73.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 30 15.00 O 1175 8.00 N 1034 7.00 C 3624 6.00 H 4120 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.39 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " Number of angles added : 6 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 55.2% alpha, 6.7% beta 15 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.534A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 355 removed outlier: 4.022A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.944A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.927A pdb=" N TYR A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.549A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.599A pdb=" N GLU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 455 through 476 removed outlier: 3.933A pdb=" N MET A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.790A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.825A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.616A pdb=" N GLU A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.992A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 692 removed outlier: 4.291A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 716 removed outlier: 3.845A pdb=" N GLN A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 741 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 790 through 796 removed outlier: 3.831A pdb=" N GLU A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 790 through 796' Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.863A pdb=" N GLU A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.985A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 987 Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.562A pdb=" N GLU A1005 " --> pdb=" O LYS A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1019 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.754A pdb=" N ILE A 326 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 364 removed outlier: 6.091A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER A 413 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 362 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 722 through 723 Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 915 removed outlier: 6.549A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AA6, first strand: chain 'A' and resid 940 through 942 removed outlier: 6.350A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4109 1.03 - 1.23: 27 1.23 - 1.42: 2506 1.42 - 1.62: 3476 1.62 - 1.81: 52 Bond restraints: 10170 Sorted by residual: bond pdb=" CB MET A 459 " pdb=" CG MET A 459 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.43e+00 bond pdb=" N ASN A 379 " pdb=" CA ASN A 379 " ideal model delta sigma weight residual 1.462 1.448 0.014 7.70e-03 1.69e+04 3.31e+00 bond pdb=" CB VAL A 360 " pdb=" CG1 VAL A 360 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CG LYS A 466 " pdb=" CD LYS A 466 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CG LEU A 418 " pdb=" CD1 LEU A 418 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.43e+00 ... (remaining 10165 not shown) Histogram of bond angle deviations from ideal: 62.45 - 77.55: 6 77.55 - 92.66: 0 92.66 - 107.76: 1424 107.76 - 122.87: 15032 122.87 - 137.97: 1235 Bond angle restraints: 17697 Sorted by residual: angle pdb=" C LYS A 451 " pdb=" N GLU A 452 " pdb=" H GLU A 452 " ideal model delta sigma weight residual 124.11 70.97 53.14 3.00e+00 1.11e-01 3.14e+02 angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 124.56 72.49 52.07 3.00e+00 1.11e-01 3.01e+02 angle pdb=" CA GLU A 452 " pdb=" N GLU A 452 " pdb=" H GLU A 452 " ideal model delta sigma weight residual 113.81 62.45 51.36 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C ILE A 399 " pdb=" N SER A 400 " pdb=" H SER A 400 " ideal model delta sigma weight residual 124.49 73.30 51.19 3.00e+00 1.11e-01 2.91e+02 angle pdb=" CA SER A 400 " pdb=" N SER A 400 " pdb=" H SER A 400 " ideal model delta sigma weight residual 114.19 63.54 50.65 3.00e+00 1.11e-01 2.85e+02 ... (remaining 17692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 4549 14.77 - 29.53: 386 29.53 - 44.30: 83 44.30 - 59.06: 26 59.06 - 73.82: 32 Dihedral angle restraints: 5076 sinusoidal: 2871 harmonic: 2205 Sorted by residual: dihedral pdb=" CA LYS A 477 " pdb=" C LYS A 477 " pdb=" N PRO A 478 " pdb=" CA PRO A 478 " ideal model delta harmonic sigma weight residual 180.00 142.23 37.77 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" CA GLN A 999 " pdb=" C GLN A 999 " pdb=" N TYR A1000 " pdb=" CA TYR A1000 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA LEU A 902 " pdb=" C LEU A 902 " pdb=" N ILE A 903 " pdb=" CA ILE A 903 " ideal model delta harmonic sigma weight residual 180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 593 0.033 - 0.065: 238 0.065 - 0.098: 89 0.098 - 0.131: 45 0.131 - 0.163: 10 Chirality restraints: 975 Sorted by residual: chirality pdb=" CA PRO A 933 " pdb=" N PRO A 933 " pdb=" C PRO A 933 " pdb=" CB PRO A 933 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ILE A 417 " pdb=" N ILE A 417 " pdb=" C ILE A 417 " pdb=" CB ILE A 417 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE A 618 " pdb=" N ILE A 618 " pdb=" C ILE A 618 " pdb=" CB ILE A 618 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 972 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 987 " 0.027 2.00e-02 2.50e+03 1.58e-02 7.52e+00 pdb=" CG PHE A 987 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 987 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 987 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 987 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 987 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 987 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 987 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 987 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 987 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 987 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 987 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 460 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ARG A 460 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 460 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG A 461 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 491 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO A 492 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 492 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 492 " -0.029 5.00e-02 4.00e+02 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 244 2.15 - 2.76: 16443 2.76 - 3.37: 24632 3.37 - 3.99: 32075 3.99 - 4.60: 49773 Nonbonded interactions: 123167 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.532 1.816 nonbonded pdb=" H SER A 400 " pdb=" HA SER A 400 " model vdw 1.576 1.816 nonbonded pdb=" O SER A 357 " pdb=" HG SER A 439 " model vdw 1.657 1.850 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' U X 5 " model vdw 1.692 1.850 nonbonded pdb=" O ILE A 614 " pdb=" H ILE A 618 " model vdw 1.702 1.850 ... (remaining 123162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.170 Extract box with map and model: 3.070 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 41.560 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.008 0.056 6050 Z= 0.537 Angle : 0.885 16.792 8289 Z= 0.504 Chirality : 0.046 0.163 975 Planarity : 0.006 0.052 939 Dihedral : 12.769 73.825 2471 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.45 % Favored : 89.40 % Rotamer: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.28), residues: 651 helix: -0.66 (0.25), residues: 308 sheet: -3.20 (0.45), residues: 85 loop : -3.36 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 582 HIS 0.007 0.002 HIS A 447 PHE 0.046 0.004 PHE A 987 TYR 0.016 0.003 TYR A 312 ARG 0.009 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 0.817 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 TYR cc_start: 0.7495 (t80) cc_final: 0.7272 (t80) REVERT: A 603 GLU cc_start: 0.7977 (tt0) cc_final: 0.6979 (tm-30) REVERT: A 612 LEU cc_start: 0.9079 (mt) cc_final: 0.8862 (tt) REVERT: A 620 MET cc_start: 0.7780 (ptp) cc_final: 0.7562 (ptp) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.4438 time to fit residues: 95.2410 Evaluate side-chains 95 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6050 Z= 0.153 Angle : 0.631 23.337 8289 Z= 0.341 Chirality : 0.037 0.164 975 Planarity : 0.004 0.048 939 Dihedral : 14.384 73.752 1150 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.32), residues: 651 helix: 1.12 (0.29), residues: 314 sheet: -2.78 (0.52), residues: 74 loop : -3.04 (0.31), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1003 HIS 0.013 0.001 HIS A 928 PHE 0.010 0.001 PHE A 551 TYR 0.011 0.001 TYR A 939 ARG 0.005 0.001 ARG A 860 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.858 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: 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 585 GLN cc_start: 0.8653 (mp10) cc_final: 0.8224 (tp-100) REVERT: A 603 GLU cc_start: 0.7777 (tt0) cc_final: 0.7000 (tm-30) REVERT: A 864 MET cc_start: 0.7955 (ttt) cc_final: 0.7737 (ttt) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2990 time to fit residues: 52.6541 Evaluate side-chains 98 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6050 Z= 0.205 Angle : 0.634 23.065 8289 Z= 0.344 Chirality : 0.038 0.165 975 Planarity : 0.004 0.040 939 Dihedral : 14.305 74.144 1150 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.32), residues: 651 helix: 1.62 (0.29), residues: 311 sheet: -2.67 (0.52), residues: 85 loop : -2.90 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 582 HIS 0.009 0.001 HIS A 928 PHE 0.010 0.001 PHE A 438 TYR 0.016 0.002 TYR A 579 ARG 0.006 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.825 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 GLU cc_start: 0.7834 (tt0) cc_final: 0.7010 (tm-30) REVERT: A 864 MET cc_start: 0.7739 (ttt) cc_final: 0.7392 (ttt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3234 time to fit residues: 51.2988 Evaluate side-chains 89 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 0.0970 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6050 Z= 0.192 Angle : 0.629 23.294 8289 Z= 0.336 Chirality : 0.037 0.193 975 Planarity : 0.003 0.039 939 Dihedral : 14.276 73.986 1150 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.33), residues: 651 helix: 2.00 (0.29), residues: 311 sheet: -2.64 (0.52), residues: 87 loop : -2.70 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 737 HIS 0.007 0.001 HIS A 928 PHE 0.011 0.001 PHE A 551 TYR 0.011 0.002 TYR A 579 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.786 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.7820 (t0) cc_final: 0.7483 (t0) REVERT: A 585 GLN cc_start: 0.8721 (mp-120) cc_final: 0.8347 (tp-100) REVERT: A 603 GLU cc_start: 0.7911 (tt0) cc_final: 0.7048 (tm-30) REVERT: A 723 ILE cc_start: 0.9531 (mt) cc_final: 0.9159 (mm) REVERT: A 864 MET cc_start: 0.7693 (ttt) cc_final: 0.7288 (ttt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2853 time to fit residues: 45.0526 Evaluate side-chains 89 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 862 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6050 Z= 0.163 Angle : 0.606 23.030 8289 Z= 0.326 Chirality : 0.036 0.169 975 Planarity : 0.003 0.036 939 Dihedral : 14.314 73.976 1150 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.34), residues: 651 helix: 2.26 (0.29), residues: 311 sheet: -2.55 (0.53), residues: 87 loop : -2.60 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.005 0.001 HIS A 928 PHE 0.009 0.001 PHE A 551 TYR 0.012 0.001 TYR A 579 ARG 0.003 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.825 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.7728 (t0) cc_final: 0.7458 (t0) REVERT: A 603 GLU cc_start: 0.7899 (tt0) cc_final: 0.7065 (tm-30) REVERT: A 723 ILE cc_start: 0.9533 (mt) cc_final: 0.9197 (mm) REVERT: A 864 MET cc_start: 0.7717 (ttt) cc_final: 0.7350 (ttt) REVERT: A 912 MET cc_start: 0.7146 (ptt) cc_final: 0.6714 (ptt) REVERT: A 923 ILE cc_start: 0.9009 (pt) cc_final: 0.8728 (pt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2835 time to fit residues: 42.6171 Evaluate side-chains 87 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6050 Z= 0.177 Angle : 0.598 23.003 8289 Z= 0.323 Chirality : 0.036 0.187 975 Planarity : 0.003 0.034 939 Dihedral : 14.126 74.047 1150 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.34), residues: 651 helix: 2.37 (0.29), residues: 314 sheet: -2.51 (0.54), residues: 87 loop : -2.51 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.006 0.001 HIS A 928 PHE 0.014 0.001 PHE A 551 TYR 0.011 0.001 TYR A 579 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.814 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: 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: 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 515 ASP cc_start: 0.7872 (t0) cc_final: 0.7613 (t0) REVERT: A 603 GLU cc_start: 0.7920 (tt0) cc_final: 0.7117 (tm-30) REVERT: A 615 ASN cc_start: 0.7805 (t0) cc_final: 0.7454 (t0) REVERT: A 723 ILE cc_start: 0.9545 (mt) cc_final: 0.9211 (mm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2971 time to fit residues: 45.5396 Evaluate side-chains 93 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6050 Z= 0.219 Angle : 0.625 23.099 8289 Z= 0.335 Chirality : 0.037 0.176 975 Planarity : 0.003 0.035 939 Dihedral : 14.131 73.970 1150 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.34), residues: 651 helix: 2.30 (0.29), residues: 313 sheet: -2.55 (0.56), residues: 87 loop : -2.50 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1003 HIS 0.006 0.001 HIS A 928 PHE 0.017 0.001 PHE A 551 TYR 0.011 0.002 TYR A 579 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.882 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 GLU cc_start: 0.7974 (tt0) cc_final: 0.7138 (tm-30) REVERT: A 723 ILE cc_start: 0.9555 (mt) cc_final: 0.9248 (mm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3261 time to fit residues: 47.3203 Evaluate side-chains 91 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6050 Z= 0.159 Angle : 0.589 22.913 8289 Z= 0.316 Chirality : 0.036 0.175 975 Planarity : 0.003 0.031 939 Dihedral : 14.081 73.971 1150 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.35), residues: 651 helix: 2.36 (0.29), residues: 320 sheet: -2.47 (0.56), residues: 87 loop : -2.40 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.004 0.001 HIS A 928 PHE 0.007 0.001 PHE A 551 TYR 0.010 0.001 TYR A 579 ARG 0.004 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.029 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.7031 (ttt) cc_final: 0.6741 (ttp) REVERT: A 603 GLU cc_start: 0.7936 (tt0) cc_final: 0.7156 (tm-30) REVERT: A 723 ILE cc_start: 0.9540 (mt) cc_final: 0.9231 (mm) REVERT: A 877 GLN cc_start: 0.8106 (mt0) cc_final: 0.7642 (mm-40) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2773 time to fit residues: 42.5804 Evaluate side-chains 87 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6050 Z= 0.202 Angle : 0.613 23.277 8289 Z= 0.330 Chirality : 0.037 0.169 975 Planarity : 0.003 0.033 939 Dihedral : 14.124 73.999 1150 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.35), residues: 651 helix: 2.16 (0.29), residues: 321 sheet: -2.47 (0.57), residues: 87 loop : -2.37 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 737 HIS 0.005 0.001 HIS A 928 PHE 0.018 0.001 PHE A 551 TYR 0.009 0.001 TYR A 579 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.953 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.7096 (ttt) cc_final: 0.6734 (ttp) REVERT: A 603 GLU cc_start: 0.7949 (tt0) cc_final: 0.7175 (tm-30) REVERT: A 613 GLN cc_start: 0.8613 (pm20) cc_final: 0.8185 (pm20) REVERT: A 723 ILE cc_start: 0.9530 (mt) cc_final: 0.9226 (mm) REVERT: A 769 THR cc_start: 0.9519 (p) cc_final: 0.9274 (t) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2845 time to fit residues: 40.8661 Evaluate side-chains 87 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 0.0670 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6050 Z= 0.136 Angle : 0.582 23.071 8289 Z= 0.311 Chirality : 0.036 0.178 975 Planarity : 0.003 0.029 939 Dihedral : 14.008 73.950 1150 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.35), residues: 651 helix: 2.45 (0.29), residues: 321 sheet: -2.32 (0.57), residues: 85 loop : -2.30 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.003 0.001 HIS A 928 PHE 0.006 0.001 PHE A 935 TYR 0.010 0.001 TYR A 579 ARG 0.002 0.000 ARG A 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.887 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.7153 (ttt) cc_final: 0.6683 (ttp) REVERT: A 603 GLU cc_start: 0.7995 (tt0) cc_final: 0.7217 (tm-30) REVERT: A 607 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8697 (mmmm) REVERT: A 613 GLN cc_start: 0.8581 (pm20) cc_final: 0.8256 (pm20) REVERT: A 723 ILE cc_start: 0.9525 (mt) cc_final: 0.9229 (mm) REVERT: A 864 MET cc_start: 0.7853 (ttt) cc_final: 0.7467 (ttt) REVERT: A 877 GLN cc_start: 0.8128 (mt0) cc_final: 0.7622 (mm-40) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2917 time to fit residues: 41.3083 Evaluate side-chains 87 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.0000 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086830 restraints weight = 40685.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.090325 restraints weight = 19279.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092527 restraints weight = 12071.293| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6050 Z= 0.185 Angle : 0.598 23.196 8289 Z= 0.320 Chirality : 0.036 0.168 975 Planarity : 0.003 0.032 939 Dihedral : 14.083 74.003 1150 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.35), residues: 651 helix: 2.34 (0.29), residues: 322 sheet: -2.47 (0.56), residues: 85 loop : -2.28 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 737 HIS 0.004 0.001 HIS A 928 PHE 0.007 0.001 PHE A 849 TYR 0.011 0.001 TYR A 462 ARG 0.003 0.000 ARG A 461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.77 seconds wall clock time: 47 minutes 14.77 seconds (2834.77 seconds total)