Starting phenix.real_space_refine on Fri Feb 14 14:38:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h66_0145/02_2025/6h66_0145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h66_0145/02_2025/6h66_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/cci-nas-00/data/ceres_data/6h66_0145/02_2025/6h66_0145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h66_0145/02_2025/6h66_0145.map" model { file = "/net/cci-nas-00/data/ceres_data/6h66_0145/02_2025/6h66_0145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h66_0145/02_2025/6h66_0145.cif" } 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. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.50, per 1000 atoms: 0.55 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 648.4 milliseconds 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: 3.92 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: 3.48 Time building geometry restraints manager: 3.19 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: 0.00 - 10.63: 17688 10.63 - 21.26: 3 21.26 - 31.88: 0 31.88 - 42.51: 0 42.51 - 53.14: 6 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: 4562 14.77 - 29.53: 408 29.53 - 44.30: 97 44.30 - 59.06: 45 59.06 - 73.82: 34 Dihedral angle restraints: 5146 sinusoidal: 2941 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 5143 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 2.450 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' U X 5 " model vdw 1.692 2.450 nonbonded pdb=" O ILE A 614 " pdb=" H ILE A 618 " model vdw 1.702 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.960 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- 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 : 13.218 73.825 2495 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 to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.782 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: 0.4431 time to fit residues: 94.6254 Evaluate side-chains 95 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 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 563 GLN A 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090538 restraints weight = 40211.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094445 restraints weight = 18800.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096786 restraints weight = 11447.324| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6050 Z= 0.181 Angle : 0.649 23.258 8289 Z= 0.353 Chirality : 0.038 0.161 975 Planarity : 0.004 0.048 939 Dihedral : 15.201 73.906 1174 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % 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: -1.56 (0.31), residues: 651 helix: 1.02 (0.28), residues: 314 sheet: -2.95 (0.51), residues: 74 loop : -3.12 (0.31), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 582 HIS 0.014 0.002 HIS A 928 PHE 0.011 0.001 PHE A 551 TYR 0.010 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 130 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.913 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: A 444 ASP cc_start: 0.7602 (t70) cc_final: 0.7209 (p0) REVERT: A 540 PHE cc_start: 0.6682 (m-10) cc_final: 0.6156 (p90) REVERT: A 585 GLN cc_start: 0.8755 (mp10) cc_final: 0.8378 (tp40) REVERT: A 603 GLU cc_start: 0.8178 (tt0) cc_final: 0.7203 (tm-30) REVERT: A 864 MET cc_start: 0.7991 (ttt) cc_final: 0.7727 (ttt) REVERT: A 923 ILE cc_start: 0.9286 (pt) cc_final: 0.9071 (pt) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.3076 time to fit residues: 54.4422 Evaluate side-chains 97 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN A 993 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084966 restraints weight = 42212.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088559 restraints weight = 19801.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090809 restraints weight = 12298.979| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6050 Z= 0.331 Angle : 0.727 23.156 8289 Z= 0.394 Chirality : 0.040 0.148 975 Planarity : 0.005 0.043 939 Dihedral : 15.189 74.116 1174 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -1.60 (0.31), residues: 651 helix: 1.10 (0.28), residues: 314 sheet: -3.25 (0.45), residues: 87 loop : -3.16 (0.31), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.012 0.002 HIS A 928 PHE 0.013 0.002 PHE A 849 TYR 0.014 0.002 TYR A 381 ARG 0.007 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 110 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.815 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: A 342 TYR cc_start: 0.7785 (t80) cc_final: 0.7560 (t80) REVERT: A 446 CYS cc_start: 0.8379 (m) cc_final: 0.8076 (m) REVERT: A 540 PHE cc_start: 0.6966 (m-10) cc_final: 0.6414 (p90) REVERT: A 585 GLN cc_start: 0.8877 (mp10) cc_final: 0.8405 (tp-100) REVERT: A 603 GLU cc_start: 0.8192 (tt0) cc_final: 0.7151 (tm-30) REVERT: A 832 LEU cc_start: 0.8159 (tp) cc_final: 0.7940 (mt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3176 time to fit residues: 46.6869 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086414 restraints weight = 41268.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090175 restraints weight = 19409.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092466 restraints weight = 11874.986| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6050 Z= 0.159 Angle : 0.625 23.078 8289 Z= 0.332 Chirality : 0.037 0.157 975 Planarity : 0.003 0.037 939 Dihedral : 15.123 73.964 1174 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.83 (0.32), residues: 651 helix: 1.78 (0.29), residues: 315 sheet: -2.89 (0.50), residues: 75 loop : -2.91 (0.32), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A1003 HIS 0.007 0.001 HIS A 928 PHE 0.008 0.001 PHE A 849 TYR 0.010 0.001 TYR A 939 ARG 0.003 0.000 ARG A 599 *********************** 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 107 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.818 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 540 PHE cc_start: 0.6928 (m-10) cc_final: 0.6387 (p90) REVERT: A 581 GLN cc_start: 0.8613 (tt0) cc_final: 0.8381 (tt0) REVERT: A 585 GLN cc_start: 0.8825 (mp10) cc_final: 0.8400 (tp-100) REVERT: A 603 GLU cc_start: 0.8264 (tt0) cc_final: 0.7199 (tm-30) REVERT: A 723 ILE cc_start: 0.9461 (mt) cc_final: 0.9062 (mm) REVERT: A 864 MET cc_start: 0.7706 (ttt) cc_final: 0.7277 (ttt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3031 time to fit residues: 44.1851 Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 60 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088007 restraints weight = 40792.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.091703 restraints weight = 19045.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093994 restraints weight = 11669.621| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6050 Z= 0.134 Angle : 0.584 22.944 8289 Z= 0.313 Chirality : 0.036 0.149 975 Planarity : 0.003 0.034 939 Dihedral : 15.023 73.966 1174 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.34), residues: 651 helix: 2.26 (0.29), residues: 317 sheet: -2.71 (0.51), residues: 75 loop : -2.74 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 737 HIS 0.004 0.001 HIS A 928 PHE 0.005 0.001 PHE A 401 TYR 0.008 0.001 TYR A 565 ARG 0.003 0.000 ARG A 375 *********************** 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 106 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.647 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: A 540 PHE cc_start: 0.6992 (m-10) cc_final: 0.6238 (p90) REVERT: A 581 GLN cc_start: 0.8568 (tt0) cc_final: 0.8302 (tt0) REVERT: A 585 GLN cc_start: 0.8795 (mp10) cc_final: 0.8396 (tp-100) REVERT: A 603 GLU cc_start: 0.8221 (tt0) cc_final: 0.7221 (tm-30) REVERT: A 723 ILE cc_start: 0.9497 (mt) cc_final: 0.9124 (mm) REVERT: A 864 MET cc_start: 0.7749 (ttt) cc_final: 0.7337 (ttt) REVERT: A 923 ILE cc_start: 0.9119 (pt) cc_final: 0.8839 (pt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3068 time to fit residues: 43.3790 Evaluate side-chains 86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086841 restraints weight = 40710.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090611 restraints weight = 18651.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.092940 restraints weight = 11299.300| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6050 Z= 0.163 Angle : 0.595 23.085 8289 Z= 0.318 Chirality : 0.036 0.145 975 Planarity : 0.003 0.033 939 Dihedral : 15.018 73.998 1174 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % 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: -0.08 (0.34), residues: 651 helix: 2.44 (0.29), residues: 315 sheet: -2.58 (0.53), residues: 75 loop : -2.58 (0.35), residues: 261 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 0.006 0.001 PHE A 401 TYR 0.008 0.001 TYR A 624 ARG 0.005 0.000 ARG A 596 *********************** 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 103 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 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: A 540 PHE cc_start: 0.7073 (m-10) cc_final: 0.6225 (p90) REVERT: A 559 MET cc_start: 0.7996 (mtp) cc_final: 0.7730 (mtp) REVERT: A 603 GLU cc_start: 0.8307 (tt0) cc_final: 0.7254 (tm-30) REVERT: A 723 ILE cc_start: 0.9488 (mt) cc_final: 0.9128 (mm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2889 time to fit residues: 40.7319 Evaluate side-chains 86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.084953 restraints weight = 41920.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088551 restraints weight = 19814.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090792 restraints weight = 12377.883| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6050 Z= 0.238 Angle : 0.641 23.096 8289 Z= 0.344 Chirality : 0.037 0.140 975 Planarity : 0.003 0.035 939 Dihedral : 15.195 74.090 1174 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -0.27 (0.34), residues: 651 helix: 2.25 (0.29), residues: 319 sheet: -2.77 (0.50), residues: 87 loop : -2.62 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1003 HIS 0.006 0.001 HIS A 928 PHE 0.012 0.001 PHE A 551 TYR 0.009 0.002 TYR A1018 ARG 0.004 0.001 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 101 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.159 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: A 446 CYS cc_start: 0.8228 (m) cc_final: 0.7887 (m) REVERT: A 488 LEU cc_start: 0.8736 (mt) cc_final: 0.8296 (mt) REVERT: A 540 PHE cc_start: 0.7074 (m-10) cc_final: 0.6309 (p90) REVERT: A 603 GLU cc_start: 0.8400 (tt0) cc_final: 0.7273 (tm-30) REVERT: A 613 GLN cc_start: 0.8499 (pm20) cc_final: 0.8295 (pm20) REVERT: A 723 ILE cc_start: 0.9514 (mt) cc_final: 0.9172 (mm) REVERT: A 1009 ARG cc_start: 0.7721 (mmp80) cc_final: 0.7499 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2998 time to fit residues: 41.2314 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 0.0060 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.086146 restraints weight = 41165.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089775 restraints weight = 19487.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.092032 restraints weight = 12029.868| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6050 Z= 0.166 Angle : 0.604 23.000 8289 Z= 0.326 Chirality : 0.037 0.157 975 Planarity : 0.003 0.030 939 Dihedral : 14.915 74.045 1174 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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: -0.10 (0.34), residues: 651 helix: 2.42 (0.29), residues: 316 sheet: -2.63 (0.52), residues: 85 loop : -2.55 (0.35), residues: 250 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 0.011 0.001 PHE A 630 TYR 0.013 0.002 TYR A 631 ARG 0.002 0.000 ARG A 461 *********************** 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 100 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.826 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: A 446 CYS cc_start: 0.8099 (m) cc_final: 0.7814 (m) REVERT: A 488 LEU cc_start: 0.8621 (mt) cc_final: 0.8217 (mt) REVERT: A 540 PHE cc_start: 0.7019 (m-10) cc_final: 0.6286 (p90) REVERT: A 603 GLU cc_start: 0.8282 (tt0) cc_final: 0.7228 (tm-30) REVERT: A 613 GLN cc_start: 0.8328 (pm20) cc_final: 0.8117 (pm20) REVERT: A 615 ASN cc_start: 0.8179 (t0) cc_final: 0.7896 (t0) REVERT: A 723 ILE cc_start: 0.9527 (mt) cc_final: 0.9180 (mm) REVERT: A 769 THR cc_start: 0.9451 (p) cc_final: 0.9241 (t) REVERT: A 877 GLN cc_start: 0.8217 (mt0) cc_final: 0.7761 (mm-40) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3008 time to fit residues: 40.9875 Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN A 615 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084156 restraints weight = 41712.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.087656 restraints weight = 19900.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089888 restraints weight = 12489.276| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6050 Z= 0.253 Angle : 0.648 23.258 8289 Z= 0.349 Chirality : 0.038 0.137 975 Planarity : 0.003 0.033 939 Dihedral : 15.102 74.087 1174 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % 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 : 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: -0.38 (0.34), residues: 651 helix: 2.06 (0.29), residues: 323 sheet: -2.78 (0.51), residues: 87 loop : -2.61 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 737 HIS 0.008 0.001 HIS A 927 PHE 0.021 0.002 PHE A 630 TYR 0.011 0.002 TYR A 455 ARG 0.004 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 97 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.875 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: A 322 ASP cc_start: 0.8672 (p0) cc_final: 0.8211 (p0) REVERT: A 446 CYS cc_start: 0.7932 (m) cc_final: 0.7694 (m) REVERT: A 488 LEU cc_start: 0.8687 (mt) cc_final: 0.8328 (mt) REVERT: A 540 PHE cc_start: 0.7089 (m-10) cc_final: 0.6383 (p90) REVERT: A 723 ILE cc_start: 0.9533 (mt) cc_final: 0.9187 (mm) REVERT: A 769 THR cc_start: 0.9530 (p) cc_final: 0.9321 (t) REVERT: A 864 MET cc_start: 0.7792 (ttt) cc_final: 0.7344 (ttt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3044 time to fit residues: 40.3219 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 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 = 0.3518 r_free = 0.3518 target = 0.102803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085048 restraints weight = 41606.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088628 restraints weight = 19655.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.090872 restraints weight = 12224.376| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6050 Z= 0.209 Angle : 0.630 23.162 8289 Z= 0.337 Chirality : 0.037 0.159 975 Planarity : 0.003 0.032 939 Dihedral : 15.042 74.050 1174 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % 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: -0.27 (0.34), residues: 651 helix: 2.17 (0.29), residues: 322 sheet: -2.49 (0.59), residues: 73 loop : -2.71 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 968 HIS 0.004 0.001 HIS A 928 PHE 0.013 0.001 PHE A 630 TYR 0.008 0.001 TYR A1000 ARG 0.003 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 98 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.868 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: A 322 ASP cc_start: 0.8576 (p0) cc_final: 0.8116 (p0) REVERT: A 446 CYS cc_start: 0.8081 (m) cc_final: 0.7843 (m) REVERT: A 488 LEU cc_start: 0.8636 (mt) cc_final: 0.8311 (mt) REVERT: A 540 PHE cc_start: 0.7016 (m-10) cc_final: 0.6354 (p90) REVERT: A 613 GLN cc_start: 0.8511 (pm20) cc_final: 0.8251 (pm20) REVERT: A 864 MET cc_start: 0.7721 (ttt) cc_final: 0.7361 (ttt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2969 time to fit residues: 39.6951 Evaluate side-chains 83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 44 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087151 restraints weight = 40835.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090940 restraints weight = 18735.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093309 restraints weight = 11360.382| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6050 Z= 0.124 Angle : 0.589 23.010 8289 Z= 0.312 Chirality : 0.037 0.151 975 Planarity : 0.003 0.027 939 Dihedral : 14.843 73.918 1174 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 2.60 (0.29), residues: 322 sheet: -2.39 (0.59), residues: 73 loop : -2.53 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 927 PHE 0.014 0.001 PHE A 630 TYR 0.015 0.001 TYR A 631 ARG 0.004 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.24 seconds wall clock time: 57 minutes 30.30 seconds (3450.30 seconds total)