Starting phenix.real_space_refine on Wed Sep 17 18:04:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h61_0143/09_2025/6h61_0143.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h61_0143/09_2025/6h61_0143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2025/6h61_0143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2025/6h61_0143.map" model { file = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2025/6h61_0143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2025/6h61_0143.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.009 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 3597 2.51 5 N 1025 2.21 5 O 1169 1.98 5 H 4057 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9912 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 9272 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 639} Chain breaks: 9 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 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 7821 SG CYS A 907 78.601 38.750 37.827 1.00160.60 S ATOM 7868 SG CYS A 910 82.314 38.522 37.781 1.00169.21 S ATOM 8477 SG CYS A 962 80.773 39.778 41.111 1.00174.46 S ATOM 8492 SG CYS A 964 80.765 42.477 39.020 1.00180.02 S Time building chain proxies: 2.08, per 1000 atoms: 0.21 Number of scatterers: 9912 At special positions: 0 Unit cell: (97.76, 87.36, 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 1169 8.00 N 1025 7.00 C 3597 6.00 H 4057 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: 1.10 Conformation dependent library (CDL) restraints added in 254.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 54.8% alpha, 8.3% beta 15 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.855A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.934A 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 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.767A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.948A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.765A pdb=" N HIS A 448 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 476 removed outlier: 3.746A 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: 3.533A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 566 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.904A pdb=" N GLU A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.848A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 692 removed outlier: 4.198A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 716 removed outlier: 3.588A pdb=" N GLU A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.564A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 780 Processing helix chain 'A' and resid 812 through 823 removed outlier: 4.022A pdb=" N ARG A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.508A pdb=" N GLU A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.744A 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 Processing helix chain 'A' and resid 1014 through 1018 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.635A pdb=" N ILE A 326 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 361 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER A 413 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL A 362 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 389 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR A 414 " --> pdb=" O ILE A 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 751 through 753 removed outlier: 6.899A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ALA A 788 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 723 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 722 " --> pdb=" O ILE A 805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.644A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 916 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 903 " --> pdb=" O SER A 916 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AA5, first strand: chain 'A' and resid 940 through 942 removed outlier: 3.845A pdb=" N GLY A 969 " --> pdb=" O ILE A 960 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.48 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: 4046 1.03 - 1.23: 19 1.23 - 1.42: 2497 1.42 - 1.62: 3448 1.62 - 1.81: 52 Bond restraints: 10062 Sorted by residual: bond pdb=" CA LYS A 366 " pdb=" CB LYS A 366 " ideal model delta sigma weight residual 1.535 1.501 0.034 2.09e-02 2.29e+03 2.72e+00 bond pdb=" CB CYS A 446 " pdb=" SG CYS A 446 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CB TYR A 408 " pdb=" CG TYR A 408 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.20e-02 2.07e+03 2.03e+00 bond pdb=" CG LYS A 466 " pdb=" CD LYS A 466 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CG1 ILE A 458 " pdb=" CD1 ILE A 458 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.88e+00 ... (remaining 10057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.01: 17489 10.01 - 20.02: 0 20.02 - 30.03: 1 30.03 - 40.04: 0 40.04 - 50.04: 2 Bond angle restraints: 17492 Sorted by residual: angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 124.58 74.53 50.04 3.00e+00 1.11e-01 2.78e+02 angle pdb=" CA LYS A 498 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 114.28 67.64 46.64 3.00e+00 1.11e-01 2.42e+02 angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 121.15 142.14 -20.99 1.85e+00 2.92e-01 1.29e+02 angle pdb=" C LEU A 472 " pdb=" N LYS A 473 " pdb=" CA LYS A 473 " ideal model delta sigma weight residual 120.79 124.95 -4.16 1.39e+00 5.18e-01 8.95e+00 angle pdb=" N SER A 761 " pdb=" CA SER A 761 " pdb=" C SER A 761 " ideal model delta sigma weight residual 110.80 116.99 -6.19 2.13e+00 2.20e-01 8.43e+00 ... (remaining 17487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4613 17.29 - 34.57: 335 34.57 - 51.86: 85 51.86 - 69.14: 51 69.14 - 86.43: 11 Dihedral angle restraints: 5095 sinusoidal: 2910 harmonic: 2185 Sorted by residual: dihedral pdb=" CA SER A 760 " pdb=" C SER A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+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 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ARG A 375 " pdb=" C ARG A 375 " pdb=" N LYS A 376 " pdb=" CA LYS A 376 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 5092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 570 0.031 - 0.062: 234 0.062 - 0.092: 108 0.092 - 0.123: 42 0.123 - 0.154: 14 Chirality restraints: 968 Sorted by residual: chirality pdb=" CB ILE A 399 " pdb=" CA ILE A 399 " pdb=" CG1 ILE A 399 " pdb=" CG2 ILE A 399 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 412 " pdb=" N ILE A 412 " pdb=" C ILE A 412 " pdb=" CB ILE A 412 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 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 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 965 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 490 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C ALA A 490 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA A 490 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 491 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 829 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C THR A 829 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 829 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 830 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 457 " -0.008 2.00e-02 2.50e+03 1.29e-02 2.50e+00 pdb=" CG ASN A 457 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 457 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 457 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 457 " -0.005 2.00e-02 2.50e+03 pdb="HD22 ASN A 457 " -0.002 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 334 2.17 - 2.77: 16899 2.77 - 3.38: 24460 3.38 - 3.99: 32097 3.99 - 4.60: 49603 Nonbonded interactions: 123393 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.557 1.816 nonbonded pdb=" O LYS A 750 " pdb=" H ASN A 784 " model vdw 1.724 2.450 nonbonded pdb=" HZ2 LYS A 638 " pdb=" O CYS A 964 " model vdw 1.726 2.450 nonbonded pdb="HH12 ARG A 599 " pdb=" OD1 ASN A 909 " model vdw 1.727 2.450 nonbonded pdb=" O GLU A 628 " pdb=" HG1 THR A 632 " model vdw 1.729 2.450 ... (remaining 123388 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: 0.830 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: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.010 0.582 6009 Z= 0.420 Angle : 0.970 33.455 8232 Z= 0.475 Chirality : 0.045 0.154 968 Planarity : 0.005 0.039 930 Dihedral : 13.660 74.317 2476 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.18 % Allowed : 2.11 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.28), residues: 640 helix: -1.19 (0.24), residues: 311 sheet: -2.07 (0.59), residues: 71 loop : -2.88 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 599 TYR 0.013 0.002 TYR A 830 PHE 0.023 0.003 PHE A 378 TRP 0.011 0.002 TRP A 968 HIS 0.006 0.002 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 6005) covalent geometry : angle 0.83953 ( 8226) hydrogen bonds : bond 0.12053 ( 302) hydrogen bonds : angle 5.87584 ( 822) metal coordination : bond 0.29710 ( 4) metal coordination : angle 18.00099 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 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 178 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8765 (mt) cc_final: 0.8498 (mt) REVERT: A 398 LYS cc_start: 0.8275 (mtpp) cc_final: 0.7865 (pttp) REVERT: A 446 CYS cc_start: 0.8193 (m) cc_final: 0.7885 (m) REVERT: A 586 MET cc_start: 0.8426 (tpp) cc_final: 0.8036 (tpp) REVERT: A 603 GLU cc_start: 0.9072 (tt0) cc_final: 0.8704 (mt-10) REVERT: A 631 TYR cc_start: 0.8312 (m-80) cc_final: 0.8065 (m-80) REVERT: A 869 TYR cc_start: 0.8223 (t80) cc_final: 0.8008 (t80) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1910 time to fit residues: 41.9968 Evaluate side-chains 106 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 476 ASN A 683 ASN A 693 ASN A 729 GLN A 784 ASN A 899 ASN A 957 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.088626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071961 restraints weight = 54694.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.074963 restraints weight = 25048.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.076833 restraints weight = 15539.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.077976 restraints weight = 11523.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.078646 restraints weight = 9543.887| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6009 Z= 0.218 Angle : 0.674 18.989 8232 Z= 0.357 Chirality : 0.039 0.153 968 Planarity : 0.004 0.036 930 Dihedral : 15.439 74.274 1166 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.53 % Allowed : 2.11 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.32), residues: 640 helix: 0.52 (0.27), residues: 312 sheet: -1.86 (0.61), residues: 65 loop : -2.79 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 599 TYR 0.011 0.001 TYR A 830 PHE 0.016 0.002 PHE A 378 TRP 0.008 0.001 TRP A 582 HIS 0.014 0.002 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6005) covalent geometry : angle 0.66113 ( 8226) hydrogen bonds : bond 0.03976 ( 302) hydrogen bonds : angle 4.86186 ( 822) metal coordination : bond 0.01334 ( 4) metal coordination : angle 4.83869 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 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 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8825 (mt) cc_final: 0.8589 (mt) REVERT: A 365 ASN cc_start: 0.8586 (p0) cc_final: 0.8218 (p0) REVERT: A 446 CYS cc_start: 0.8064 (m) cc_final: 0.7843 (m) REVERT: A 586 MET cc_start: 0.8319 (tpp) cc_final: 0.7724 (tpp) REVERT: A 603 GLU cc_start: 0.9066 (tt0) cc_final: 0.8704 (mt-10) REVERT: A 609 ASN cc_start: 0.8933 (t0) cc_final: 0.8638 (t0) REVERT: A 797 ASP cc_start: 0.8073 (t70) cc_final: 0.7734 (t0) REVERT: A 869 TYR cc_start: 0.8199 (t80) cc_final: 0.7994 (t80) REVERT: A 886 MET cc_start: 0.7549 (mtp) cc_final: 0.7315 (mtp) REVERT: A 1018 TYR cc_start: 0.7171 (t80) cc_final: 0.6718 (t80) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 0.1600 time to fit residues: 25.6827 Evaluate side-chains 96 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN A 643 ASN A 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.086981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070256 restraints weight = 53885.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.073172 restraints weight = 24111.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.074947 restraints weight = 14831.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076001 restraints weight = 11028.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076695 restraints weight = 9199.045| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6009 Z= 0.195 Angle : 0.613 19.024 8232 Z= 0.329 Chirality : 0.038 0.143 968 Planarity : 0.004 0.035 930 Dihedral : 15.281 74.218 1166 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.18 % Allowed : 1.93 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.33), residues: 640 helix: 1.42 (0.29), residues: 319 sheet: -1.76 (0.60), residues: 65 loop : -2.88 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.009 0.002 TYR A 830 PHE 0.012 0.001 PHE A 378 TRP 0.006 0.001 TRP A 582 HIS 0.008 0.002 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6005) covalent geometry : angle 0.60679 ( 8226) hydrogen bonds : bond 0.03712 ( 302) hydrogen bonds : angle 4.52876 ( 822) metal coordination : bond 0.00571 ( 4) metal coordination : angle 3.33136 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8858 (mt) cc_final: 0.8615 (mt) REVERT: A 397 LEU cc_start: 0.9291 (tp) cc_final: 0.9062 (tp) REVERT: A 424 ASN cc_start: 0.9102 (m-40) cc_final: 0.8856 (m-40) REVERT: A 446 CYS cc_start: 0.8323 (m) cc_final: 0.7995 (m) REVERT: A 452 GLU cc_start: 0.8176 (tp30) cc_final: 0.7912 (tp30) REVERT: A 555 LEU cc_start: 0.9557 (tt) cc_final: 0.9268 (mt) REVERT: A 603 GLU cc_start: 0.9091 (tt0) cc_final: 0.8795 (mt-10) REVERT: A 674 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8678 (mm-30) REVERT: A 797 ASP cc_start: 0.8209 (t70) cc_final: 0.7854 (t0) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1533 time to fit residues: 22.9437 Evaluate side-chains 88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.085313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.068715 restraints weight = 54017.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071538 restraints weight = 23865.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.073288 restraints weight = 14664.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.074350 restraints weight = 10900.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.074904 restraints weight = 9085.765| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6009 Z= 0.229 Angle : 0.640 18.820 8232 Z= 0.337 Chirality : 0.038 0.147 968 Planarity : 0.004 0.040 930 Dihedral : 15.214 74.200 1166 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.18 % Allowed : 1.93 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.34), residues: 640 helix: 1.69 (0.29), residues: 320 sheet: -1.76 (0.60), residues: 65 loop : -2.87 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 599 TYR 0.014 0.002 TYR A 455 PHE 0.012 0.001 PHE A 378 TRP 0.008 0.001 TRP A 582 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 6005) covalent geometry : angle 0.62417 ( 8226) hydrogen bonds : bond 0.03854 ( 302) hydrogen bonds : angle 4.68020 ( 822) metal coordination : bond 0.00987 ( 4) metal coordination : angle 5.20967 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.285 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 327 ILE cc_start: 0.8899 (mt) cc_final: 0.8693 (mt) REVERT: A 424 ASN cc_start: 0.8939 (m-40) cc_final: 0.8648 (m-40) REVERT: A 446 CYS cc_start: 0.8385 (m) cc_final: 0.8152 (m) REVERT: A 452 GLU cc_start: 0.8332 (tp30) cc_final: 0.8062 (tp30) REVERT: A 488 LEU cc_start: 0.8974 (mp) cc_final: 0.8668 (mp) REVERT: A 555 LEU cc_start: 0.9546 (tt) cc_final: 0.9244 (mt) REVERT: A 586 MET cc_start: 0.8487 (tpp) cc_final: 0.7960 (tpp) REVERT: A 603 GLU cc_start: 0.9068 (tt0) cc_final: 0.8762 (mt-10) REVERT: A 755 ILE cc_start: 0.8611 (pt) cc_final: 0.8392 (pt) REVERT: A 924 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7742 (mm-30) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1566 time to fit residues: 23.3212 Evaluate side-chains 86 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 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 = 0.3602 r_free = 0.3602 target = 0.087607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071168 restraints weight = 52390.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074078 restraints weight = 23068.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.075829 restraints weight = 14078.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076921 restraints weight = 10432.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077627 restraints weight = 8645.135| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6009 Z= 0.130 Angle : 0.552 19.094 8232 Z= 0.291 Chirality : 0.037 0.141 968 Planarity : 0.003 0.037 930 Dihedral : 15.123 74.090 1166 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.34), residues: 640 helix: 2.15 (0.29), residues: 319 sheet: -1.62 (0.61), residues: 65 loop : -2.71 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.007 0.001 TYR A 462 PHE 0.016 0.001 PHE A 517 TRP 0.007 0.001 TRP A 582 HIS 0.019 0.002 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6005) covalent geometry : angle 0.54367 ( 8226) hydrogen bonds : bond 0.03311 ( 302) hydrogen bonds : angle 4.32331 ( 822) metal coordination : bond 0.00526 ( 4) metal coordination : angle 3.50359 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 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 113 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.8876 (m-40) cc_final: 0.8572 (m-40) REVERT: A 446 CYS cc_start: 0.8523 (m) cc_final: 0.8068 (m) REVERT: A 452 GLU cc_start: 0.8257 (tp30) cc_final: 0.7850 (tp30) REVERT: A 488 LEU cc_start: 0.8947 (mp) cc_final: 0.8725 (mp) REVERT: A 555 LEU cc_start: 0.9518 (tt) cc_final: 0.9272 (mt) REVERT: A 580 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 586 MET cc_start: 0.8410 (tpp) cc_final: 0.8100 (tpp) REVERT: A 603 GLU cc_start: 0.9037 (tt0) cc_final: 0.8668 (mt-10) REVERT: A 755 ILE cc_start: 0.8540 (pt) cc_final: 0.8328 (pt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1334 time to fit residues: 20.5923 Evaluate side-chains 94 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN A 879 GLN A 957 ASN A 974 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072648 restraints weight = 53098.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.075639 restraints weight = 23207.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077500 restraints weight = 14077.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078651 restraints weight = 10277.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079337 restraints weight = 8420.741| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6009 Z= 0.100 Angle : 0.513 19.139 8232 Z= 0.270 Chirality : 0.037 0.147 968 Planarity : 0.003 0.033 930 Dihedral : 14.986 74.021 1166 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.18 % Allowed : 1.23 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.35), residues: 640 helix: 2.60 (0.29), residues: 320 sheet: -1.54 (0.61), residues: 67 loop : -2.47 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.008 0.001 TYR A 631 PHE 0.010 0.001 PHE A 517 TRP 0.006 0.001 TRP A 582 HIS 0.014 0.002 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6005) covalent geometry : angle 0.50867 ( 8226) hydrogen bonds : bond 0.03033 ( 302) hydrogen bonds : angle 4.04220 ( 822) metal coordination : bond 0.00356 ( 4) metal coordination : angle 2.62928 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.292 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 327 ILE cc_start: 0.8859 (mt) cc_final: 0.8639 (mt) REVERT: A 424 ASN cc_start: 0.8889 (m-40) cc_final: 0.8586 (m-40) REVERT: A 431 ASP cc_start: 0.7659 (m-30) cc_final: 0.7190 (t70) REVERT: A 446 CYS cc_start: 0.8380 (m) cc_final: 0.8057 (m) REVERT: A 452 GLU cc_start: 0.8330 (tp30) cc_final: 0.7892 (tp30) REVERT: A 488 LEU cc_start: 0.8997 (mp) cc_final: 0.8722 (mp) REVERT: A 555 LEU cc_start: 0.9501 (tt) cc_final: 0.9087 (mt) REVERT: A 586 MET cc_start: 0.8411 (tpp) cc_final: 0.8102 (tpp) REVERT: A 603 GLU cc_start: 0.9028 (tt0) cc_final: 0.8732 (mt-10) REVERT: A 755 ILE cc_start: 0.8533 (pt) cc_final: 0.8278 (pt) REVERT: A 851 GLU cc_start: 0.8721 (tt0) cc_final: 0.8464 (tp30) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1450 time to fit residues: 22.7966 Evaluate side-chains 93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.087875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071361 restraints weight = 53861.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074314 restraints weight = 24158.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.076087 restraints weight = 14898.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.077225 restraints weight = 11075.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.077894 restraints weight = 9119.321| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6009 Z= 0.183 Angle : 0.587 18.719 8232 Z= 0.307 Chirality : 0.037 0.152 968 Planarity : 0.003 0.036 930 Dihedral : 14.980 74.152 1166 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.35), residues: 640 helix: 2.25 (0.29), residues: 333 sheet: -1.62 (0.54), residues: 80 loop : -2.82 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.013 0.001 TYR A 455 PHE 0.011 0.001 PHE A 517 TRP 0.007 0.001 TRP A 582 HIS 0.016 0.002 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6005) covalent geometry : angle 0.58087 ( 8226) hydrogen bonds : bond 0.03500 ( 302) hydrogen bonds : angle 4.37958 ( 822) metal coordination : bond 0.00764 ( 4) metal coordination : angle 3.14495 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 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 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.292 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 327 ILE cc_start: 0.8930 (mt) cc_final: 0.8673 (mt) REVERT: A 336 LYS cc_start: 0.8396 (ptmt) cc_final: 0.8072 (ttpt) REVERT: A 424 ASN cc_start: 0.8835 (m-40) cc_final: 0.8506 (m-40) REVERT: A 431 ASP cc_start: 0.7686 (m-30) cc_final: 0.7199 (t70) REVERT: A 446 CYS cc_start: 0.8388 (m) cc_final: 0.8110 (m) REVERT: A 452 GLU cc_start: 0.8484 (tp30) cc_final: 0.8227 (tp30) REVERT: A 586 MET cc_start: 0.8427 (tpp) cc_final: 0.7924 (tpp) REVERT: A 603 GLU cc_start: 0.9035 (tt0) cc_final: 0.8757 (mt-10) REVERT: A 755 ILE cc_start: 0.8520 (pt) cc_final: 0.8303 (pt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1405 time to fit residues: 20.9934 Evaluate side-chains 88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 0.0470 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.091014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074913 restraints weight = 54229.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077906 restraints weight = 24112.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.079697 restraints weight = 14693.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080845 restraints weight = 10841.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.081581 restraints weight = 8890.794| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6009 Z= 0.118 Angle : 0.526 18.923 8232 Z= 0.275 Chirality : 0.037 0.142 968 Planarity : 0.003 0.036 930 Dihedral : 14.927 73.980 1166 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.18 % Allowed : 0.00 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.35), residues: 640 helix: 2.54 (0.29), residues: 327 sheet: -1.20 (0.62), residues: 65 loop : -2.50 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 599 TYR 0.007 0.001 TYR A 408 PHE 0.010 0.001 PHE A 517 TRP 0.006 0.001 TRP A 582 HIS 0.014 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6005) covalent geometry : angle 0.52307 ( 8226) hydrogen bonds : bond 0.03117 ( 302) hydrogen bonds : angle 4.08775 ( 822) metal coordination : bond 0.00509 ( 4) metal coordination : angle 2.25492 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 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 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.291 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 327 ILE cc_start: 0.8868 (mt) cc_final: 0.8630 (mt) REVERT: A 336 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7981 (ttpt) REVERT: A 424 ASN cc_start: 0.8773 (m-40) cc_final: 0.8424 (m-40) REVERT: A 431 ASP cc_start: 0.7581 (m-30) cc_final: 0.7176 (t70) REVERT: A 446 CYS cc_start: 0.8390 (m) cc_final: 0.7958 (m) REVERT: A 520 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7497 (mmmt) REVERT: A 586 MET cc_start: 0.8322 (tpp) cc_final: 0.7812 (tpp) REVERT: A 603 GLU cc_start: 0.8987 (tt0) cc_final: 0.8725 (mt-10) REVERT: A 755 ILE cc_start: 0.8558 (pt) cc_final: 0.8328 (pt) REVERT: A 926 MET cc_start: 0.8555 (ttt) cc_final: 0.8339 (tpp) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1293 time to fit residues: 19.6044 Evaluate side-chains 92 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075926 restraints weight = 53734.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078853 restraints weight = 23868.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.080665 restraints weight = 14590.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.081807 restraints weight = 10733.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082394 restraints weight = 8792.879| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6009 Z= 0.092 Angle : 0.509 19.088 8232 Z= 0.265 Chirality : 0.037 0.140 968 Planarity : 0.003 0.032 930 Dihedral : 14.863 73.998 1166 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.18 % Allowed : 0.70 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.35), residues: 640 helix: 2.75 (0.29), residues: 326 sheet: -1.10 (0.62), residues: 65 loop : -2.37 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 599 TYR 0.007 0.001 TYR A 631 PHE 0.010 0.001 PHE A 517 TRP 0.006 0.001 TRP A 582 HIS 0.013 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 6005) covalent geometry : angle 0.50590 ( 8226) hydrogen bonds : bond 0.02891 ( 302) hydrogen bonds : angle 3.89419 ( 822) metal coordination : bond 0.00308 ( 4) metal coordination : angle 2.25643 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 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 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.324 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 327 ILE cc_start: 0.8715 (mt) cc_final: 0.8487 (mt) REVERT: A 336 LYS cc_start: 0.8223 (ptmt) cc_final: 0.7850 (ttpt) REVERT: A 424 ASN cc_start: 0.8768 (m-40) cc_final: 0.8423 (m-40) REVERT: A 446 CYS cc_start: 0.8268 (m) cc_final: 0.7951 (m) REVERT: A 520 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7464 (mmmt) REVERT: A 586 MET cc_start: 0.8304 (tpp) cc_final: 0.7799 (tpp) REVERT: A 603 GLU cc_start: 0.8979 (tt0) cc_final: 0.8736 (mt-10) REVERT: A 624 TYR cc_start: 0.6814 (t80) cc_final: 0.6335 (t80) REVERT: A 755 ILE cc_start: 0.8533 (pt) cc_final: 0.8243 (pt) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1234 time to fit residues: 18.2983 Evaluate side-chains 90 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 60 optimal weight: 0.0030 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075630 restraints weight = 53091.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.078532 restraints weight = 23588.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080315 restraints weight = 14410.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081430 restraints weight = 10635.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082119 restraints weight = 8730.131| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6009 Z= 0.106 Angle : 0.514 18.905 8232 Z= 0.268 Chirality : 0.037 0.142 968 Planarity : 0.003 0.032 930 Dihedral : 14.838 73.952 1166 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.35), residues: 640 helix: 2.65 (0.29), residues: 332 sheet: -0.97 (0.63), residues: 65 loop : -2.48 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 599 TYR 0.006 0.001 TYR A 408 PHE 0.011 0.001 PHE A 517 TRP 0.007 0.001 TRP A 582 HIS 0.012 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6005) covalent geometry : angle 0.51139 ( 8226) hydrogen bonds : bond 0.02908 ( 302) hydrogen bonds : angle 3.86507 ( 822) metal coordination : bond 0.00425 ( 4) metal coordination : angle 1.80375 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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 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 VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 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 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 105 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8739 (mt) cc_final: 0.8501 (mt) REVERT: A 336 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7874 (ttpt) REVERT: A 424 ASN cc_start: 0.8764 (m-40) cc_final: 0.8429 (m-40) REVERT: A 446 CYS cc_start: 0.8190 (m) cc_final: 0.7921 (m) REVERT: A 520 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7512 (mmmt) REVERT: A 586 MET cc_start: 0.8312 (tpp) cc_final: 0.7820 (tpp) REVERT: A 603 GLU cc_start: 0.8976 (tt0) cc_final: 0.8756 (mt-10) REVERT: A 755 ILE cc_start: 0.8546 (pt) cc_final: 0.8199 (pt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1171 time to fit residues: 16.9133 Evaluate side-chains 86 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.0970 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.090447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074540 restraints weight = 54207.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077461 restraints weight = 23833.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079287 restraints weight = 14481.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080436 restraints weight = 10584.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080919 restraints weight = 8593.125| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6009 Z= 0.139 Angle : 0.543 18.774 8232 Z= 0.285 Chirality : 0.037 0.175 968 Planarity : 0.003 0.044 930 Dihedral : 14.891 74.102 1166 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.35), residues: 640 helix: 2.55 (0.29), residues: 332 sheet: -1.20 (0.65), residues: 60 loop : -2.54 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.008 0.001 TYR A1018 PHE 0.012 0.001 PHE A 517 TRP 0.007 0.001 TRP A 582 HIS 0.012 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6005) covalent geometry : angle 0.53988 ( 8226) hydrogen bonds : bond 0.03138 ( 302) hydrogen bonds : angle 3.94665 ( 822) metal coordination : bond 0.00624 ( 4) metal coordination : angle 2.27704 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.51 seconds wall clock time: 33 minutes 38.52 seconds (2018.52 seconds total)