Starting phenix.real_space_refine on Fri Sep 11 16:17:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_0143.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_0143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_0143.cif" model { file = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_0143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_0143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_0143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h61_0143/09_2026/6h61_0143.map" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 1.95, per 1000 atoms: 0.20 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: 0.99 Conformation dependent library (CDL) restraints added in 198.8 milliseconds 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: 1.57 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: 2.08 Time building geometry restraints manager: 1.31 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: 4544 17.29 - 34.57: 338 34.57 - 51.86: 81 51.86 - 69.14: 16 69.14 - 86.43: 2 Dihedral angle restraints: 4981 sinusoidal: 2796 harmonic: 2185 Sorted by residual: dihedral pdb=" O5' G X 15 " pdb=" C5' G X 15 " pdb=" C4' G X 15 " pdb=" C3' G X 15 " ideal model delta sinusoidal sigma weight residual 60.00 105.84 -45.84 3 6.40e+00 2.44e-02 4.52e+01 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=" O5' U X 1 " pdb=" C5' U X 1 " pdb=" C4' U X 1 " pdb=" C3' U X 1 " ideal model delta sinusoidal sigma weight residual 60.00 21.67 38.33 3 6.40e+00 2.44e-02 3.70e+01 ... (remaining 4978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 679 0.046 - 0.092: 203 0.092 - 0.137: 49 0.137 - 0.183: 10 0.183 - 0.229: 27 Chirality restraints: 968 Sorted by residual: chirality pdb=" P A Y 11 " pdb=" OP1 A Y 11 " pdb=" OP2 A Y 11 " pdb=" O5' A Y 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" P C X 9 " pdb=" OP1 C X 9 " pdb=" OP2 C X 9 " pdb=" O5' C X 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" P G X 8 " pdb=" OP1 G X 8 " pdb=" OP2 G X 8 " pdb=" O5' G X 8 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.999 33.455 8232 Z= 0.478 Chirality : 0.058 0.229 968 Planarity : 0.005 0.039 930 Dihedral : 10.799 71.444 2362 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 are 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/Z covalent geometry : bond 0.00691 / 0.33 ( 6005) covalent geometry : angle 0.87285 / 0.47 ( 8226) hydrogen bonds : bond 0.12053 / 8.00 ( 302) hydrogen bonds : angle 5.87584 / 4.08 ( 822) metal coordination : bond 0.29710 / 15.60 ( 4) metal coordination : angle 18.00099 / 10.80 ( 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 : 0.306 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: 0.7864 (pttp) REVERT: A 446 CYS cc_start: 0.8194 (m) cc_final: 0.7884 (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: 0.8224 (t80) cc_final: 0.8008 (t80) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1803 time to fit residues: 40.1246 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 : 0.272 ------------------------------------------------------------------------------- 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... 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 = 0.3624 r_free = 0.3624 target = 0.087751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071292 restraints weight = 53591.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.074305 restraints weight = 24151.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.076191 restraints weight = 14690.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.077347 restraints weight = 10702.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.078063 restraints weight = 8765.535| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6009 Z= 0.223 Angle : 0.748 18.982 8232 Z= 0.369 Chirality : 0.043 0.152 968 Planarity : 0.004 0.036 930 Dihedral : 9.988 60.864 1052 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % 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 are not related in a simple way. whole: -1.55 (0.32), residues: 640 helix: 0.53 (0.27), residues: 312 sheet: -1.85 (0.61), residues: 65 loop : -2.80 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 599 TYR 0.010 0.002 TYR A1018 PHE 0.016 0.002 PHE A 378 TRP 0.008 0.001 TRP A 582 HIS 0.015 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 ( 6005) covalent geometry : angle 0.73664 / 0.37 ( 8226) hydrogen bonds : bond 0.04061 / 2.67 ( 302) hydrogen bonds : angle 4.83770 / 3.37 ( 822) metal coordination : bond 0.01041 / 0.52 ( 4) metal coordination : angle 4.80644 / 2.45 ( 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 126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.186 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: A 327 ILE cc_start: 0.8841 (mt) cc_final: 0.8601 (mt) REVERT: A 365 ASN cc_start: 0.8625 (p0) cc_final: 0.8285 (p0) REVERT: A 446 CYS cc_start: 0.8104 (m) cc_final: 0.7873 (m) REVERT: A 586 MET cc_start: 0.8322 (tpp) cc_final: 0.7967 (tpp) REVERT: A 603 GLU cc_start: 0.9074 (tt0) cc_final: 0.8708 (mt-10) REVERT: A 609 ASN cc_start: 0.8945 (t0) cc_final: 0.8640 (t0) REVERT: A 797 ASP cc_start: 0.8094 (t70) cc_final: 0.7751 (t0) REVERT: A 886 MET cc_start: 0.7566 (mtp) cc_final: 0.7330 (mtp) REVERT: A 1018 TYR cc_start: 0.7091 (t80) cc_final: 0.6648 (t80) outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.1424 time to fit residues: 23.2502 Evaluate side-chains 98 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 0.0270 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.090592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.074270 restraints weight = 53548.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077169 restraints weight = 23620.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.078981 restraints weight = 14258.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080109 restraints weight = 10447.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.080698 restraints weight = 8561.423| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6009 Z= 0.151 Angle : 0.634 19.308 8232 Z= 0.318 Chirality : 0.041 0.143 968 Planarity : 0.003 0.036 930 Dihedral : 9.442 56.841 1052 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.18 % Allowed : 1.41 % Favored : 98.42 % 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 are not related in a simple way. whole: -0.68 (0.33), residues: 640 helix: 1.50 (0.29), residues: 319 sheet: -1.77 (0.60), residues: 67 loop : -2.77 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.008 0.001 TYR A 312 PHE 0.011 0.001 PHE A 378 TRP 0.005 0.001 TRP A 582 HIS 0.008 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 6005) covalent geometry : angle 0.62824 / 0.32 ( 8226) hydrogen bonds : bond 0.03445 / 2.33 ( 302) hydrogen bonds : angle 4.35977 / 3.00 ( 822) metal coordination : bond 0.00428 / 0.21 ( 4) metal coordination : angle 3.25853 / 1.79 ( 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 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.234 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: 0.8789 (mt) cc_final: 0.8567 (mt) REVERT: A 424 ASN cc_start: 0.9133 (m-40) cc_final: 0.8877 (m-40) REVERT: A 446 CYS cc_start: 0.8346 (m) cc_final: 0.7951 (m) REVERT: A 580 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 586 MET cc_start: 0.8419 (tpp) cc_final: 0.8048 (tpp) REVERT: A 603 GLU cc_start: 0.9029 (tt0) cc_final: 0.8740 (mt-10) REVERT: A 674 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 797 ASP cc_start: 0.8130 (t70) cc_final: 0.7784 (t0) REVERT: A 912 MET cc_start: 0.8491 (ptt) cc_final: 0.8213 (ptt) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1393 time to fit residues: 21.8444 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 : 0.194 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN A 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.086703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.069929 restraints weight = 53896.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072809 restraints weight = 24308.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.074574 restraints weight = 15015.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075643 restraints weight = 11197.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.076214 restraints weight = 9312.383| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6009 Z= 0.204 Angle : 0.678 18.870 8232 Z= 0.334 Chirality : 0.042 0.144 968 Planarity : 0.004 0.036 930 Dihedral : 9.532 60.651 1052 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.18 % Allowed : 1.58 % Favored : 98.24 % 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 are not related in a simple way. whole: -0.34 (0.34), residues: 640 helix: 1.88 (0.29), residues: 320 sheet: -1.55 (0.61), residues: 65 loop : -2.79 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 599 TYR 0.017 0.002 TYR A1018 PHE 0.011 0.001 PHE A 378 TRP 0.008 0.001 TRP A 582 HIS 0.006 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 ( 6005) covalent geometry : angle 0.67367 / 0.33 ( 8226) hydrogen bonds : bond 0.03656 / 2.48 ( 302) hydrogen bonds : angle 4.40611 / 3.03 ( 822) metal coordination : bond 0.00716 / 0.36 ( 4) metal coordination : angle 2.77334 / 1.54 ( 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 : 0.222 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: 0.8870 (mt) cc_final: 0.8617 (mt) REVERT: A 424 ASN cc_start: 0.8979 (m-40) cc_final: 0.8672 (m-40) REVERT: A 446 CYS cc_start: 0.8329 (m) cc_final: 0.8087 (m) REVERT: A 488 LEU cc_start: 0.8893 (mp) cc_final: 0.8527 (mp) REVERT: A 586 MET cc_start: 0.8501 (tpp) cc_final: 0.7935 (tpp) REVERT: A 603 GLU cc_start: 0.9069 (tt0) cc_final: 0.8758 (mt-10) REVERT: A 674 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8635 (mm-30) REVERT: A 677 MET cc_start: 0.9120 (mtp) cc_final: 0.8856 (mtp) REVERT: A 755 ILE cc_start: 0.8654 (pt) cc_final: 0.8443 (pt) REVERT: A 797 ASP cc_start: 0.8300 (t70) cc_final: 0.8074 (t0) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1381 time to fit residues: 20.9278 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 : 0.259 ------------------------------------------------------------------------------- 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: 8.9990 chunk 66 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 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 = 0.3612 r_free = 0.3612 target = 0.088058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071401 restraints weight = 52585.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.074343 restraints weight = 22994.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.076152 restraints weight = 13941.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077241 restraints weight = 10264.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.077811 restraints weight = 8480.928| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6009 Z= 0.126 Angle : 0.592 19.180 8232 Z= 0.295 Chirality : 0.041 0.149 968 Planarity : 0.003 0.034 930 Dihedral : 9.108 55.928 1052 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.18 % Allowed : 1.05 % 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 are not related in a simple way. whole: 0.06 (0.34), residues: 640 helix: 2.27 (0.29), residues: 320 sheet: -1.47 (0.61), residues: 67 loop : -2.67 (0.36), 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 408 PHE 0.008 0.001 PHE A 517 TRP 0.006 0.001 TRP A 582 HIS 0.019 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 6005) covalent geometry : angle 0.58977 / 0.30 ( 8226) hydrogen bonds : bond 0.03174 / 2.15 ( 302) hydrogen bonds : angle 4.27969 / 2.89 ( 822) metal coordination : bond 0.00452 / 0.23 ( 4) metal coordination : angle 1.78075 / 1.13 ( 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 114 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.8963 (m-40) cc_final: 0.8638 (m-40) REVERT: A 446 CYS cc_start: 0.8466 (m) cc_final: 0.8004 (m) REVERT: A 488 LEU cc_start: 0.8907 (mp) cc_final: 0.8637 (mp) REVERT: A 520 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7676 (mmmt) REVERT: A 555 LEU cc_start: 0.9558 (tt) cc_final: 0.9236 (mt) REVERT: A 580 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 586 MET cc_start: 0.8483 (tpp) cc_final: 0.7933 (tpp) REVERT: A 603 GLU cc_start: 0.9058 (tt0) cc_final: 0.8680 (mt-10) REVERT: A 755 ILE cc_start: 0.8556 (pt) cc_final: 0.8334 (pt) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1392 time to fit residues: 21.2146 Evaluate side-chains 97 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 0.6980 chunk 44 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3649 r_free = 0.3649 target = 0.090190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.073687 restraints weight = 54318.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076671 restraints weight = 23941.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.078578 restraints weight = 14569.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079731 restraints weight = 10602.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080346 restraints weight = 8676.357| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6009 Z= 0.096 Angle : 0.557 19.222 8232 Z= 0.279 Chirality : 0.041 0.165 968 Planarity : 0.003 0.032 930 Dihedral : 8.827 50.885 1052 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.35), residues: 640 helix: 2.59 (0.29), residues: 320 sheet: -1.31 (0.62), residues: 67 loop : -2.44 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.007 0.001 TYR A 631 PHE 0.016 0.001 PHE A 517 TRP 0.006 0.001 TRP A 582 HIS 0.015 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 6005) covalent geometry : angle 0.55615 / 0.28 ( 8226) hydrogen bonds : bond 0.02912 / 1.97 ( 302) hydrogen bonds : angle 3.98368 / 2.71 ( 822) metal coordination : bond 0.00255 / 0.13 ( 4) metal coordination : angle 1.32692 / 0.79 ( 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 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.276 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: A 327 ILE cc_start: 0.8823 (mt) cc_final: 0.8590 (mt) REVERT: A 336 LYS cc_start: 0.8438 (ptmt) cc_final: 0.8029 (ttpt) REVERT: A 424 ASN cc_start: 0.8937 (m-40) cc_final: 0.8617 (m-40) REVERT: A 431 ASP cc_start: 0.7607 (m-30) cc_final: 0.7353 (t70) REVERT: A 446 CYS cc_start: 0.8347 (m) cc_final: 0.8039 (m) REVERT: A 555 LEU cc_start: 0.9366 (tt) cc_final: 0.9070 (mt) REVERT: A 586 MET cc_start: 0.8405 (tpp) cc_final: 0.7851 (tpp) REVERT: A 603 GLU cc_start: 0.9011 (tt0) cc_final: 0.8713 (mt-10) REVERT: A 755 ILE cc_start: 0.8543 (pt) cc_final: 0.8280 (pt) REVERT: A 797 ASP cc_start: 0.8245 (t70) cc_final: 0.8044 (t0) REVERT: A 851 GLU cc_start: 0.8690 (tt0) cc_final: 0.8475 (tp30) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1382 time to fit residues: 22.0818 Evaluate side-chains 98 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** 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** A 974 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.087442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071041 restraints weight = 54349.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073938 restraints weight = 24488.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075774 restraints weight = 15122.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.076885 restraints weight = 11200.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.077469 restraints weight = 9179.747| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6009 Z= 0.198 Angle : 0.672 18.782 8232 Z= 0.327 Chirality : 0.042 0.151 968 Planarity : 0.003 0.035 930 Dihedral : 9.224 56.238 1052 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.18 % Allowed : 0.88 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.34), residues: 640 helix: 2.27 (0.28), residues: 328 sheet: -1.45 (0.61), residues: 67 loop : -2.55 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 375 TYR 0.013 0.001 TYR A 455 PHE 0.016 0.001 PHE A 517 TRP 0.009 0.001 TRP A 385 HIS 0.014 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 ( 6005) covalent geometry : angle 0.66903 / 0.33 ( 8226) hydrogen bonds : bond 0.03536 / 2.40 ( 302) hydrogen bonds : angle 4.31727 / 2.93 ( 822) metal coordination : bond 0.00900 / 0.46 ( 4) metal coordination : angle 2.32765 / 1.31 ( 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: 1 poor density : 110 time to evaluate : 0.296 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: A 327 ILE cc_start: 0.8916 (mt) cc_final: 0.8630 (mt) REVERT: A 336 LYS cc_start: 0.8404 (ptmt) cc_final: 0.8021 (ttpt) REVERT: A 424 ASN cc_start: 0.8916 (m-40) cc_final: 0.8590 (m-40) REVERT: A 446 CYS cc_start: 0.8357 (m) cc_final: 0.8053 (m) REVERT: A 586 MET cc_start: 0.8425 (tpp) cc_final: 0.8109 (tpp) REVERT: A 603 GLU cc_start: 0.9053 (tt0) cc_final: 0.8750 (mt-10) REVERT: A 755 ILE cc_start: 0.8536 (pt) cc_final: 0.8292 (pt) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1488 time to fit residues: 22.0933 Evaluate side-chains 87 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.089639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.073599 restraints weight = 54947.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.076535 restraints weight = 24424.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078366 restraints weight = 14929.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079512 restraints weight = 10937.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.080102 restraints weight = 8905.093| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6009 Z= 0.199 Angle : 0.650 18.656 8232 Z= 0.321 Chirality : 0.042 0.160 968 Planarity : 0.003 0.036 930 Dihedral : 9.219 56.135 1052 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % 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 are not related in a simple way. whole: -0.02 (0.34), residues: 640 helix: 2.05 (0.28), residues: 333 sheet: -1.44 (0.66), residues: 60 loop : -2.72 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 599 TYR 0.012 0.001 TYR A1018 PHE 0.013 0.001 PHE A 517 TRP 0.011 0.001 TRP A 385 HIS 0.015 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 ( 6005) covalent geometry : angle 0.64799 / 0.32 ( 8226) hydrogen bonds : bond 0.03473 / 2.39 ( 302) hydrogen bonds : angle 4.35670 / 2.97 ( 822) metal coordination : bond 0.00822 / 0.42 ( 4) metal coordination : angle 2.10276 / 1.25 ( 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 108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.314 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: 0.8834 (mt) cc_final: 0.8585 (mt) REVERT: A 336 LYS cc_start: 0.8406 (ptmt) cc_final: 0.8017 (ttpt) REVERT: A 424 ASN cc_start: 0.8791 (m-40) cc_final: 0.8424 (m-40) REVERT: A 446 CYS cc_start: 0.8477 (m) cc_final: 0.8122 (m) REVERT: A 586 MET cc_start: 0.8342 (tpp) cc_final: 0.7847 (tpp) REVERT: A 603 GLU cc_start: 0.9046 (tt0) cc_final: 0.8749 (mt-10) REVERT: A 755 ILE cc_start: 0.8533 (pt) cc_final: 0.8308 (pt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1370 time to fit residues: 20.1905 Evaluate side-chains 81 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3585 r_free = 0.3585 target = 0.087240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.071143 restraints weight = 55168.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074007 restraints weight = 24739.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.075740 restraints weight = 15296.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.076854 restraints weight = 11355.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.077478 restraints weight = 9317.187| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6009 Z= 0.209 Angle : 0.664 18.551 8232 Z= 0.329 Chirality : 0.042 0.164 968 Planarity : 0.003 0.040 930 Dihedral : 9.324 56.724 1052 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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 are not related in a simple way. whole: -0.16 (0.34), residues: 640 helix: 1.91 (0.28), residues: 334 sheet: -1.46 (0.66), residues: 60 loop : -2.77 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 599 TYR 0.013 0.002 TYR A1018 PHE 0.012 0.001 PHE A 680 TRP 0.011 0.001 TRP A 385 HIS 0.014 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 ( 6005) covalent geometry : angle 0.66221 / 0.33 ( 8226) hydrogen bonds : bond 0.03608 / 2.45 ( 302) hydrogen bonds : angle 4.40312 / 3.01 ( 822) metal coordination : bond 0.00915 / 0.46 ( 4) metal coordination : angle 2.14416 / 1.45 ( 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 102 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.286 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 327 ILE cc_start: 0.8855 (mt) cc_final: 0.8606 (mt) REVERT: A 336 LYS cc_start: 0.8341 (ptmt) cc_final: 0.7947 (ttpt) REVERT: A 446 CYS cc_start: 0.8426 (m) cc_final: 0.8159 (m) REVERT: A 586 MET cc_start: 0.8352 (tpp) cc_final: 0.7872 (tpp) REVERT: A 603 GLU cc_start: 0.9058 (tt0) cc_final: 0.8767 (mt-10) REVERT: A 677 MET cc_start: 0.9146 (mtp) cc_final: 0.8925 (mtp) REVERT: A 755 ILE cc_start: 0.8491 (pt) cc_final: 0.8243 (pt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1258 time to fit residues: 17.8965 Evaluate side-chains 81 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 0.8980 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 974 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.086930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070418 restraints weight = 53869.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.073372 restraints weight = 23274.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075185 restraints weight = 14170.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076322 restraints weight = 10437.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.077006 restraints weight = 8582.643| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6009 Z= 0.171 Angle : 0.627 18.643 8232 Z= 0.310 Chirality : 0.041 0.159 968 Planarity : 0.003 0.038 930 Dihedral : 9.163 56.128 1052 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % 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 are not related in a simple way. whole: -0.08 (0.34), residues: 640 helix: 1.98 (0.28), residues: 334 sheet: -1.56 (0.61), residues: 67 loop : -2.72 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 599 TYR 0.008 0.001 TYR A 408 PHE 0.008 0.001 PHE A 517 TRP 0.007 0.001 TRP A 582 HIS 0.014 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 6005) covalent geometry : angle 0.62510 / 0.31 ( 8226) hydrogen bonds : bond 0.03335 / 2.28 ( 302) hydrogen bonds : angle 4.27394 / 2.93 ( 822) metal coordination : bond 0.00727 / 0.37 ( 4) metal coordination : angle 2.07596 / 1.46 ( 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 99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8839 (mt) cc_final: 0.8602 (mt) REVERT: A 336 LYS cc_start: 0.8460 (ptmt) cc_final: 0.8076 (ttpt) REVERT: A 446 CYS cc_start: 0.8237 (m) cc_final: 0.8002 (m) REVERT: A 586 MET cc_start: 0.8428 (tpp) cc_final: 0.7922 (tpp) REVERT: A 603 GLU cc_start: 0.9076 (tt0) cc_final: 0.8746 (mt-10) REVERT: A 677 MET cc_start: 0.9199 (mtp) cc_final: 0.8921 (mtp) REVERT: A 755 ILE cc_start: 0.8461 (pt) cc_final: 0.8078 (pt) REVERT: A 971 MET cc_start: 0.8324 (mmm) cc_final: 0.7596 (mmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1374 time to fit residues: 18.4494 Evaluate side-chains 83 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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: 6.9990 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.084707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068489 restraints weight = 55830.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071298 restraints weight = 24401.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.073034 restraints weight = 14958.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074103 restraints weight = 11150.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074609 restraints weight = 9223.986| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6009 Z= 0.314 Angle : 0.804 18.048 8232 Z= 0.393 Chirality : 0.047 0.212 968 Planarity : 0.004 0.040 930 Dihedral : 10.006 60.577 1052 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 30.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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 are not related in a simple way. whole: -0.77 (0.33), residues: 640 helix: 1.35 (0.28), residues: 333 sheet: -1.91 (0.60), residues: 69 loop : -2.90 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 599 TYR 0.020 0.002 TYR A1018 PHE 0.016 0.002 PHE A 680 TRP 0.014 0.002 TRP A 385 HIS 0.013 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.31 ( 6005) covalent geometry : angle 0.79820 / 0.39 ( 8226) hydrogen bonds : bond 0.04297 / 2.89 ( 302) hydrogen bonds : angle 4.77752 / 3.28 ( 822) metal coordination : bond 0.01312 / 0.67 ( 4) metal coordination : angle 3.67687 / 2.26 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.01 seconds wall clock time: 31 minutes 58.59 seconds (1918.59 seconds total)