Starting phenix.real_space_refine on Mon Jun 9 04:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h61_0143/06_2025/6h61_0143.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h61_0143/06_2025/6h61_0143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h61_0143/06_2025/6h61_0143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h61_0143/06_2025/6h61_0143.map" model { file = "/net/cci-nas-00/data/ceres_data/6h61_0143/06_2025/6h61_0143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h61_0143/06_2025/6h61_0143.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 11, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "X" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7821 SG CYS A 907 78.601 38.750 37.827 1.00160.60 S ATOM 7868 SG CYS A 910 82.314 38.522 37.781 1.00169.21 S ATOM 8477 SG CYS A 962 80.773 39.778 41.111 1.00174.46 S ATOM 8492 SG CYS A 964 80.765 42.477 39.020 1.00180.02 S Time building chain proxies: 5.78, per 1000 atoms: 0.58 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: 2.80 Conformation dependent library (CDL) restraints added in 664.7 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: 4.11 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: 3.54 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4046 1.03 - 1.23: 19 1.23 - 1.42: 2497 1.42 - 1.62: 3448 1.62 - 1.81: 52 Bond restraints: 10062 Sorted by residual: bond pdb=" CA LYS A 366 " pdb=" CB LYS A 366 " ideal model delta sigma weight residual 1.535 1.501 0.034 2.09e-02 2.29e+03 2.72e+00 bond pdb=" CB CYS A 446 " pdb=" SG CYS A 446 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CB TYR A 408 " pdb=" CG TYR A 408 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.20e-02 2.07e+03 2.03e+00 bond pdb=" CG LYS A 466 " pdb=" CD LYS A 466 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CG1 ILE A 458 " pdb=" CD1 ILE A 458 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.88e+00 ... (remaining 10057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.01: 17489 10.01 - 20.02: 0 20.02 - 30.03: 1 30.03 - 40.04: 0 40.04 - 50.04: 2 Bond angle restraints: 17492 Sorted by residual: angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 124.58 74.53 50.04 3.00e+00 1.11e-01 2.78e+02 angle pdb=" CA LYS A 498 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 114.28 67.64 46.64 3.00e+00 1.11e-01 2.42e+02 angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 121.15 142.14 -20.99 1.85e+00 2.92e-01 1.29e+02 angle pdb=" C LEU A 472 " pdb=" N LYS A 473 " pdb=" CA LYS A 473 " ideal model delta sigma weight residual 120.79 124.95 -4.16 1.39e+00 5.18e-01 8.95e+00 angle pdb=" N SER A 761 " pdb=" CA SER A 761 " pdb=" C SER A 761 " ideal model delta sigma weight residual 110.80 116.99 -6.19 2.13e+00 2.20e-01 8.43e+00 ... (remaining 17487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4613 17.29 - 34.57: 335 34.57 - 51.86: 85 51.86 - 69.14: 51 69.14 - 86.43: 11 Dihedral angle restraints: 5095 sinusoidal: 2910 harmonic: 2185 Sorted by residual: dihedral pdb=" CA SER A 760 " pdb=" C SER A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA LEU A 902 " pdb=" C LEU A 902 " pdb=" N ILE A 903 " pdb=" CA ILE A 903 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ARG A 375 " pdb=" C ARG A 375 " pdb=" N LYS A 376 " pdb=" CA LYS A 376 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 5092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 570 0.031 - 0.062: 234 0.062 - 0.092: 108 0.092 - 0.123: 42 0.123 - 0.154: 14 Chirality restraints: 968 Sorted by residual: chirality pdb=" CB ILE A 399 " pdb=" CA ILE A 399 " pdb=" CG1 ILE A 399 " pdb=" CG2 ILE A 399 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 412 " pdb=" N ILE A 412 " pdb=" C ILE A 412 " pdb=" CB ILE A 412 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA PRO A 933 " pdb=" N PRO A 933 " pdb=" C PRO A 933 " pdb=" CB PRO A 933 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 965 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 490 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C ALA A 490 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA A 490 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 491 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 829 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C THR A 829 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 829 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 830 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 457 " -0.008 2.00e-02 2.50e+03 1.29e-02 2.50e+00 pdb=" CG ASN A 457 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 457 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 457 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 457 " -0.005 2.00e-02 2.50e+03 pdb="HD22 ASN A 457 " -0.002 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 334 2.17 - 2.77: 16899 2.77 - 3.38: 24460 3.38 - 3.99: 32097 3.99 - 4.60: 49603 Nonbonded interactions: 123393 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.557 1.816 nonbonded pdb=" O LYS A 750 " pdb=" H ASN A 784 " model vdw 1.724 2.450 nonbonded pdb=" HZ2 LYS A 638 " pdb=" O CYS A 964 " model vdw 1.726 2.450 nonbonded pdb="HH12 ARG A 599 " pdb=" OD1 ASN A 909 " model vdw 1.727 2.450 nonbonded pdb=" O GLU A 628 " pdb=" HG1 THR A 632 " model vdw 1.729 2.450 ... (remaining 123388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.200 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.582 6009 Z= 0.420 Angle : 0.970 33.455 8232 Z= 0.475 Chirality : 0.045 0.154 968 Planarity : 0.005 0.039 930 Dihedral : 13.660 74.317 2476 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.18 % Allowed : 2.11 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP A 968 HIS 0.006 0.002 HIS A 506 PHE 0.023 0.003 PHE A 378 TYR 0.013 0.002 TYR A 830 ARG 0.009 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.12053 ( 302) hydrogen bonds : angle 5.87584 ( 822) metal coordination : bond 0.29710 ( 4) metal coordination : angle 18.00099 ( 6) covalent geometry : bond 0.00687 ( 6005) covalent geometry : angle 0.83953 ( 8226) *********************** 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 : 0.798 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: 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: 0.7868 (pttp) REVERT: A 446 CYS cc_start: 0.8193 (m) cc_final: 0.7886 (m) REVERT: A 586 MET cc_start: 0.8426 (tpp) cc_final: 0.8037 (tpp) REVERT: A 603 GLU cc_start: 0.9072 (tt0) cc_final: 0.8706 (mt-10) REVERT: A 631 TYR cc_start: 0.8312 (m-80) cc_final: 0.8065 (m-80) REVERT: A 869 TYR cc_start: 0.8223 (t80) cc_final: 0.8010 (t80) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.4194 time to fit residues: 91.9068 Evaluate side-chains 103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 693 ASN A 729 GLN A 784 ASN A 899 ASN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.089572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073238 restraints weight = 51830.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.076285 restraints weight = 23057.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078189 restraints weight = 13879.546| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6009 Z= 0.147 Angle : 0.611 19.479 8232 Z= 0.321 Chirality : 0.038 0.152 968 Planarity : 0.004 0.037 930 Dihedral : 15.538 74.188 1166 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.32), residues: 640 helix: 0.63 (0.27), residues: 312 sheet: -1.67 (0.63), residues: 65 loop : -2.66 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.015 0.002 HIS A 626 PHE 0.016 0.002 PHE A 517 TYR 0.009 0.001 TYR A 342 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 302) hydrogen bonds : angle 4.67046 ( 822) metal coordination : bond 0.00757 ( 4) metal coordination : angle 5.36871 ( 6) covalent geometry : bond 0.00298 ( 6005) covalent geometry : angle 0.59356 ( 8226) *********************** 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 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.820 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: 0.8742 (mt) cc_final: 0.8501 (mt) REVERT: A 365 ASN cc_start: 0.8692 (p0) cc_final: 0.8338 (p0) REVERT: A 403 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 446 CYS cc_start: 0.8079 (m) cc_final: 0.7854 (m) REVERT: A 586 MET cc_start: 0.8368 (tpp) cc_final: 0.8010 (tpp) REVERT: A 603 GLU cc_start: 0.9046 (tt0) cc_final: 0.8696 (mt-10) REVERT: A 797 ASP cc_start: 0.8262 (t70) cc_final: 0.7973 (t0) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.3321 time to fit residues: 55.3364 Evaluate side-chains 105 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.0040 chunk 60 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 615 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN A 879 GLN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.087731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071519 restraints weight = 52108.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074467 restraints weight = 22685.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076249 restraints weight = 13713.835| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4042 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= 0.196 Angle : 0.619 18.998 8232 Z= 0.330 Chirality : 0.038 0.143 968 Planarity : 0.004 0.034 930 Dihedral : 15.204 74.241 1166 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.33), residues: 640 helix: 1.51 (0.29), residues: 319 sheet: -1.78 (0.60), residues: 65 loop : -2.83 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.007 0.002 HIS A 626 PHE 0.011 0.001 PHE A 378 TYR 0.014 0.002 TYR A 830 ARG 0.006 0.001 ARG A 860 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 302) hydrogen bonds : angle 4.39373 ( 822) metal coordination : bond 0.00679 ( 4) metal coordination : angle 3.42340 ( 6) covalent geometry : bond 0.00386 ( 6005) covalent geometry : angle 0.61247 ( 8226) *********************** 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: 0 poor density : 119 time to evaluate : 0.753 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: 0.8850 (mt) cc_final: 0.8602 (mt) REVERT: A 419 GLU cc_start: 0.9013 (tp30) cc_final: 0.8811 (tp30) REVERT: A 446 CYS cc_start: 0.8232 (m) cc_final: 0.8014 (m) REVERT: A 452 GLU cc_start: 0.8236 (tp30) cc_final: 0.7918 (tp30) REVERT: A 488 LEU cc_start: 0.8768 (mp) cc_final: 0.8422 (mp) REVERT: A 586 MET cc_start: 0.8453 (tpp) cc_final: 0.8134 (tpp) REVERT: A 603 GLU cc_start: 0.9085 (tt0) cc_final: 0.8719 (mt-10) REVERT: A 606 ARG cc_start: 0.8904 (tpt-90) cc_final: 0.8618 (tpt-90) REVERT: A 674 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8684 (mm-30) REVERT: A 797 ASP cc_start: 0.8257 (t70) cc_final: 0.7904 (t0) REVERT: A 912 MET cc_start: 0.8434 (ptt) cc_final: 0.8166 (ptt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3379 time to fit residues: 53.5322 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 : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 46 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 643 ASN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.069924 restraints weight = 53201.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072857 restraints weight = 23222.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.074621 restraints weight = 14108.703| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6009 Z= 0.218 Angle : 0.622 18.773 8232 Z= 0.331 Chirality : 0.038 0.145 968 Planarity : 0.004 0.036 930 Dihedral : 15.127 74.160 1166 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.33), residues: 640 helix: 1.80 (0.28), residues: 319 sheet: -1.83 (0.56), residues: 72 loop : -2.92 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 385 HIS 0.006 0.001 HIS A 626 PHE 0.020 0.002 PHE A 517 TYR 0.018 0.002 TYR A1018 ARG 0.004 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 302) hydrogen bonds : angle 4.55950 ( 822) metal coordination : bond 0.00819 ( 4) metal coordination : angle 2.99987 ( 6) covalent geometry : bond 0.00432 ( 6005) covalent geometry : angle 0.61703 ( 8226) *********************** 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 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.851 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: 0.8868 (mt) cc_final: 0.8603 (mt) REVERT: A 446 CYS cc_start: 0.8455 (m) cc_final: 0.8109 (m) REVERT: A 452 GLU cc_start: 0.8320 (tp30) cc_final: 0.7995 (tp30) REVERT: A 488 LEU cc_start: 0.8931 (mp) cc_final: 0.8653 (mp) REVERT: A 557 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 603 GLU cc_start: 0.9115 (tt0) cc_final: 0.8778 (mt-10) REVERT: A 755 ILE cc_start: 0.8547 (pt) cc_final: 0.8329 (pt) REVERT: A 797 ASP cc_start: 0.8415 (t70) cc_final: 0.8190 (t0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2972 time to fit residues: 44.3767 Evaluate side-chains 84 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.087111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070567 restraints weight = 52521.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.073540 restraints weight = 23168.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075346 restraints weight = 14150.227| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5168 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= 0.151 Angle : 0.550 19.017 8232 Z= 0.293 Chirality : 0.037 0.143 968 Planarity : 0.003 0.037 930 Dihedral : 15.028 74.086 1166 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.34), residues: 640 helix: 2.10 (0.29), residues: 327 sheet: -1.63 (0.60), residues: 65 loop : -2.82 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.021 0.002 HIS A 626 PHE 0.012 0.001 PHE A 517 TYR 0.011 0.001 TYR A 342 ARG 0.003 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 302) hydrogen bonds : angle 4.22131 ( 822) metal coordination : bond 0.00589 ( 4) metal coordination : angle 1.84190 ( 6) covalent geometry : bond 0.00300 ( 6005) covalent geometry : angle 0.54779 ( 8226) *********************** 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 108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.886 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: 0.8850 (mt) cc_final: 0.8613 (mt) REVERT: A 336 LYS cc_start: 0.8480 (ptmt) cc_final: 0.8098 (ttpt) REVERT: A 424 ASN cc_start: 0.9118 (m-40) cc_final: 0.8818 (m-40) REVERT: A 446 CYS cc_start: 0.8375 (m) cc_final: 0.8112 (m) REVERT: A 452 GLU cc_start: 0.8293 (tp30) cc_final: 0.7973 (tp30) REVERT: A 555 LEU cc_start: 0.9533 (tt) cc_final: 0.9256 (mt) REVERT: A 557 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 586 MET cc_start: 0.8495 (tpp) cc_final: 0.7959 (tpp) REVERT: A 603 GLU cc_start: 0.9097 (tt0) cc_final: 0.8731 (mt-10) REVERT: A 606 ARG cc_start: 0.9013 (tpt-90) cc_final: 0.8785 (tpt-90) REVERT: A 755 ILE cc_start: 0.8523 (pt) cc_final: 0.8314 (pt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3582 time to fit residues: 53.3570 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 : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.085945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069629 restraints weight = 54394.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072541 restraints weight = 24310.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.074306 restraints weight = 15133.085| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6009 Z= 0.220 Angle : 0.609 18.638 8232 Z= 0.324 Chirality : 0.038 0.149 968 Planarity : 0.004 0.035 930 Dihedral : 15.239 74.296 1166 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.34), residues: 640 helix: 1.92 (0.29), residues: 333 sheet: -1.86 (0.63), residues: 60 loop : -2.88 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 385 HIS 0.016 0.002 HIS A 626 PHE 0.012 0.002 PHE A 680 TYR 0.015 0.002 TYR A 455 ARG 0.004 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 302) hydrogen bonds : angle 4.39354 ( 822) metal coordination : bond 0.00883 ( 4) metal coordination : angle 2.54313 ( 6) covalent geometry : bond 0.00435 ( 6005) covalent geometry : angle 0.60513 ( 8226) *********************** 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 108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.737 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 327 ILE cc_start: 0.8930 (mt) cc_final: 0.8704 (mt) REVERT: A 446 CYS cc_start: 0.8379 (m) cc_final: 0.8105 (m) REVERT: A 467 LEU cc_start: 0.8980 (mt) cc_final: 0.8755 (tt) REVERT: A 488 LEU cc_start: 0.9036 (mp) cc_final: 0.8703 (mp) REVERT: A 555 LEU cc_start: 0.9529 (tt) cc_final: 0.9252 (mt) REVERT: A 557 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8383 (tm-30) REVERT: A 586 MET cc_start: 0.8415 (tpp) cc_final: 0.7914 (tpp) REVERT: A 603 GLU cc_start: 0.9071 (tt0) cc_final: 0.8777 (mt-10) REVERT: A 606 ARG cc_start: 0.9040 (tpt-90) cc_final: 0.8835 (tpt-90) REVERT: A 755 ILE cc_start: 0.8439 (pt) cc_final: 0.8235 (pt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3400 time to fit residues: 48.3286 Evaluate side-chains 82 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073153 restraints weight = 53283.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.076198 restraints weight = 23379.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078093 restraints weight = 14230.400| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6009 Z= 0.137 Angle : 0.554 18.907 8232 Z= 0.293 Chirality : 0.037 0.144 968 Planarity : 0.003 0.036 930 Dihedral : 15.178 74.041 1166 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.35), residues: 640 helix: 2.09 (0.29), residues: 333 sheet: -1.49 (0.58), residues: 72 loop : -2.81 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.014 0.002 HIS A 626 PHE 0.009 0.001 PHE A 374 TYR 0.011 0.001 TYR A 342 ARG 0.008 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 302) hydrogen bonds : angle 4.26313 ( 822) metal coordination : bond 0.00713 ( 4) metal coordination : angle 1.71002 ( 6) covalent geometry : bond 0.00278 ( 6005) covalent geometry : angle 0.55214 ( 8226) *********************** 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 113 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.457 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 336 LYS cc_start: 0.8386 (ptmt) cc_final: 0.7990 (ttpt) REVERT: A 431 ASP cc_start: 0.7701 (m-30) cc_final: 0.7223 (t70) REVERT: A 446 CYS cc_start: 0.8550 (m) cc_final: 0.8119 (m) REVERT: A 467 LEU cc_start: 0.8995 (mt) cc_final: 0.8751 (tt) REVERT: A 586 MET cc_start: 0.8409 (tpp) cc_final: 0.7886 (tpp) REVERT: A 603 GLU cc_start: 0.9033 (tt0) cc_final: 0.8737 (mt-10) REVERT: A 606 ARG cc_start: 0.8995 (tpt-90) cc_final: 0.8769 (tpt-90) REVERT: A 755 ILE cc_start: 0.8456 (pt) cc_final: 0.8239 (pt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.4053 time to fit residues: 60.8656 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 : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.0000 chunk 63 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.089919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073867 restraints weight = 54088.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076852 restraints weight = 23879.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.078729 restraints weight = 14572.214| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6009 Z= 0.102 Angle : 0.520 19.068 8232 Z= 0.274 Chirality : 0.037 0.149 968 Planarity : 0.003 0.032 930 Dihedral : 15.059 74.009 1166 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.35), residues: 640 helix: 2.31 (0.29), residues: 333 sheet: -1.19 (0.64), residues: 64 loop : -2.59 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 582 HIS 0.013 0.001 HIS A 626 PHE 0.010 0.001 PHE A 374 TYR 0.010 0.001 TYR A 342 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 302) hydrogen bonds : angle 3.94864 ( 822) metal coordination : bond 0.00363 ( 4) metal coordination : angle 1.27422 ( 6) covalent geometry : bond 0.00210 ( 6005) covalent geometry : angle 0.51885 ( 8226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue VAL 810 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8933 (mt) cc_final: 0.8655 (mt) REVERT: A 336 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7852 (ttpt) REVERT: A 419 GLU cc_start: 0.8813 (tp30) cc_final: 0.8602 (tp30) REVERT: A 446 CYS cc_start: 0.8418 (m) cc_final: 0.8136 (m) REVERT: A 467 LEU cc_start: 0.8986 (mt) cc_final: 0.8750 (tt) REVERT: A 603 GLU cc_start: 0.8990 (tt0) cc_final: 0.8724 (mt-10) REVERT: A 606 ARG cc_start: 0.8955 (tpt-90) cc_final: 0.8716 (tpt-90) REVERT: A 755 ILE cc_start: 0.8515 (pt) cc_final: 0.8269 (pt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3098 time to fit residues: 45.4416 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 : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 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 = 0.3605 r_free = 0.3605 target = 0.087820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071439 restraints weight = 53462.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.074410 restraints weight = 23873.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076249 restraints weight = 14660.628| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6009 Z= 0.166 Angle : 0.575 18.730 8232 Z= 0.303 Chirality : 0.038 0.165 968 Planarity : 0.003 0.034 930 Dihedral : 15.103 74.196 1166 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.35), residues: 640 helix: 2.25 (0.29), residues: 332 sheet: -1.20 (0.64), residues: 65 loop : -2.68 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 385 HIS 0.012 0.001 HIS A 626 PHE 0.010 0.001 PHE A 517 TYR 0.010 0.001 TYR A1018 ARG 0.004 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 302) hydrogen bonds : angle 4.13729 ( 822) metal coordination : bond 0.00722 ( 4) metal coordination : angle 2.22716 ( 6) covalent geometry : bond 0.00331 ( 6005) covalent geometry : angle 0.57166 ( 8226) *********************** 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 99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.847 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: 0.8943 (mt) cc_final: 0.8651 (mt) REVERT: A 336 LYS cc_start: 0.8399 (ptmt) cc_final: 0.8054 (ttpt) REVERT: A 446 CYS cc_start: 0.8257 (m) cc_final: 0.7953 (m) REVERT: A 467 LEU cc_start: 0.8978 (mt) cc_final: 0.8752 (tt) REVERT: A 603 GLU cc_start: 0.9035 (tt0) cc_final: 0.8792 (mt-10) REVERT: A 606 ARG cc_start: 0.9005 (tpt-90) cc_final: 0.8744 (tpt-90) REVERT: A 624 TYR cc_start: 0.7168 (t80) cc_final: 0.6659 (t80) REVERT: A 755 ILE cc_start: 0.8468 (pt) cc_final: 0.8210 (pt) REVERT: A 931 MET cc_start: 0.6381 (mmt) cc_final: 0.5556 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3013 time to fit residues: 40.0296 Evaluate side-chains 77 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** 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 = 0.3617 r_free = 0.3617 target = 0.088469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072127 restraints weight = 53027.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075163 restraints weight = 23663.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077011 restraints weight = 14505.735| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6009 Z= 0.120 Angle : 0.532 18.825 8232 Z= 0.279 Chirality : 0.037 0.146 968 Planarity : 0.003 0.034 930 Dihedral : 15.059 74.038 1166 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.35), residues: 640 helix: 2.41 (0.29), residues: 326 sheet: -1.02 (0.64), residues: 64 loop : -2.56 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 582 HIS 0.012 0.001 HIS A 626 PHE 0.008 0.001 PHE A 378 TYR 0.009 0.001 TYR A 631 ARG 0.006 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 302) hydrogen bonds : angle 3.99569 ( 822) metal coordination : bond 0.00451 ( 4) metal coordination : angle 1.27447 ( 6) covalent geometry : bond 0.00244 ( 6005) covalent geometry : angle 0.53087 ( 8226) ********************** 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 : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8920 (mt) cc_final: 0.8640 (mt) REVERT: A 336 LYS cc_start: 0.8413 (ptmt) cc_final: 0.8044 (ttpt) REVERT: A 446 CYS cc_start: 0.8225 (m) cc_final: 0.7928 (m) REVERT: A 467 LEU cc_start: 0.8996 (mt) cc_final: 0.8769 (tt) REVERT: A 603 GLU cc_start: 0.9025 (tt0) cc_final: 0.8787 (mt-10) REVERT: A 606 ARG cc_start: 0.8994 (tpt-90) cc_final: 0.8720 (tpt-90) REVERT: A 755 ILE cc_start: 0.8497 (pt) cc_final: 0.8127 (pt) REVERT: A 931 MET cc_start: 0.6258 (mmt) cc_final: 0.5638 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3558 time to fit residues: 48.4793 Evaluate side-chains 79 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072673 restraints weight = 52547.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.075715 restraints weight = 23611.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077599 restraints weight = 14456.101| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6009 Z= 0.108 Angle : 0.533 18.956 8232 Z= 0.280 Chirality : 0.036 0.145 968 Planarity : 0.003 0.034 930 Dihedral : 15.032 73.980 1166 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.35), residues: 640 helix: 2.38 (0.29), residues: 327 sheet: -0.93 (0.65), residues: 64 loop : -2.54 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 582 HIS 0.011 0.001 HIS A 626 PHE 0.009 0.001 PHE A 374 TYR 0.010 0.001 TYR A 631 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 302) hydrogen bonds : angle 3.90494 ( 822) metal coordination : bond 0.00397 ( 4) metal coordination : angle 1.14790 ( 6) covalent geometry : bond 0.00224 ( 6005) covalent geometry : angle 0.53224 ( 8226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.66 seconds wall clock time: 64 minutes 37.13 seconds (3877.13 seconds total)