Starting phenix.real_space_refine on Thu Mar 14 21:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h61_0143/03_2024/6h61_0143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h61_0143/03_2024/6h61_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h61_0143/03_2024/6h61_0143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h61_0143/03_2024/6h61_0143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h61_0143/03_2024/6h61_0143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h61_0143/03_2024/6h61_0143.pdb" } 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 Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.97, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.23 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 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: 4.06 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: 3.46 Time building geometry restraints manager: 7.51 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: 67.64 - 82.54: 2 82.54 - 97.44: 1 97.44 - 112.34: 10808 112.34 - 127.24: 6577 127.24 - 142.14: 104 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 1.850 nonbonded pdb=" HZ2 LYS A 638 " pdb=" O CYS A 964 " model vdw 1.726 1.850 nonbonded pdb="HH12 ARG A 599 " pdb=" OD1 ASN A 909 " model vdw 1.727 1.850 nonbonded pdb=" O GLU A 628 " pdb=" HG1 THR A 632 " model vdw 1.729 1.850 ... (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 ========== 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 3.060 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 38.460 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- 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 : 0.007 0.064 6005 Z= 0.445 Angle : 0.840 20.993 8226 Z= 0.467 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.775 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: 0.4055 time to fit residues: 88.3205 Evaluate side-chains 103 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 643 ASN A 693 ASN A 784 ASN A 899 ASN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6005 Z= 0.153 Angle : 0.574 19.430 8226 Z= 0.306 Chirality : 0.037 0.144 968 Planarity : 0.003 0.036 930 Dihedral : 15.469 74.112 1166 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.35 % Allowed : 1.58 % 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: -1.24 (0.32), residues: 640 helix: 0.69 (0.27), residues: 314 sheet: -1.44 (0.63), residues: 65 loop : -2.61 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.016 0.001 HIS A 626 PHE 0.016 0.002 PHE A 517 TYR 0.010 0.001 TYR A 342 ARG 0.004 0.000 ARG A 599 *********************** 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 135 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8752 (mt) cc_final: 0.8536 (mt) REVERT: A 365 ASN cc_start: 0.8691 (p0) cc_final: 0.8321 (p0) REVERT: A 403 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 446 CYS cc_start: 0.8048 (m) cc_final: 0.7824 (m) REVERT: A 586 MET cc_start: 0.8379 (tpp) cc_final: 0.8015 (tpp) REVERT: A 603 GLU cc_start: 0.9082 (tt0) cc_final: 0.8709 (mt-10) REVERT: A 609 ASN cc_start: 0.8869 (t0) cc_final: 0.8649 (t0) REVERT: A 797 ASP cc_start: 0.8144 (t70) cc_final: 0.7873 (t0) REVERT: A 879 GLN cc_start: 0.9015 (tt0) cc_final: 0.8733 (mm110) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.3356 time to fit residues: 57.7407 Evaluate side-chains 104 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 17 optimal weight: 0.0670 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 overall best weight: 1.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN A 643 ASN A 683 ASN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6005 Z= 0.149 Angle : 0.534 19.398 8226 Z= 0.285 Chirality : 0.037 0.144 968 Planarity : 0.003 0.037 930 Dihedral : 15.208 74.084 1166 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.34), residues: 640 helix: 1.86 (0.29), residues: 314 sheet: -1.34 (0.61), residues: 67 loop : -2.49 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 582 HIS 0.007 0.001 HIS A 626 PHE 0.017 0.001 PHE A 517 TYR 0.013 0.001 TYR A 869 ARG 0.003 0.000 ARG A 599 *********************** 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 128 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.862 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: 0.8822 (mt) cc_final: 0.8582 (mt) REVERT: A 403 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 446 CYS cc_start: 0.8170 (m) cc_final: 0.7903 (m) REVERT: A 488 LEU cc_start: 0.8724 (mp) cc_final: 0.8414 (mp) REVERT: A 515 ASP cc_start: 0.8399 (t0) cc_final: 0.8190 (t70) REVERT: A 580 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 586 MET cc_start: 0.8381 (tpp) cc_final: 0.7723 (tpp) REVERT: A 603 GLU cc_start: 0.9054 (tt0) cc_final: 0.8722 (mt-10) REVERT: A 797 ASP cc_start: 0.8161 (t70) cc_final: 0.7809 (t0) REVERT: A 869 TYR cc_start: 0.8140 (t80) cc_final: 0.7754 (t80) REVERT: A 1018 TYR cc_start: 0.7009 (t80) cc_final: 0.6578 (t80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3537 time to fit residues: 58.3096 Evaluate side-chains 98 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 476 ASN A 643 ASN A 678 ASN A 729 GLN A 859 ASN A 863 ASN A 879 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6005 Z= 0.332 Angle : 0.673 18.508 8226 Z= 0.360 Chirality : 0.039 0.148 968 Planarity : 0.004 0.040 930 Dihedral : 15.252 74.424 1166 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 28.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.33), residues: 640 helix: 1.81 (0.28), residues: 319 sheet: -1.67 (0.61), residues: 68 loop : -2.87 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 385 HIS 0.020 0.002 HIS A 626 PHE 0.013 0.002 PHE A 680 TYR 0.019 0.002 TYR A 830 ARG 0.004 0.001 ARG A 599 *********************** 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 112 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.813 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: 0.8910 (mt) cc_final: 0.8688 (mt) REVERT: A 397 LEU cc_start: 0.9325 (tp) cc_final: 0.9106 (tp) REVERT: A 446 CYS cc_start: 0.8349 (m) cc_final: 0.8021 (m) REVERT: A 557 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 603 GLU cc_start: 0.9139 (tt0) cc_final: 0.8759 (mt-10) REVERT: A 609 ASN cc_start: 0.8806 (t0) cc_final: 0.8517 (t0) REVERT: A 797 ASP cc_start: 0.8204 (t70) cc_final: 0.7984 (t0) REVERT: A 912 MET cc_start: 0.8119 (ptt) cc_final: 0.7838 (ptt) REVERT: A 924 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7656 (mm-30) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3305 time to fit residues: 48.1925 Evaluate side-chains 90 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6005 Z= 0.190 Angle : 0.544 19.024 8226 Z= 0.292 Chirality : 0.037 0.137 968 Planarity : 0.003 0.039 930 Dihedral : 15.155 74.020 1166 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % 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: -0.04 (0.34), residues: 640 helix: 2.20 (0.29), residues: 319 sheet: -1.55 (0.62), residues: 70 loop : -2.70 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.014 0.001 HIS A 626 PHE 0.016 0.001 PHE A 374 TYR 0.011 0.001 TYR A 342 ARG 0.003 0.000 ARG A 599 *********************** 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 117 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.832 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 397 LEU cc_start: 0.9293 (tp) cc_final: 0.9081 (tp) REVERT: A 424 ASN cc_start: 0.9042 (m-40) cc_final: 0.8773 (m-40) REVERT: A 446 CYS cc_start: 0.8330 (m) cc_final: 0.8037 (m) REVERT: A 488 LEU cc_start: 0.8710 (mp) cc_final: 0.8452 (mp) REVERT: A 557 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 603 GLU cc_start: 0.9120 (tt0) cc_final: 0.8741 (mt-10) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3276 time to fit residues: 49.8326 Evaluate side-chains 86 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6005 Z= 0.212 Angle : 0.557 18.758 8226 Z= 0.297 Chirality : 0.037 0.153 968 Planarity : 0.003 0.042 930 Dihedral : 15.114 74.089 1166 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.35), residues: 640 helix: 2.38 (0.29), residues: 321 sheet: -1.63 (0.62), residues: 70 loop : -2.68 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.011 0.001 HIS A 626 PHE 0.010 0.001 PHE A 374 TYR 0.013 0.001 TYR A 455 ARG 0.004 0.000 ARG A 599 *********************** 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 114 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8980 (mt) cc_final: 0.8710 (mt) REVERT: A 397 LEU cc_start: 0.9292 (tp) cc_final: 0.9091 (tp) REVERT: A 424 ASN cc_start: 0.8911 (m-40) cc_final: 0.8540 (m-40) REVERT: A 446 CYS cc_start: 0.8379 (m) cc_final: 0.8135 (m) REVERT: A 488 LEU cc_start: 0.8624 (mp) cc_final: 0.8346 (mp) REVERT: A 555 LEU cc_start: 0.9576 (tt) cc_final: 0.9306 (mt) REVERT: A 557 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 580 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 603 GLU cc_start: 0.9112 (tt0) cc_final: 0.8752 (mt-10) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3030 time to fit residues: 45.9297 Evaluate side-chains 93 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 ASN ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6005 Z= 0.283 Angle : 0.607 18.572 8226 Z= 0.325 Chirality : 0.038 0.150 968 Planarity : 0.004 0.042 930 Dihedral : 15.250 74.275 1166 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.34), residues: 640 helix: 2.06 (0.29), residues: 326 sheet: -1.91 (0.57), residues: 82 loop : -2.75 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 385 HIS 0.010 0.001 HIS A 626 PHE 0.015 0.002 PHE A 374 TYR 0.017 0.002 TYR A1018 ARG 0.004 0.000 ARG A 599 *********************** 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 109 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.892 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: 0.9035 (mt) cc_final: 0.8808 (mt) REVERT: A 446 CYS cc_start: 0.8295 (m) cc_final: 0.8044 (m) REVERT: A 488 LEU cc_start: 0.8595 (mp) cc_final: 0.8183 (mp) REVERT: A 555 LEU cc_start: 0.9571 (tt) cc_final: 0.9312 (mt) REVERT: A 557 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 603 GLU cc_start: 0.9133 (tt0) cc_final: 0.8794 (mt-10) REVERT: A 677 MET cc_start: 0.9334 (mtp) cc_final: 0.9094 (mtp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3141 time to fit residues: 44.9695 Evaluate side-chains 89 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6005 Z= 0.164 Angle : 0.526 18.877 8226 Z= 0.280 Chirality : 0.036 0.146 968 Planarity : 0.003 0.042 930 Dihedral : 15.123 74.018 1166 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % 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: 0.25 (0.35), residues: 640 helix: 2.38 (0.29), residues: 325 sheet: -1.25 (0.61), residues: 74 loop : -2.66 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 385 HIS 0.009 0.001 HIS A 626 PHE 0.008 0.001 PHE A 378 TYR 0.011 0.001 TYR A 342 ARG 0.004 0.000 ARG A 599 *********************** 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 fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.970 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: 0.8985 (mt) cc_final: 0.8735 (mt) REVERT: A 397 LEU cc_start: 0.9279 (tp) cc_final: 0.9069 (tp) REVERT: A 446 CYS cc_start: 0.8288 (m) cc_final: 0.7998 (m) REVERT: A 488 LEU cc_start: 0.8846 (mp) cc_final: 0.8067 (tt) REVERT: A 557 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 603 GLU cc_start: 0.9107 (tt0) cc_final: 0.8757 (mt-10) REVERT: A 677 MET cc_start: 0.9310 (mtp) cc_final: 0.9081 (mtp) REVERT: A 684 LYS cc_start: 0.9254 (tmmt) cc_final: 0.9012 (tmtt) REVERT: A 755 ILE cc_start: 0.8453 (pt) cc_final: 0.8235 (pt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3161 time to fit residues: 46.3578 Evaluate side-chains 88 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6005 Z= 0.152 Angle : 0.518 18.949 8226 Z= 0.274 Chirality : 0.036 0.145 968 Planarity : 0.003 0.040 930 Dihedral : 15.057 73.986 1166 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % 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: 0.48 (0.36), residues: 640 helix: 2.55 (0.29), residues: 325 sheet: -1.46 (0.60), residues: 79 loop : -2.41 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.009 0.001 HIS A 626 PHE 0.008 0.001 PHE A 374 TYR 0.020 0.001 TYR A 624 ARG 0.004 0.000 ARG A 310 *********************** 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 109 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ILE cc_start: 0.8997 (mt) cc_final: 0.8788 (mt) REVERT: A 446 CYS cc_start: 0.8218 (m) cc_final: 0.7967 (m) REVERT: A 557 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8554 (tm-30) REVERT: A 580 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 603 GLU cc_start: 0.9085 (tt0) cc_final: 0.8748 (mt-10) REVERT: A 624 TYR cc_start: 0.7720 (t80) cc_final: 0.7208 (t80) REVERT: A 677 MET cc_start: 0.9303 (mtp) cc_final: 0.9100 (mtp) REVERT: A 755 ILE cc_start: 0.8439 (pt) cc_final: 0.8141 (pt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3109 time to fit residues: 45.0255 Evaluate side-chains 90 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6005 Z= 0.218 Angle : 0.560 18.607 8226 Z= 0.298 Chirality : 0.037 0.144 968 Planarity : 0.003 0.044 930 Dihedral : 15.161 74.149 1166 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % 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: 0.25 (0.35), residues: 640 helix: 2.30 (0.29), residues: 325 sheet: -1.40 (0.61), residues: 77 loop : -2.49 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 385 HIS 0.010 0.001 HIS A 626 PHE 0.009 0.001 PHE A 374 TYR 0.034 0.002 TYR A 624 ARG 0.004 0.000 ARG A 599 ********************** 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 97 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.836 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: 0.9074 (mt) cc_final: 0.8853 (mt) REVERT: A 446 CYS cc_start: 0.8235 (m) cc_final: 0.7996 (m) REVERT: A 557 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8544 (tm-30) REVERT: A 603 GLU cc_start: 0.9132 (tt0) cc_final: 0.8806 (mt-10) REVERT: A 677 MET cc_start: 0.9287 (mtp) cc_final: 0.9065 (mtp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3224 time to fit residues: 41.4200 Evaluate side-chains 79 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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 = 0.3594 r_free = 0.3594 target = 0.089051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.072945 restraints weight = 53953.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.075910 restraints weight = 23147.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077707 restraints weight = 14003.574| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6005 Z= 0.156 Angle : 0.516 18.843 8226 Z= 0.273 Chirality : 0.036 0.142 968 Planarity : 0.003 0.045 930 Dihedral : 15.143 74.015 1166 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % 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: 0.47 (0.35), residues: 640 helix: 2.48 (0.29), residues: 325 sheet: -1.31 (0.61), residues: 77 loop : -2.38 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 385 HIS 0.010 0.001 HIS A 626 PHE 0.010 0.001 PHE A 374 TYR 0.010 0.001 TYR A 624 ARG 0.004 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.65 seconds wall clock time: 44 minutes 58.05 seconds (2698.05 seconds total)