Starting phenix.real_space_refine on Sun Dec 29 05:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q4c_13801/12_2024/7q4c_13801_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q4c_13801/12_2024/7q4c_13801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q4c_13801/12_2024/7q4c_13801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q4c_13801/12_2024/7q4c_13801.map" model { file = "/net/cci-nas-00/data/ceres_data/7q4c_13801/12_2024/7q4c_13801_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q4c_13801/12_2024/7q4c_13801_trim.cif" } resolution = 4.08 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= 0.003 sd= 0.063 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: 6 Type Number sf(0) Gaussians S 24 5.16 5 Cl 1 4.86 5 C 3133 2.51 5 N 822 2.21 5 O 925 1.98 5 H 4598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9503 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 9368 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 551} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.15, per 1000 atoms: 0.54 Number of scatterers: 9503 At special positions: 0 Unit cell: (78.44, 79.5, 81.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 24 16.00 O 925 8.00 N 822 7.00 C 3133 6.00 H 4598 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A 928 " - pdb=" SG CYS A 946 " distance=2.03 Simple disulfide: pdb=" SG CYS A1114 " - pdb=" SG CYS A1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A3002 " - " ASN A 666 " " NAG A3003 " - " ASN A 913 " " NAG B 1 " - " ASN A 648 " " NAG C 1 " - " ASN A 685 " " NAG D 1 " - " ASN A 731 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 618.0 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 71.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 617 through 648 removed outlier: 4.034A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 removed outlier: 3.581A pdb=" N SER A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 678 No H-bonds generated for 'chain 'A' and resid 677 through 678' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.705A pdb=" N GLN A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 725 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.845A pdb=" N ARG A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.871A pdb=" N MET A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 836 removed outlier: 3.614A pdb=" N LEU A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 818 - end of helix Processing helix chain 'A' and resid 859 through 861 No H-bonds generated for 'chain 'A' and resid 859 through 861' Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 887 through 902 Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 950 through 970 Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 982 through 996 removed outlier: 3.719A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 990 " --> pdb=" O HIS A 986 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 996 " --> pdb=" O VAL A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1006 Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.802A pdb=" N ASP A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1049 removed outlier: 3.897A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1056 through 1070 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1096 through 1118 removed outlier: 3.799A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.775A pdb=" N GLN A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 4.146A pdb=" N ALA A1153 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 Processing helix chain 'A' and resid 1172 through 1186 Processing sheet with id=AA1, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA2, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.257A pdb=" N ILE A 846 " --> pdb=" O CYS A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 931 through 934 276 hydrogen bonds defined for protein. 789 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 3.60 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: 4597 1.03 - 1.23: 7 1.23 - 1.42: 2169 1.42 - 1.62: 2829 1.62 - 1.81: 41 Bond restraints: 9643 Sorted by residual: bond pdb=" C1 NAG A3002 " pdb=" O5 NAG A3002 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 NAG B 1 " pdb=" C2 NAG B 1 " ideal model delta sigma weight residual 1.532 1.496 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.95e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 9638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 15824 1.26 - 2.51: 1296 2.51 - 3.77: 149 3.77 - 5.03: 49 5.03 - 6.29: 12 Bond angle restraints: 17330 Sorted by residual: angle pdb=" CA TYR A 970 " pdb=" CB TYR A 970 " pdb=" CG TYR A 970 " ideal model delta sigma weight residual 113.90 120.18 -6.28 1.80e+00 3.09e-01 1.22e+01 angle pdb=" N GLY A1080 " pdb=" CA GLY A1080 " pdb=" C GLY A1080 " ideal model delta sigma weight residual 114.64 109.84 4.80 1.40e+00 5.10e-01 1.18e+01 angle pdb=" CA TRP A1062 " pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 113.60 107.59 6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" C CYS A 928 " pdb=" N HIS A 929 " pdb=" CA HIS A 929 " ideal model delta sigma weight residual 121.24 116.86 4.38 1.44e+00 4.82e-01 9.25e+00 angle pdb=" N ASN A1196 " pdb=" CA ASN A1196 " pdb=" C ASN A1196 " ideal model delta sigma weight residual 107.41 113.43 -6.02 2.02e+00 2.45e-01 8.87e+00 ... (remaining 17325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 4424 20.74 - 41.49: 213 41.49 - 62.23: 57 62.23 - 82.97: 24 82.97 - 103.71: 7 Dihedral angle restraints: 4725 sinusoidal: 2602 harmonic: 2123 Sorted by residual: dihedral pdb=" CB CYS A 928 " pdb=" SG CYS A 928 " pdb=" SG CYS A 946 " pdb=" CB CYS A 946 " ideal model delta sinusoidal sigma weight residual 93.00 168.88 -75.88 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CA PRO A 873 " pdb=" C PRO A 873 " pdb=" N SER A 874 " pdb=" CA SER A 874 " ideal model delta harmonic sigma weight residual 180.00 152.54 27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA PHE A 869 " pdb=" C PHE A 869 " pdb=" N PRO A 870 " pdb=" CA PRO A 870 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 565 0.054 - 0.107: 144 0.107 - 0.161: 34 0.161 - 0.214: 2 0.214 - 0.268: 4 Chirality restraints: 749 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG A3003 " pdb=" ND2 ASN A 913 " pdb=" C2 NAG A3003 " pdb=" O5 NAG A3003 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLN A 969 " pdb=" N GLN A 969 " pdb=" C GLN A 969 " pdb=" CB GLN A 969 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 746 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1197 " 0.016 2.00e-02 2.50e+03 1.92e-02 1.48e+01 pdb=" CG TRP A1197 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A1197 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A1197 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1197 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A1197 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1197 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1197 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1197 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A1197 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A1197 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A1197 " 0.041 2.00e-02 2.50e+03 pdb=" HE3 TRP A1197 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP A1197 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP A1197 " 0.011 2.00e-02 2.50e+03 pdb=" HH2 TRP A1197 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1148 " 0.320 9.50e-02 1.11e+02 1.07e-01 1.36e+01 pdb=" NE ARG A1148 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A1148 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A1148 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A1148 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A1148 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A1148 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A1148 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A1148 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1160 " -0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A1161 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A1161 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A1161 " -0.048 5.00e-02 4.00e+02 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.02: 117 2.02 - 2.66: 13556 2.66 - 3.31: 28651 3.31 - 3.95: 35281 3.95 - 4.60: 56027 Nonbonded interactions: 133632 Sorted by model distance: nonbonded pdb=" OD2 ASP A1041 " pdb=" H ILE A1097 " model vdw 1.373 2.450 nonbonded pdb=" H THR A 948 " pdb=" OD2 ASP A 953 " model vdw 1.513 2.450 nonbonded pdb=" OE1 GLU A 707 " pdb="HE22 GLN A 782 " model vdw 1.561 2.450 nonbonded pdb=" HE1 TRP A 855 " pdb=" O ALA A1086 " model vdw 1.586 2.450 nonbonded pdb=" O GLU A 719 " pdb=" HG SER A 723 " model vdw 1.600 2.450 ... (remaining 133627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.720 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 0.053 5045 Z= 0.478 Angle : 0.916 6.285 6861 Z= 0.510 Chirality : 0.052 0.268 749 Planarity : 0.010 0.138 872 Dihedral : 14.779 103.712 2000 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.44 (0.31), residues: 583 helix: -1.08 (0.23), residues: 359 sheet: -0.64 (1.40), residues: 10 loop : -0.40 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP A1197 HIS 0.011 0.003 HIS A1089 PHE 0.021 0.004 PHE A 813 TYR 0.034 0.006 TYR A1068 ARG 0.021 0.004 ARG A1148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.795 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 854 MET cc_start: 0.7952 (tpp) cc_final: 0.7640 (tpt) REVERT: A 914 LYS cc_start: 0.8216 (mttt) cc_final: 0.7991 (mttt) REVERT: A 961 MET cc_start: 0.9058 (mmm) cc_final: 0.8854 (mmm) REVERT: A 968 MET cc_start: 0.7227 (mtm) cc_final: 0.7006 (mtm) REVERT: A 1051 SER cc_start: 0.8965 (p) cc_final: 0.8695 (t) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4002 time to fit residues: 66.6153 Evaluate side-chains 80 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5045 Z= 0.227 Angle : 0.708 8.138 6861 Z= 0.381 Chirality : 0.043 0.210 749 Planarity : 0.008 0.109 872 Dihedral : 8.722 68.145 842 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.20 % Allowed : 2.54 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.35), residues: 583 helix: 0.04 (0.26), residues: 358 sheet: -0.06 (1.50), residues: 10 loop : 0.04 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 761 HIS 0.012 0.002 HIS A1089 PHE 0.014 0.002 PHE A1033 TYR 0.023 0.002 TYR A 970 ARG 0.005 0.001 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.728 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: A 676 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8421 (ttm110) REVERT: A 855 TRP cc_start: 0.8479 (m-90) cc_final: 0.8164 (m-90) REVERT: A 961 MET cc_start: 0.9024 (mmm) cc_final: 0.8797 (mmm) REVERT: A 1051 SER cc_start: 0.8811 (p) cc_final: 0.8452 (t) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.3325 time to fit residues: 44.9131 Evaluate side-chains 80 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 5045 Z= 0.279 Angle : 0.652 6.763 6861 Z= 0.351 Chirality : 0.041 0.196 749 Planarity : 0.006 0.063 872 Dihedral : 6.243 32.436 842 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.35), residues: 583 helix: 0.29 (0.26), residues: 358 sheet: -0.14 (1.41), residues: 10 loop : 0.18 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1150 HIS 0.010 0.002 HIS A 832 PHE 0.020 0.002 PHE A1082 TYR 0.021 0.002 TYR A 970 ARG 0.003 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 946 CYS cc_start: 0.5636 (m) cc_final: 0.5384 (m) REVERT: A 1051 SER cc_start: 0.8780 (p) cc_final: 0.8403 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3404 time to fit residues: 40.4120 Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0470 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5045 Z= 0.204 Angle : 0.602 5.794 6861 Z= 0.321 Chirality : 0.039 0.191 749 Planarity : 0.005 0.057 872 Dihedral : 5.267 26.034 842 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.35), residues: 583 helix: 0.38 (0.26), residues: 361 sheet: -0.06 (1.70), residues: 10 loop : 0.21 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 855 HIS 0.005 0.001 HIS A 963 PHE 0.017 0.002 PHE A1033 TYR 0.033 0.002 TYR A 966 ARG 0.003 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1051 SER cc_start: 0.8880 (p) cc_final: 0.8467 (t) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3116 time to fit residues: 40.2524 Evaluate side-chains 75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 5045 Z= 0.338 Angle : 0.665 16.957 6861 Z= 0.356 Chirality : 0.041 0.204 749 Planarity : 0.005 0.054 872 Dihedral : 5.329 26.731 842 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.49 (0.35), residues: 583 helix: 0.53 (0.27), residues: 361 sheet: -0.11 (1.83), residues: 10 loop : 0.25 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 761 HIS 0.006 0.002 HIS A 729 PHE 0.017 0.002 PHE A 985 TYR 0.021 0.002 TYR A 970 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1051 SER cc_start: 0.8911 (p) cc_final: 0.8471 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3205 time to fit residues: 38.3163 Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 5045 Z= 0.222 Angle : 0.615 15.536 6861 Z= 0.327 Chirality : 0.040 0.257 749 Planarity : 0.006 0.117 872 Dihedral : 5.085 26.789 842 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.96 (0.36), residues: 583 helix: 0.87 (0.27), residues: 359 sheet: -0.35 (1.86), residues: 10 loop : 0.53 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 761 HIS 0.011 0.001 HIS A 832 PHE 0.015 0.002 PHE A 935 TYR 0.018 0.001 TYR A 970 ARG 0.012 0.001 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.746 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 945 GLN cc_start: 0.8022 (tt0) cc_final: 0.7762 (tt0) REVERT: A 1051 SER cc_start: 0.8895 (p) cc_final: 0.8416 (t) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2996 time to fit residues: 38.4877 Evaluate side-chains 78 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 5045 Z= 0.229 Angle : 0.600 13.365 6861 Z= 0.319 Chirality : 0.040 0.238 749 Planarity : 0.005 0.071 872 Dihedral : 4.956 26.794 842 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.15 (0.36), residues: 583 helix: 1.03 (0.27), residues: 359 sheet: -0.29 (1.92), residues: 10 loop : 0.60 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 761 HIS 0.006 0.001 HIS A 832 PHE 0.017 0.002 PHE A1036 TYR 0.015 0.001 TYR A 970 ARG 0.004 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 TRP cc_start: 0.8326 (t60) cc_final: 0.8117 (t60) REVERT: A 1051 SER cc_start: 0.8892 (p) cc_final: 0.8381 (t) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3579 time to fit residues: 42.0955 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5045 Z= 0.206 Angle : 0.574 11.188 6861 Z= 0.303 Chirality : 0.039 0.204 749 Planarity : 0.005 0.067 872 Dihedral : 4.799 27.000 842 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.25 (0.36), residues: 583 helix: 1.19 (0.27), residues: 365 sheet: -0.24 (2.03), residues: 10 loop : 0.43 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 761 HIS 0.007 0.001 HIS A 832 PHE 0.017 0.002 PHE A1022 TYR 0.015 0.001 TYR A 970 ARG 0.003 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 945 GLN cc_start: 0.8010 (tt0) cc_final: 0.7736 (tt0) REVERT: A 1051 SER cc_start: 0.8874 (p) cc_final: 0.8351 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3024 time to fit residues: 36.7084 Evaluate side-chains 74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7509 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5045 Z= 0.213 Angle : 0.571 10.268 6861 Z= 0.302 Chirality : 0.039 0.189 749 Planarity : 0.005 0.065 872 Dihedral : 4.795 26.898 842 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.32 (0.37), residues: 583 helix: 1.27 (0.27), residues: 365 sheet: -0.54 (1.98), residues: 10 loop : 0.43 (0.50), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 761 HIS 0.008 0.001 HIS A1089 PHE 0.012 0.001 PHE A1033 TYR 0.014 0.001 TYR A 970 ARG 0.003 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 TRP cc_start: 0.8412 (t60) cc_final: 0.8172 (t60) REVERT: A 945 GLN cc_start: 0.8025 (tt0) cc_final: 0.7694 (tt0) REVERT: A 1051 SER cc_start: 0.8871 (p) cc_final: 0.8322 (t) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3898 time to fit residues: 43.7758 Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.0870 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.7507 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5045 Z= 0.192 Angle : 0.553 8.937 6861 Z= 0.291 Chirality : 0.038 0.177 749 Planarity : 0.005 0.064 872 Dihedral : 4.675 26.981 842 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.52 (0.37), residues: 583 helix: 1.42 (0.27), residues: 366 sheet: -0.57 (2.03), residues: 10 loop : 0.54 (0.50), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 761 HIS 0.005 0.001 HIS A 832 PHE 0.009 0.001 PHE A1033 TYR 0.024 0.001 TYR A1096 ARG 0.004 0.000 ARG A 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.731 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: A 802 THR cc_start: 0.9087 (m) cc_final: 0.8865 (p) REVERT: A 945 GLN cc_start: 0.8030 (tt0) cc_final: 0.7713 (tt0) REVERT: A 1051 SER cc_start: 0.8877 (p) cc_final: 0.8373 (t) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3204 time to fit residues: 35.9223 Evaluate side-chains 71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117318 restraints weight = 25841.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122104 restraints weight = 12820.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125316 restraints weight = 7656.749| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5045 Z= 0.286 Angle : 0.599 8.303 6861 Z= 0.320 Chirality : 0.040 0.192 749 Planarity : 0.005 0.063 872 Dihedral : 4.894 28.181 842 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.38 (0.36), residues: 583 helix: 1.34 (0.27), residues: 366 sheet: -0.85 (1.87), residues: 10 loop : 0.42 (0.50), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 761 HIS 0.008 0.002 HIS A1089 PHE 0.013 0.002 PHE A 898 TYR 0.011 0.002 TYR A 966 ARG 0.004 0.001 ARG A 942 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.75 seconds wall clock time: 54 minutes 13.32 seconds (3253.32 seconds total)