Starting phenix.real_space_refine on Thu Jul 2 19:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q4c_13801/07_2026/7q4c_13801_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q4c_13801/07_2026/7q4c_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_13801/07_2026/7q4c_13801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q4c_13801/07_2026/7q4c_13801.map" model { file = "/net/cci-nas-00/data/ceres_data/7q4c_13801/07_2026/7q4c_13801_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q4c_13801/07_2026/7q4c_13801_trim.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 28 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.87, per 1000 atoms: 0.20 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: 0.96 Conformation dependent library (CDL) restraints added in 317.5 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: 0.21 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: 2.13 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 5058 Z= 0.349 Angle : 0.961 10.815 6897 Z= 0.519 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (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 ARG 0.021 0.004 ARG A1148 TYR 0.034 0.006 TYR A1068 PHE 0.021 0.004 PHE A 813 TRP 0.031 0.005 TRP A1197 HIS 0.011 0.003 HIS A1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.35 ( 5045) covalent geometry : angle 0.91573 / 0.51 ( 6861) SS BOND : bond 0.00574 / 0.29 ( 3) SS BOND : angle 2.97521 / 1.57 ( 6) hydrogen bonds : bond 0.20566 / 13.87 ( 276) hydrogen bonds : angle 8.87200 / 7.02 ( 789) link_ALPHA1-6 : bond 0.00736 / 0.39 ( 1) link_ALPHA1-6 : angle 1.50431 / 0.85 ( 3) link_BETA1-4 : bond 0.00728 / 0.38 ( 4) link_BETA1-4 : angle 3.58578 / 1.84 ( 12) link_NAG-ASN : bond 0.00729 / 0.39 ( 5) link_NAG-ASN : angle 5.13638 / 2.70 ( 15) *********************** 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 : 0.245 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 846 ILE cc_start: 0.8985 (mt) cc_final: 0.8785 (mt) REVERT: A 854 MET cc_start: 0.7952 (tpp) cc_final: 0.7638 (tpt) REVERT: A 914 LYS cc_start: 0.8216 (mttt) cc_final: 0.7985 (mttt) REVERT: A 961 MET cc_start: 0.9058 (mmm) cc_final: 0.8846 (mmm) REVERT: A 968 MET cc_start: 0.7227 (mtm) cc_final: 0.7000 (mtm) REVERT: A 1051 SER cc_start: 0.8965 (p) cc_final: 0.8693 (t) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1729 time to fit residues: 29.2237 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 : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 857 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121469 restraints weight = 25410.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125618 restraints weight = 13503.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128456 restraints weight = 8423.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.130341 restraints weight = 5789.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131594 restraints weight = 4271.033| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5058 Z= 0.191 Angle : 0.750 9.022 6897 Z= 0.399 Chirality : 0.044 0.216 749 Planarity : 0.008 0.117 872 Dihedral : 8.695 67.117 842 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.20 % Allowed : 2.74 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.34), residues: 583 helix: -0.06 (0.25), residues: 358 sheet: -0.51 (1.33), residues: 10 loop : -0.09 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 890 TYR 0.024 0.002 TYR A 970 PHE 0.015 0.002 PHE A1033 TRP 0.020 0.002 TRP A1062 HIS 0.012 0.002 HIS A1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 5045) covalent geometry : angle 0.72861 / 0.39 ( 6861) SS BOND : bond 0.01121 / 0.53 ( 3) SS BOND : angle 4.04208 / 2.04 ( 6) hydrogen bonds : bond 0.06092 / 4.15 ( 276) hydrogen bonds : angle 5.88287 / 4.62 ( 789) link_ALPHA1-6 : bond 0.00647 / 0.34 ( 1) link_ALPHA1-6 : angle 1.41098 / 0.80 ( 3) link_BETA1-4 : bond 0.00365 / 0.18 ( 4) link_BETA1-4 : angle 2.33598 / 1.18 ( 12) link_NAG-ASN : bond 0.00524 / 0.28 ( 5) link_NAG-ASN : angle 2.12226 / 1.14 ( 15) *********************** 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 106 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 TRP cc_start: 0.8488 (m-90) cc_final: 0.8153 (m-90) REVERT: A 961 MET cc_start: 0.9077 (mmm) cc_final: 0.8830 (mmm) REVERT: A 1051 SER cc_start: 0.8883 (p) cc_final: 0.8593 (t) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1417 time to fit residues: 19.9013 Evaluate side-chains 81 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 832 HIS ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122029 restraints weight = 25675.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126255 restraints weight = 13464.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129058 restraints weight = 8198.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130914 restraints weight = 5543.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132023 restraints weight = 4037.181| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 5058 Z= 0.167 Angle : 0.657 6.987 6897 Z= 0.347 Chirality : 0.041 0.196 749 Planarity : 0.006 0.070 872 Dihedral : 6.490 37.216 842 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.20 % Allowed : 3.13 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.35), residues: 583 helix: 0.30 (0.26), residues: 358 sheet: -0.03 (1.37), residues: 10 loop : 0.17 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 829 TYR 0.021 0.002 TYR A 970 PHE 0.018 0.002 PHE A1033 TRP 0.015 0.001 TRP A1150 HIS 0.006 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 5045) covalent geometry : angle 0.64072 / 0.34 ( 6861) SS BOND : bond 0.00396 / 0.20 ( 3) SS BOND : angle 2.87748 / 1.49 ( 6) hydrogen bonds : bond 0.05469 / 3.73 ( 276) hydrogen bonds : angle 5.51136 / 4.33 ( 789) link_ALPHA1-6 : bond 0.00737 / 0.39 ( 1) link_ALPHA1-6 : angle 1.54937 / 0.83 ( 3) link_BETA1-4 : bond 0.00305 / 0.15 ( 4) link_BETA1-4 : angle 2.20244 / 1.12 ( 12) link_NAG-ASN : bond 0.00333 / 0.17 ( 5) link_NAG-ASN : angle 1.76798 / 0.97 ( 15) *********************** 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 94 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.200 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 855 TRP cc_start: 0.8493 (m-90) cc_final: 0.8284 (m-90) REVERT: A 961 MET cc_start: 0.9014 (mmm) cc_final: 0.8793 (mmm) REVERT: A 1051 SER cc_start: 0.8852 (p) cc_final: 0.8505 (t) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1117 time to fit residues: 14.4162 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 : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121991 restraints weight = 25978.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126462 restraints weight = 13322.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129382 restraints weight = 7988.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131270 restraints weight = 5362.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132603 restraints weight = 3895.797| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5058 Z= 0.177 Angle : 0.627 5.854 6897 Z= 0.334 Chirality : 0.040 0.191 749 Planarity : 0.005 0.058 872 Dihedral : 5.426 26.438 842 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.35), residues: 583 helix: 0.44 (0.26), residues: 359 sheet: -0.27 (1.62), residues: 10 loop : 0.29 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1065 TYR 0.036 0.002 TYR A 966 PHE 0.020 0.002 PHE A1033 TRP 0.012 0.002 TRP A1150 HIS 0.006 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 5045) covalent geometry : angle 0.61470 / 0.33 ( 6861) SS BOND : bond 0.00346 / 0.17 ( 3) SS BOND : angle 1.53948 / 0.80 ( 6) hydrogen bonds : bond 0.04876 / 3.30 ( 276) hydrogen bonds : angle 5.27338 / 4.13 ( 789) link_ALPHA1-6 : bond 0.00423 / 0.22 ( 1) link_ALPHA1-6 : angle 1.93160 / 1.01 ( 3) link_BETA1-4 : bond 0.00359 / 0.18 ( 4) link_BETA1-4 : angle 2.16038 / 1.08 ( 12) link_NAG-ASN : bond 0.00367 / 0.19 ( 5) link_NAG-ASN : angle 1.49627 / 0.84 ( 15) *********************** 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 98 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 961 MET cc_start: 0.9003 (mmm) cc_final: 0.8759 (mmm) REVERT: A 1051 SER cc_start: 0.8941 (p) cc_final: 0.8635 (t) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1267 time to fit residues: 16.9860 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 : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 857 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120699 restraints weight = 25368.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125067 restraints weight = 13096.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127984 restraints weight = 7914.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129920 restraints weight = 5300.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131324 restraints weight = 3823.513| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5058 Z= 0.147 Angle : 0.577 5.948 6897 Z= 0.305 Chirality : 0.039 0.187 749 Planarity : 0.005 0.064 872 Dihedral : 5.139 25.902 842 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.13 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.36), residues: 583 helix: 0.76 (0.27), residues: 359 sheet: -0.18 (1.74), residues: 10 loop : 0.52 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 811 TYR 0.019 0.002 TYR A 970 PHE 0.020 0.002 PHE A1033 TRP 0.013 0.001 TRP A 758 HIS 0.005 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 5045) covalent geometry : angle 0.56838 / 0.30 ( 6861) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 0.95889 / 0.44 ( 6) hydrogen bonds : bond 0.04393 / 2.96 ( 276) hydrogen bonds : angle 4.97670 / 3.89 ( 789) link_ALPHA1-6 : bond 0.00393 / 0.21 ( 1) link_ALPHA1-6 : angle 1.58203 / 0.86 ( 3) link_BETA1-4 : bond 0.00284 / 0.14 ( 4) link_BETA1-4 : angle 1.79819 / 0.91 ( 12) link_NAG-ASN : bond 0.00312 / 0.16 ( 5) link_NAG-ASN : angle 1.32884 / 0.77 ( 15) *********************** 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 : 0.177 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 1051 SER cc_start: 0.8992 (p) cc_final: 0.8611 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1020 time to fit residues: 12.5299 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 : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1089 HIS ** 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 = 0.136434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119795 restraints weight = 25471.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124284 restraints weight = 13155.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127287 restraints weight = 7969.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129330 restraints weight = 5385.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130719 restraints weight = 3892.974| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 5058 Z= 0.166 Angle : 0.640 17.101 6897 Z= 0.335 Chirality : 0.040 0.277 749 Planarity : 0.006 0.084 872 Dihedral : 5.062 26.270 842 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.36), residues: 583 helix: 0.92 (0.27), residues: 359 sheet: -0.83 (1.67), residues: 10 loop : 0.62 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 942 TYR 0.016 0.001 TYR A 970 PHE 0.015 0.002 PHE A1033 TRP 0.018 0.002 TRP A 761 HIS 0.006 0.001 HIS A 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 5045) covalent geometry : angle 0.61689 / 0.33 ( 6861) SS BOND : bond 0.01131 / 0.59 ( 3) SS BOND : angle 4.99068 / 2.74 ( 6) hydrogen bonds : bond 0.04233 / 2.83 ( 276) hydrogen bonds : angle 4.92767 / 3.87 ( 789) link_ALPHA1-6 : bond 0.00301 / 0.16 ( 1) link_ALPHA1-6 : angle 1.58562 / 0.87 ( 3) link_BETA1-4 : bond 0.00303 / 0.15 ( 4) link_BETA1-4 : angle 1.72752 / 0.86 ( 12) link_NAG-ASN : bond 0.00375 / 0.19 ( 5) link_NAG-ASN : angle 1.29476 / 0.75 ( 15) *********************** 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 89 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.207 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 737 LEU cc_start: 0.8327 (tt) cc_final: 0.8072 (tp) REVERT: A 854 MET cc_start: 0.8672 (tpp) cc_final: 0.8215 (tpp) REVERT: A 945 GLN cc_start: 0.8178 (tt0) cc_final: 0.7891 (tt0) REVERT: A 1051 SER cc_start: 0.9006 (p) cc_final: 0.8636 (t) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1023 time to fit residues: 12.4935 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 : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 857 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116990 restraints weight = 25665.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121502 restraints weight = 12875.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124573 restraints weight = 7715.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126692 restraints weight = 5177.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127887 restraints weight = 3737.074| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 5058 Z= 0.209 Angle : 0.657 13.903 6897 Z= 0.349 Chirality : 0.042 0.265 749 Planarity : 0.005 0.072 872 Dihedral : 5.228 26.489 842 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.36), residues: 583 helix: 0.96 (0.27), residues: 356 sheet: -1.05 (1.68), residues: 10 loop : 0.48 (0.48), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 942 TYR 0.014 0.002 TYR A1096 PHE 0.016 0.002 PHE A1033 TRP 0.014 0.002 TRP A1150 HIS 0.005 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 5045) covalent geometry : angle 0.63907 / 0.34 ( 6861) SS BOND : bond 0.01243 / 0.65 ( 3) SS BOND : angle 3.99920 / 2.19 ( 6) hydrogen bonds : bond 0.04256 / 2.81 ( 276) hydrogen bonds : angle 4.97945 / 3.88 ( 789) link_ALPHA1-6 : bond 0.00401 / 0.21 ( 1) link_ALPHA1-6 : angle 1.68150 / 0.94 ( 3) link_BETA1-4 : bond 0.00325 / 0.16 ( 4) link_BETA1-4 : angle 1.81033 / 0.90 ( 12) link_NAG-ASN : bond 0.00387 / 0.20 ( 5) link_NAG-ASN : angle 1.36718 / 0.81 ( 15) *********************** 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 90 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.182 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 737 LEU cc_start: 0.8356 (tt) cc_final: 0.8024 (tp) REVERT: A 854 MET cc_start: 0.8545 (tpp) cc_final: 0.8227 (tpp) REVERT: A 945 GLN cc_start: 0.8112 (tt0) cc_final: 0.7784 (tt0) REVERT: A 1051 SER cc_start: 0.9030 (p) cc_final: 0.8574 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1118 time to fit residues: 13.6379 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1089 HIS ** 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 = 0.3676 r_free = 0.3676 target = 0.135521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117356 restraints weight = 25417.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122289 restraints weight = 12669.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125570 restraints weight = 7546.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127793 restraints weight = 5049.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129332 restraints weight = 3634.848| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.003 0.078 5058 Z= 0.142 Angle : 0.610 13.072 6897 Z= 0.321 Chirality : 0.040 0.237 749 Planarity : 0.005 0.074 872 Dihedral : 5.114 26.609 842 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.36), residues: 583 helix: 1.15 (0.27), residues: 359 sheet: -1.12 (1.71), residues: 10 loop : 0.44 (0.50), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 942 TYR 0.014 0.001 TYR A 970 PHE 0.013 0.001 PHE A1036 TRP 0.014 0.002 TRP A 761 HIS 0.011 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 5045) covalent geometry : angle 0.59593 / 0.32 ( 6861) SS BOND : bond 0.01106 / 0.58 ( 3) SS BOND : angle 3.29281 / 1.81 ( 6) hydrogen bonds : bond 0.04008 / 2.65 ( 276) hydrogen bonds : angle 4.76174 / 3.72 ( 789) link_ALPHA1-6 : bond 0.00266 / 0.14 ( 1) link_ALPHA1-6 : angle 1.66064 / 0.92 ( 3) link_BETA1-4 : bond 0.00291 / 0.14 ( 4) link_BETA1-4 : angle 1.64619 / 0.81 ( 12) link_NAG-ASN : bond 0.00306 / 0.16 ( 5) link_NAG-ASN : angle 1.20804 / 0.72 ( 15) *********************** 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 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.164 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: 0.8593 (t60) cc_final: 0.8328 (t60) REVERT: A 737 LEU cc_start: 0.8379 (tt) cc_final: 0.8107 (tp) REVERT: A 945 GLN cc_start: 0.8183 (tt0) cc_final: 0.7823 (tt0) REVERT: A 1022 PHE cc_start: 0.9069 (t80) cc_final: 0.8772 (t80) REVERT: A 1051 SER cc_start: 0.9027 (p) cc_final: 0.8608 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1203 time to fit residues: 14.9013 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 : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117430 restraints weight = 25494.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122306 restraints weight = 12698.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125572 restraints weight = 7521.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127785 restraints weight = 5032.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129271 restraints weight = 3648.162| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5058 Z= 0.157 Angle : 0.601 11.457 6897 Z= 0.316 Chirality : 0.040 0.214 749 Planarity : 0.005 0.075 872 Dihedral : 5.053 27.470 842 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.36), residues: 583 helix: 1.23 (0.27), residues: 359 sheet: -1.27 (1.66), residues: 10 loop : 0.37 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 942 TYR 0.014 0.001 TYR A 970 PHE 0.015 0.001 PHE A1033 TRP 0.013 0.002 TRP A1062 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 5045) covalent geometry : angle 0.58857 / 0.31 ( 6861) SS BOND : bond 0.00970 / 0.51 ( 3) SS BOND : angle 2.90897 / 1.60 ( 6) hydrogen bonds : bond 0.03916 / 2.58 ( 276) hydrogen bonds : angle 4.73817 / 3.69 ( 789) link_ALPHA1-6 : bond 0.00266 / 0.14 ( 1) link_ALPHA1-6 : angle 1.61837 / 0.90 ( 3) link_BETA1-4 : bond 0.00306 / 0.15 ( 4) link_BETA1-4 : angle 1.67672 / 0.84 ( 12) link_NAG-ASN : bond 0.00328 / 0.17 ( 5) link_NAG-ASN : angle 1.23265 / 0.74 ( 15) *********************** 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 87 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.244 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: 0.8670 (t60) cc_final: 0.8383 (t60) REVERT: A 737 LEU cc_start: 0.8390 (tt) cc_final: 0.8022 (tp) REVERT: A 945 GLN cc_start: 0.8356 (tt0) cc_final: 0.7997 (tt0) REVERT: A 1022 PHE cc_start: 0.9093 (t80) cc_final: 0.8806 (t80) REVERT: A 1051 SER cc_start: 0.9048 (p) cc_final: 0.8641 (t) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1161 time to fit residues: 13.6812 Evaluate side-chains 77 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 857 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119165 restraints weight = 25836.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124079 restraints weight = 12803.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127448 restraints weight = 7557.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129590 restraints weight = 4972.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131103 restraints weight = 3585.962| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5058 Z= 0.128 Angle : 0.579 10.438 6897 Z= 0.304 Chirality : 0.039 0.193 749 Planarity : 0.005 0.076 872 Dihedral : 4.959 27.193 842 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.37), residues: 583 helix: 1.32 (0.27), residues: 361 sheet: -1.08 (1.86), residues: 10 loop : 0.62 (0.51), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 942 TYR 0.013 0.001 TYR A 970 PHE 0.013 0.001 PHE A1033 TRP 0.015 0.001 TRP A 761 HIS 0.006 0.001 HIS A1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5045) covalent geometry : angle 0.56811 / 0.30 ( 6861) SS BOND : bond 0.00898 / 0.47 ( 3) SS BOND : angle 2.65261 / 1.46 ( 6) hydrogen bonds : bond 0.03735 / 2.47 ( 276) hydrogen bonds : angle 4.63999 / 3.62 ( 789) link_ALPHA1-6 : bond 0.00233 / 0.12 ( 1) link_ALPHA1-6 : angle 1.62489 / 0.90 ( 3) link_BETA1-4 : bond 0.00280 / 0.14 ( 4) link_BETA1-4 : angle 1.58888 / 0.79 ( 12) link_NAG-ASN : bond 0.00270 / 0.14 ( 5) link_NAG-ASN : angle 1.13777 / 0.68 ( 15) ********************** 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 87 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.172 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 643 TRP cc_start: 0.8572 (t60) cc_final: 0.8313 (t60) REVERT: A 737 LEU cc_start: 0.8385 (tt) cc_final: 0.8052 (tp) REVERT: A 802 THR cc_start: 0.9028 (m) cc_final: 0.8813 (p) REVERT: A 945 GLN cc_start: 0.8350 (tt0) cc_final: 0.7964 (tt0) REVERT: A 1051 SER cc_start: 0.9016 (p) cc_final: 0.8613 (t) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1186 time to fit residues: 13.7573 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1089 HIS ** 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 = 0.3709 r_free = 0.3709 target = 0.137659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119967 restraints weight = 25395.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124924 restraints weight = 12507.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128191 restraints weight = 7357.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130383 restraints weight = 4849.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131825 restraints weight = 3469.786| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5058 Z= 0.135 Angle : 0.580 9.669 6897 Z= 0.304 Chirality : 0.039 0.181 749 Planarity : 0.005 0.075 872 Dihedral : 4.874 27.297 842 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.37), residues: 583 helix: 1.36 (0.27), residues: 366 sheet: -0.58 (1.87), residues: 10 loop : 0.48 (0.51), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 942 TYR 0.013 0.001 TYR A 970 PHE 0.016 0.001 PHE A1036 TRP 0.013 0.002 TRP A 761 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 5045) covalent geometry : angle 0.56981 / 0.30 ( 6861) SS BOND : bond 0.00817 / 0.43 ( 3) SS BOND : angle 2.43442 / 1.34 ( 6) hydrogen bonds : bond 0.03684 / 2.44 ( 276) hydrogen bonds : angle 4.60340 / 3.59 ( 789) link_ALPHA1-6 : bond 0.00264 / 0.14 ( 1) link_ALPHA1-6 : angle 1.60842 / 0.89 ( 3) link_BETA1-4 : bond 0.00294 / 0.14 ( 4) link_BETA1-4 : angle 1.60760 / 0.81 ( 12) link_NAG-ASN : bond 0.00284 / 0.15 ( 5) link_NAG-ASN : angle 1.16276 / 0.70 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.89 seconds wall clock time: 28 minutes 46.45 seconds (1726.45 seconds total)