Starting phenix.real_space_refine on Wed Mar 4 01:35:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q4c_13801/03_2026/7q4c_13801_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q4c_13801/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7q4c_13801/03_2026/7q4c_13801_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q4c_13801/03_2026/7q4c_13801_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q4c_13801/03_2026/7q4c_13801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q4c_13801/03_2026/7q4c_13801.map" } 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-5986/lib/python3.9/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, 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: 1.88, 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: 0.86 Conformation dependent library (CDL) restraints added in 195.8 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: 2.04 Time building geometry restraints manager: 1.19 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: 1.290 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.360 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.180 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.00742 ( 5045) covalent geometry : angle 0.91573 ( 6861) SS BOND : bond 0.00574 ( 3) SS BOND : angle 2.97521 ( 6) hydrogen bonds : bond 0.20566 ( 276) hydrogen bonds : angle 8.87200 ( 789) link_ALPHA1-6 : bond 0.00736 ( 1) link_ALPHA1-6 : angle 1.50431 ( 3) link_BETA1-4 : bond 0.00728 ( 4) link_BETA1-4 : angle 3.58578 ( 12) link_NAG-ASN : bond 0.00729 ( 5) link_NAG-ASN : angle 5.13638 ( 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 : 0.255 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: 0.1918 time to fit residues: 31.6237 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 : 0.252 ------------------------------------------------------------------------------- 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... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121325 restraints weight = 25416.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125560 restraints weight = 13641.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128401 restraints weight = 8485.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130055 restraints weight = 5828.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131481 restraints weight = 4451.783| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5058 Z= 0.192 Angle : 0.749 8.868 6897 Z= 0.398 Chirality : 0.044 0.216 749 Planarity : 0.008 0.117 872 Dihedral : 8.676 66.842 842 Min Nonbonded Distance : 2.296 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: -0.27 (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 0.016 0.002 PHE A1033 TRP 0.020 0.002 TRP A1062 HIS 0.013 0.002 HIS A1089 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 5045) covalent geometry : angle 0.72754 ( 6861) SS BOND : bond 0.01218 ( 3) SS BOND : angle 3.98015 ( 6) hydrogen bonds : bond 0.06085 ( 276) hydrogen bonds : angle 5.87437 ( 789) link_ALPHA1-6 : bond 0.00822 ( 1) link_ALPHA1-6 : angle 1.53354 ( 3) link_BETA1-4 : bond 0.00355 ( 4) link_BETA1-4 : angle 2.33812 ( 12) link_NAG-ASN : bond 0.00519 ( 5) link_NAG-ASN : angle 2.11520 ( 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 : 0.247 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: 0.8499 (m-90) cc_final: 0.8164 (m-90) REVERT: A 961 MET cc_start: 0.9074 (mmm) cc_final: 0.8829 (mmm) REVERT: A 1051 SER cc_start: 0.8879 (p) cc_final: 0.8578 (t) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1523 time to fit residues: 20.8028 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 : 0.264 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121749 restraints weight = 25655.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126025 restraints weight = 13618.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128838 restraints weight = 8301.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130672 restraints weight = 5644.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132054 restraints weight = 4136.264| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5058 Z= 0.158 Angle : 0.647 6.337 6897 Z= 0.342 Chirality : 0.041 0.197 749 Planarity : 0.006 0.069 872 Dihedral : 6.174 32.085 842 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % 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: 0.30 (0.35), residues: 583 helix: 0.35 (0.26), residues: 358 sheet: 0.13 (1.40), residues: 10 loop : 0.23 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 676 TYR 0.021 0.002 TYR A 970 PHE 0.020 0.002 PHE A1033 TRP 0.015 0.001 TRP A1150 HIS 0.006 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5045) covalent geometry : angle 0.63111 ( 6861) SS BOND : bond 0.00399 ( 3) SS BOND : angle 2.71545 ( 6) hydrogen bonds : bond 0.05377 ( 276) hydrogen bonds : angle 5.44734 ( 789) link_ALPHA1-6 : bond 0.00768 ( 1) link_ALPHA1-6 : angle 1.71742 ( 3) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 2.15383 ( 12) link_NAG-ASN : bond 0.00328 ( 5) link_NAG-ASN : angle 1.69568 ( 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 95 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.238 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: 0.8507 (m-90) cc_final: 0.8287 (m-90) REVERT: A 946 CYS cc_start: 0.5673 (m) cc_final: 0.5395 (m) REVERT: A 961 MET cc_start: 0.9021 (mmm) cc_final: 0.8790 (mmm) REVERT: A 1051 SER cc_start: 0.8861 (p) cc_final: 0.8524 (t) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1417 time to fit residues: 17.9729 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 : 0.218 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 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: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113788 restraints weight = 25591.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118594 restraints weight = 12769.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121849 restraints weight = 7533.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123981 restraints weight = 4954.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125427 restraints weight = 3546.926| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5058 Z= 0.186 Angle : 0.635 5.842 6897 Z= 0.339 Chirality : 0.040 0.193 749 Planarity : 0.005 0.057 872 Dihedral : 5.406 26.571 842 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 0.41 (0.35), residues: 583 helix: 0.44 (0.26), residues: 359 sheet: -0.16 (1.63), residues: 10 loop : 0.27 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1065 TYR 0.031 0.002 TYR A 966 PHE 0.022 0.002 PHE A1033 TRP 0.012 0.002 TRP A 758 HIS 0.006 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5045) covalent geometry : angle 0.62367 ( 6861) SS BOND : bond 0.00596 ( 3) SS BOND : angle 1.71600 ( 6) hydrogen bonds : bond 0.04832 ( 276) hydrogen bonds : angle 5.26729 ( 789) link_ALPHA1-6 : bond 0.00493 ( 1) link_ALPHA1-6 : angle 1.79446 ( 3) link_BETA1-4 : bond 0.00291 ( 4) link_BETA1-4 : angle 2.10151 ( 12) link_NAG-ASN : bond 0.00386 ( 5) link_NAG-ASN : angle 1.50862 ( 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 95 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.273 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 854 MET cc_start: 0.8152 (tpt) cc_final: 0.7926 (tpp) REVERT: A 961 MET cc_start: 0.9006 (mmm) cc_final: 0.8767 (mmm) REVERT: A 1051 SER cc_start: 0.9011 (p) cc_final: 0.8690 (t) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1474 time to fit residues: 18.7363 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 : 0.183 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122529 restraints weight = 24852.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127053 restraints weight = 12857.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130006 restraints weight = 7678.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131930 restraints weight = 5114.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133341 restraints weight = 3685.936| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 5058 Z= 0.152 Angle : 0.645 17.322 6897 Z= 0.335 Chirality : 0.040 0.242 749 Planarity : 0.005 0.065 872 Dihedral : 5.133 25.763 842 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 0.85 (0.35), residues: 583 helix: 0.77 (0.27), residues: 359 sheet: -0.07 (1.76), residues: 10 loop : 0.49 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 811 TYR 0.019 0.001 TYR A 970 PHE 0.021 0.002 PHE A1033 TRP 0.017 0.002 TRP A 761 HIS 0.006 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5045) covalent geometry : angle 0.61708 ( 6861) SS BOND : bond 0.00655 ( 3) SS BOND : angle 5.53072 ( 6) hydrogen bonds : bond 0.04478 ( 276) hydrogen bonds : angle 5.00425 ( 789) link_ALPHA1-6 : bond 0.00349 ( 1) link_ALPHA1-6 : angle 1.57946 ( 3) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 1.82276 ( 12) link_NAG-ASN : bond 0.00284 ( 5) link_NAG-ASN : angle 1.31199 ( 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 87 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.252 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 718 MET cc_start: 0.6981 (ptp) cc_final: 0.6715 (ptp) REVERT: A 854 MET cc_start: 0.8275 (tpt) cc_final: 0.7813 (tpp) REVERT: A 914 LYS cc_start: 0.7652 (mttm) cc_final: 0.7414 (mttt) REVERT: A 961 MET cc_start: 0.8959 (mmm) cc_final: 0.8757 (mmm) REVERT: A 1051 SER cc_start: 0.9006 (p) cc_final: 0.8639 (t) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1380 time to fit residues: 15.9895 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 : 0.291 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.137117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120723 restraints weight = 25415.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125268 restraints weight = 12856.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128381 restraints weight = 7641.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130473 restraints weight = 5038.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131897 restraints weight = 3571.764| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 5058 Z= 0.138 Angle : 0.612 15.047 6897 Z= 0.321 Chirality : 0.040 0.261 749 Planarity : 0.005 0.060 872 Dihedral : 4.946 25.955 842 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.65 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: 1.18 (0.36), residues: 583 helix: 1.04 (0.27), residues: 359 sheet: -0.37 (1.73), residues: 10 loop : 0.64 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1044 TYR 0.017 0.001 TYR A 970 PHE 0.018 0.002 PHE A1033 TRP 0.019 0.001 TRP A 761 HIS 0.007 0.001 HIS A1089 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5045) covalent geometry : angle 0.59433 ( 6861) SS BOND : bond 0.01235 ( 3) SS BOND : angle 3.96522 ( 6) hydrogen bonds : bond 0.04189 ( 276) hydrogen bonds : angle 4.88712 ( 789) link_ALPHA1-6 : bond 0.00326 ( 1) link_ALPHA1-6 : angle 1.58736 ( 3) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 1.70310 ( 12) link_NAG-ASN : bond 0.00281 ( 5) link_NAG-ASN : angle 1.22372 ( 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 88 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.206 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 854 MET cc_start: 0.8363 (tpt) cc_final: 0.7929 (tpp) REVERT: A 942 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7522 (mtt-85) REVERT: A 961 MET cc_start: 0.8970 (mmm) cc_final: 0.8749 (mmm) REVERT: A 1051 SER cc_start: 0.9009 (p) cc_final: 0.8623 (t) REVERT: A 1160 GLN cc_start: 0.8179 (tt0) cc_final: 0.7936 (mt0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1468 time to fit residues: 17.1731 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 : 0.304 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117998 restraints weight = 25358.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122399 restraints weight = 12826.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125352 restraints weight = 7678.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127296 restraints weight = 5159.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128682 restraints weight = 3753.399| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5058 Z= 0.173 Angle : 0.614 12.905 6897 Z= 0.324 Chirality : 0.040 0.239 749 Planarity : 0.005 0.058 872 Dihedral : 4.985 26.609 842 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 1.14 (0.36), residues: 583 helix: 1.08 (0.27), residues: 356 sheet: -1.07 (1.61), residues: 10 loop : 0.53 (0.48), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1044 TYR 0.015 0.001 TYR A 970 PHE 0.017 0.002 PHE A1022 TRP 0.015 0.002 TRP A 761 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5045) covalent geometry : angle 0.60044 ( 6861) SS BOND : bond 0.01126 ( 3) SS BOND : angle 3.20893 ( 6) hydrogen bonds : bond 0.04147 ( 276) hydrogen bonds : angle 4.89650 ( 789) link_ALPHA1-6 : bond 0.00298 ( 1) link_ALPHA1-6 : angle 1.59864 ( 3) link_BETA1-4 : bond 0.00272 ( 4) link_BETA1-4 : angle 1.73455 ( 12) link_NAG-ASN : bond 0.00320 ( 5) link_NAG-ASN : angle 1.27583 ( 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 88 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.167 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 854 MET cc_start: 0.8270 (tpt) cc_final: 0.7769 (tpp) REVERT: A 942 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7804 (mtt180) REVERT: A 961 MET cc_start: 0.8987 (mmm) cc_final: 0.8769 (mmm) REVERT: A 1051 SER cc_start: 0.9031 (p) cc_final: 0.8620 (t) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1472 time to fit residues: 17.3420 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 : 0.249 ------------------------------------------------------------------------------- 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: 0.5980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120935 restraints weight = 25176.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125433 restraints weight = 12660.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128460 restraints weight = 7521.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130504 restraints weight = 5023.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131915 restraints weight = 3605.217| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5058 Z= 0.134 Angle : 0.590 11.594 6897 Z= 0.311 Chirality : 0.039 0.210 749 Planarity : 0.005 0.077 872 Dihedral : 4.934 26.584 842 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 1.41 (0.37), residues: 583 helix: 1.30 (0.27), residues: 359 sheet: -0.31 (1.72), residues: 10 loop : 0.58 (0.50), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1098 TYR 0.015 0.001 TYR A 970 PHE 0.019 0.002 PHE A1036 TRP 0.016 0.001 TRP A 761 HIS 0.003 0.001 HIS A1089 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5045) covalent geometry : angle 0.57802 ( 6861) SS BOND : bond 0.00993 ( 3) SS BOND : angle 2.81841 ( 6) hydrogen bonds : bond 0.03943 ( 276) hydrogen bonds : angle 4.73627 ( 789) link_ALPHA1-6 : bond 0.00266 ( 1) link_ALPHA1-6 : angle 1.61497 ( 3) link_BETA1-4 : bond 0.00279 ( 4) link_BETA1-4 : angle 1.62436 ( 12) link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 1.15262 ( 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 92 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.259 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: 0.8304 (tp) cc_final: 0.7796 (tt) REVERT: A 854 MET cc_start: 0.8249 (tpt) cc_final: 0.7694 (tpp) REVERT: A 945 GLN cc_start: 0.8078 (tt0) cc_final: 0.7833 (tt0) REVERT: A 961 MET cc_start: 0.8968 (mmm) cc_final: 0.8727 (mmm) REVERT: A 1051 SER cc_start: 0.8987 (p) cc_final: 0.8574 (t) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1707 time to fit residues: 20.3498 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 : 0.251 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118858 restraints weight = 25147.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123720 restraints weight = 12302.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126921 restraints weight = 7189.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129036 restraints weight = 4742.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130442 restraints weight = 3411.673| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5058 Z= 0.133 Angle : 0.572 10.300 6897 Z= 0.300 Chirality : 0.039 0.190 749 Planarity : 0.005 0.074 872 Dihedral : 4.834 27.138 842 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 1.50 (0.36), residues: 583 helix: 1.33 (0.27), residues: 357 sheet: -0.14 (1.78), residues: 10 loop : 0.69 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 676 TYR 0.013 0.001 TYR A 970 PHE 0.014 0.002 PHE A1033 TRP 0.013 0.001 TRP A 761 HIS 0.003 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5045) covalent geometry : angle 0.56104 ( 6861) SS BOND : bond 0.00899 ( 3) SS BOND : angle 2.53363 ( 6) hydrogen bonds : bond 0.03813 ( 276) hydrogen bonds : angle 4.67984 ( 789) link_ALPHA1-6 : bond 0.00285 ( 1) link_ALPHA1-6 : angle 1.60352 ( 3) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 1.60361 ( 12) link_NAG-ASN : bond 0.00265 ( 5) link_NAG-ASN : angle 1.13205 ( 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 89 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.256 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 802 THR cc_start: 0.9146 (m) cc_final: 0.8924 (p) REVERT: A 945 GLN cc_start: 0.8047 (tt0) cc_final: 0.7707 (tt0) REVERT: A 1051 SER cc_start: 0.8974 (p) cc_final: 0.8561 (t) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1724 time to fit residues: 19.7295 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 : 0.249 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121472 restraints weight = 24978.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126156 restraints weight = 12294.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129355 restraints weight = 7263.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131441 restraints weight = 4818.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132630 restraints weight = 3467.072| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5058 Z= 0.120 Angle : 0.561 9.162 6897 Z= 0.292 Chirality : 0.038 0.177 749 Planarity : 0.005 0.071 872 Dihedral : 4.694 26.845 842 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 1.72 (0.37), residues: 583 helix: 1.54 (0.27), residues: 359 sheet: -0.36 (1.85), residues: 10 loop : 0.74 (0.50), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 833 TYR 0.014 0.001 TYR A 800 PHE 0.013 0.001 PHE A 985 TRP 0.013 0.001 TRP A 761 HIS 0.003 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5045) covalent geometry : angle 0.55111 ( 6861) SS BOND : bond 0.00810 ( 3) SS BOND : angle 2.20939 ( 6) hydrogen bonds : bond 0.03594 ( 276) hydrogen bonds : angle 4.58607 ( 789) link_ALPHA1-6 : bond 0.00259 ( 1) link_ALPHA1-6 : angle 1.60509 ( 3) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 1.54020 ( 12) link_NAG-ASN : bond 0.00241 ( 5) link_NAG-ASN : angle 1.08578 ( 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 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.259 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 802 THR cc_start: 0.9130 (m) cc_final: 0.8906 (p) REVERT: A 945 GLN cc_start: 0.8048 (tt0) cc_final: 0.7770 (tt0) REVERT: A 1051 SER cc_start: 0.8966 (p) cc_final: 0.8538 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1736 time to fit residues: 20.0786 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 : 0.259 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120558 restraints weight = 25232.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125652 restraints weight = 11999.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129022 restraints weight = 6886.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131209 restraints weight = 4490.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132713 restraints weight = 3192.614| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5131 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= 0.137 Angle : 0.581 8.554 6897 Z= 0.300 Chirality : 0.038 0.175 749 Planarity : 0.005 0.070 872 Dihedral : 4.705 27.015 842 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.07 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: 1.74 (0.36), residues: 583 helix: 1.59 (0.27), residues: 356 sheet: -0.64 (1.81), residues: 10 loop : 0.69 (0.49), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 833 TYR 0.012 0.001 TYR A 970 PHE 0.010 0.001 PHE A1033 TRP 0.021 0.002 TRP A 855 HIS 0.003 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5045) covalent geometry : angle 0.57132 ( 6861) SS BOND : bond 0.00746 ( 3) SS BOND : angle 2.12132 ( 6) hydrogen bonds : bond 0.03607 ( 276) hydrogen bonds : angle 4.64102 ( 789) link_ALPHA1-6 : bond 0.00278 ( 1) link_ALPHA1-6 : angle 1.60000 ( 3) link_BETA1-4 : bond 0.00294 ( 4) link_BETA1-4 : angle 1.58554 ( 12) link_NAG-ASN : bond 0.00259 ( 5) link_NAG-ASN : angle 1.15291 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.38 seconds wall clock time: 32 minutes 26.30 seconds (1946.30 seconds total)