Starting phenix.real_space_refine on Fri Jul 25 08:18:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w28_43741/07_2025/8w28_43741_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w28_43741/07_2025/8w28_43741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w28_43741/07_2025/8w28_43741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w28_43741/07_2025/8w28_43741.map" model { file = "/net/cci-nas-00/data/ceres_data/8w28_43741/07_2025/8w28_43741_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w28_43741/07_2025/8w28_43741_neut.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3298 atoms to isotropic. 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 Zn 2 6.06 5 S 28 5.16 5 C 2868 2.51 5 N 820 2.21 5 O 840 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4564 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "Q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1632 SG CYS D1081 28.969 12.512 63.980 1.00 32.93 S ATOM 1692 SG CYS D1089 28.038 15.705 65.939 1.00 35.34 S ATOM 1718 SG CYS D1092 31.730 14.856 65.255 1.00 38.99 S ATOM 3872 SG CYS Q1081 19.852 58.236 11.676 1.00 45.26 S ATOM 3932 SG CYS Q1089 20.037 55.018 9.553 1.00 27.36 S ATOM 3958 SG CYS Q1092 23.131 57.250 9.954 1.00 38.10 S Time building chain proxies: 7.65, per 1000 atoms: 1.68 Number of scatterers: 4564 At special positions: 0 Unit cell: (97.468, 87.556, 76.818, 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) Zn 2 29.99 S 28 16.00 F 6 9.00 O 840 8.00 N 820 7.00 C 2868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 511.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1202 " pdb="ZN ZN D1202 " - pdb=" ND1 HIS D1084 " pdb="ZN ZN D1202 " - pdb=" SG CYS D1092 " pdb="ZN ZN D1202 " - pdb=" SG CYS D1081 " pdb="ZN ZN D1202 " - pdb=" SG CYS D1089 " pdb=" ZN Q1202 " pdb="ZN ZN Q1202 " - pdb=" ND1 HIS Q1084 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1092 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1081 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1089 " Number of angles added : 6 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 44.0% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'D' and resid 875 through 885 removed outlier: 3.508A pdb=" N LEU D 885 " --> pdb=" O PHE D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 889 removed outlier: 5.607A pdb=" N HIS D 889 " --> pdb=" O GLY D 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 889' Processing helix chain 'D' and resid 890 through 897 Processing helix chain 'D' and resid 900 through 905 Processing helix chain 'D' and resid 908 through 915 Processing helix chain 'D' and resid 919 through 935 Processing helix chain 'D' and resid 937 through 940 Processing helix chain 'D' and resid 941 through 947 removed outlier: 3.703A pdb=" N THR D 945 " --> pdb=" O ASN D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 975 removed outlier: 3.526A pdb=" N THR D 975 " --> pdb=" O GLU D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1019 Processing helix chain 'D' and resid 1035 through 1043 Processing helix chain 'D' and resid 1045 through 1049 Processing helix chain 'D' and resid 1064 through 1070 removed outlier: 3.514A pdb=" N SER D1068 " --> pdb=" O ASN D1064 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN D1070 " --> pdb=" O SER D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1078 Processing helix chain 'D' and resid 1143 through 1145 No H-bonds generated for 'chain 'D' and resid 1143 through 1145' Processing helix chain 'Q' and resid 876 through 885 removed outlier: 3.501A pdb=" N LEU Q 885 " --> pdb=" O PHE Q 881 " (cutoff:3.500A) Processing helix chain 'Q' and resid 887 through 889 No H-bonds generated for 'chain 'Q' and resid 887 through 889' Processing helix chain 'Q' and resid 890 through 897 Processing helix chain 'Q' and resid 900 through 905 Processing helix chain 'Q' and resid 908 through 915 Processing helix chain 'Q' and resid 919 through 935 Processing helix chain 'Q' and resid 937 through 940 Processing helix chain 'Q' and resid 941 through 947 removed outlier: 3.562A pdb=" N THR Q 945 " --> pdb=" O ASN Q 941 " (cutoff:3.500A) Processing helix chain 'Q' and resid 962 through 975 Processing helix chain 'Q' and resid 1002 through 1019 Processing helix chain 'Q' and resid 1035 through 1043 Processing helix chain 'Q' and resid 1045 through 1049 Processing helix chain 'Q' and resid 1064 through 1070 removed outlier: 3.522A pdb=" N SER Q1068 " --> pdb=" O ASN Q1064 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1074 through 1078 Processing helix chain 'Q' and resid 1143 through 1145 No H-bonds generated for 'chain 'Q' and resid 1143 through 1145' Processing sheet with id=AA1, first strand: chain 'D' and resid 954 through 957 removed outlier: 5.172A pdb=" N ILE D 994 " --> pdb=" O GLN D1156 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN D1156 " --> pdb=" O ILE D 994 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU D1150 " --> pdb=" O VAL D1000 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA D1147 " --> pdb=" O THR D1102 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR D1102 " --> pdb=" O ALA D1147 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG D1100 " --> pdb=" O PRO D1149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 1059 through 1061 Processing sheet with id=AA3, first strand: chain 'Q' and resid 954 through 957 removed outlier: 4.690A pdb=" N ARG Q 991 " --> pdb=" O MET Q1158 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR Q1154 " --> pdb=" O LEU Q 995 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE Q 997 " --> pdb=" O LEU Q1152 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU Q1152 " --> pdb=" O ILE Q 997 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS Q 999 " --> pdb=" O GLU Q1150 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU Q1150 " --> pdb=" O LYS Q 999 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N CYS Q1001 " --> pdb=" O TYR Q1148 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N TYR Q1148 " --> pdb=" O CYS Q1001 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA Q1147 " --> pdb=" O THR Q1102 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR Q1102 " --> pdb=" O ALA Q1147 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG Q1100 " --> pdb=" O PRO Q1149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 1059 through 1061 removed outlier: 6.000A pdb=" N PHE Q1107 " --> pdb=" O THR Q1126 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1516 1.34 - 1.46: 1102 1.46 - 1.58: 1968 1.58 - 1.70: 0 1.70 - 1.81: 46 Bond restraints: 4632 Sorted by residual: bond pdb=" CB GLU Q 888 " pdb=" CG GLU Q 888 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CB GLU D 888 " pdb=" CG GLU D 888 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.56e-01 bond pdb=" CB GLU Q 931 " pdb=" CG GLU Q 931 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.76e-01 bond pdb=" CA GLU D 888 " pdb=" CB GLU D 888 " ideal model delta sigma weight residual 1.529 1.539 -0.010 1.64e-02 3.72e+03 3.93e-01 bond pdb=" CB MET Q 891 " pdb=" CG MET Q 891 " ideal model delta sigma weight residual 1.520 1.538 -0.018 3.00e-02 1.11e+03 3.77e-01 ... (remaining 4627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 5999 1.04 - 2.08: 195 2.08 - 3.12: 28 3.12 - 4.15: 17 4.15 - 5.19: 3 Bond angle restraints: 6242 Sorted by residual: angle pdb=" CA GLU Q 888 " pdb=" CB GLU Q 888 " pdb=" CG GLU Q 888 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.74e+00 angle pdb=" CA GLU Q 931 " pdb=" CB GLU Q 931 " pdb=" CG GLU Q 931 " ideal model delta sigma weight residual 114.10 118.42 -4.32 2.00e+00 2.50e-01 4.67e+00 angle pdb=" CA GLU D 931 " pdb=" CB GLU D 931 " pdb=" CG GLU D 931 " ideal model delta sigma weight residual 114.10 118.07 -3.97 2.00e+00 2.50e-01 3.94e+00 angle pdb=" CA GLU D 888 " pdb=" CB GLU D 888 " pdb=" CG GLU D 888 " ideal model delta sigma weight residual 114.10 118.05 -3.95 2.00e+00 2.50e-01 3.90e+00 angle pdb=" N VAL D 905 " pdb=" CA VAL D 905 " pdb=" C VAL D 905 " ideal model delta sigma weight residual 109.34 112.91 -3.57 2.08e+00 2.31e-01 2.95e+00 ... (remaining 6237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2416 17.97 - 35.93: 210 35.93 - 53.90: 57 53.90 - 71.87: 24 71.87 - 89.83: 5 Dihedral angle restraints: 2712 sinusoidal: 1098 harmonic: 1614 Sorted by residual: dihedral pdb=" CA PHE Q1098 " pdb=" C PHE Q1098 " pdb=" N CYS Q1099 " pdb=" CA CYS Q1099 " ideal model delta harmonic sigma weight residual 180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU D1018 " pdb=" C GLU D1018 " pdb=" N GLU D1019 " pdb=" CA GLU D1019 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA PHE D1098 " pdb=" C PHE D1098 " pdb=" N CYS D1099 " pdb=" CA CYS D1099 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 361 0.026 - 0.052: 183 0.052 - 0.077: 58 0.077 - 0.103: 25 0.103 - 0.129: 19 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA ILE D1059 " pdb=" N ILE D1059 " pdb=" C ILE D1059 " pdb=" CB ILE D1059 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE D 988 " pdb=" N ILE D 988 " pdb=" C ILE D 988 " pdb=" CB ILE D 988 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE D 997 " pdb=" N ILE D 997 " pdb=" C ILE D 997 " pdb=" CB ILE D 997 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 643 not shown) Planarity restraints: 808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 941 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.18e+00 pdb=" N PRO D 942 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 942 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 942 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO Q1119 " 0.015 5.00e-02 4.00e+02 2.20e-02 7.74e-01 pdb=" N PRO Q1120 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO Q1120 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO Q1120 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q1142 " -0.008 2.00e-02 2.50e+03 5.04e-03 5.07e-01 pdb=" CG TYR Q1142 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR Q1142 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR Q1142 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR Q1142 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR Q1142 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Q1142 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR Q1142 " -0.003 2.00e-02 2.50e+03 ... (remaining 805 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 16 2.52 - 3.11: 3416 3.11 - 3.71: 7153 3.71 - 4.30: 10615 4.30 - 4.90: 16853 Nonbonded interactions: 38053 Sorted by model distance: nonbonded pdb=" OE2 GLU D1138 " pdb=" O HOH D1301 " model vdw 1.920 3.040 nonbonded pdb=" OG1 THR D 900 " pdb=" OD1 ASP D 902 " model vdw 2.149 3.040 nonbonded pdb=" OE1 GLU Q1138 " pdb=" O HOH Q1301 " model vdw 2.160 3.040 nonbonded pdb=" N GLY D1052 " pdb=" O HOH D1302 " model vdw 2.395 3.120 nonbonded pdb=" O VAL D1016 " pdb=" O GLU D1019 " model vdw 2.425 3.040 ... (remaining 38048 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: 0.03 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'Q' } 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 individual isotropic 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: 85.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 30.150 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:29.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 146.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 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 : 0.002 0.033 4640 Z= 0.111 Angle : 0.485 5.193 6248 Z= 0.269 Chirality : 0.039 0.129 646 Planarity : 0.003 0.037 808 Dihedral : 16.521 89.834 1692 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.35), residues: 564 helix: 0.93 (0.37), residues: 206 sheet: 0.05 (0.48), residues: 120 loop : -0.41 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D1006 HIS 0.003 0.001 HIS D1041 PHE 0.009 0.001 PHE D1098 TYR 0.011 0.001 TYR Q1142 ARG 0.002 0.000 ARG Q1100 Details of bonding type rmsd hydrogen bonds : bond 0.14863 ( 191) hydrogen bonds : angle 6.43497 ( 519) metal coordination : bond 0.00282 ( 8) metal coordination : angle 0.43170 ( 6) covalent geometry : bond 0.00235 ( 4632) covalent geometry : angle 0.48528 ( 6242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.486 Fit side-chains REVERT: Q 963 LYS cc_start: 0.7176 (pttm) cc_final: 0.6914 (tptt) REVERT: Q 1042 LYS cc_start: 0.7005 (mtmt) cc_final: 0.6667 (pptt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 2.1545 time to fit residues: 236.4801 Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 50 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 898 GLN D1156 GLN Q 889 HIS Q 966 GLN Q1022 ASN Q1109 GLN Q1156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141053 restraints weight = 3880.623| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.40 r_work: 0.3733 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4640 Z= 0.138 Angle : 0.526 4.802 6248 Z= 0.294 Chirality : 0.044 0.140 646 Planarity : 0.004 0.037 808 Dihedral : 4.811 22.648 640 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.52 % Allowed : 13.70 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.36), residues: 564 helix: 0.76 (0.37), residues: 208 sheet: -0.03 (0.45), residues: 120 loop : -0.14 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D1006 HIS 0.005 0.001 HIS D 979 PHE 0.011 0.002 PHE D 965 TYR 0.013 0.002 TYR Q1139 ARG 0.006 0.001 ARG D1128 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 191) hydrogen bonds : angle 5.02439 ( 519) metal coordination : bond 0.00386 ( 8) metal coordination : angle 0.66946 ( 6) covalent geometry : bond 0.00304 ( 4632) covalent geometry : angle 0.52624 ( 6242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.519 Fit side-chains REVERT: D 977 ARG cc_start: 0.7044 (mmt-90) cc_final: 0.6815 (mmt-90) REVERT: D 1115 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7709 (ptm) REVERT: Q 932 ARG cc_start: 0.7382 (mtt180) cc_final: 0.6853 (mtp180) REVERT: Q 963 LYS cc_start: 0.7564 (pttm) cc_final: 0.6806 (tptt) REVERT: Q 991 ARG cc_start: 0.7509 (ptm160) cc_final: 0.7072 (ptm160) REVERT: Q 1004 LYS cc_start: 0.7406 (tttp) cc_final: 0.6904 (mptt) outliers start: 7 outliers final: 1 residues processed: 81 average time/residue: 2.8513 time to fit residues: 238.8851 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1115 MET Chi-restraints excluded: chain Q residue 1036 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139354 restraints weight = 3954.952| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.42 r_work: 0.3719 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4640 Z= 0.116 Angle : 0.472 4.275 6248 Z= 0.266 Chirality : 0.042 0.131 646 Planarity : 0.003 0.036 808 Dihedral : 4.692 21.921 640 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 13.48 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.36), residues: 564 helix: 0.83 (0.37), residues: 204 sheet: 0.10 (0.45), residues: 116 loop : -0.24 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D1006 HIS 0.004 0.001 HIS D 979 PHE 0.012 0.001 PHE D 965 TYR 0.011 0.001 TYR Q 920 ARG 0.003 0.000 ARG D 896 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 191) hydrogen bonds : angle 4.85060 ( 519) metal coordination : bond 0.00457 ( 8) metal coordination : angle 0.57489 ( 6) covalent geometry : bond 0.00244 ( 4632) covalent geometry : angle 0.47237 ( 6242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.468 Fit side-chains REVERT: D 892 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7293 (p0) REVERT: D 963 LYS cc_start: 0.6963 (pttm) cc_final: 0.5805 (tppt) REVERT: Q 963 LYS cc_start: 0.7599 (pttm) cc_final: 0.6798 (tptt) REVERT: Q 1004 LYS cc_start: 0.7424 (tttp) cc_final: 0.6956 (mptt) outliers start: 9 outliers final: 0 residues processed: 74 average time/residue: 1.5818 time to fit residues: 120.7181 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.135832 restraints weight = 3987.484| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.43 r_work: 0.3687 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4640 Z= 0.162 Angle : 0.524 4.808 6248 Z= 0.293 Chirality : 0.044 0.128 646 Planarity : 0.004 0.037 808 Dihedral : 4.887 23.018 640 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 12.83 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.35), residues: 564 helix: 0.54 (0.36), residues: 208 sheet: -0.07 (0.44), residues: 120 loop : -0.29 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D1006 HIS 0.006 0.001 HIS D 979 PHE 0.015 0.002 PHE D 965 TYR 0.014 0.002 TYR Q 920 ARG 0.002 0.000 ARG D1013 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 191) hydrogen bonds : angle 4.95663 ( 519) metal coordination : bond 0.00608 ( 8) metal coordination : angle 0.62836 ( 6) covalent geometry : bond 0.00354 ( 4632) covalent geometry : angle 0.52432 ( 6242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.473 Fit side-chains REVERT: D 963 LYS cc_start: 0.7114 (pttm) cc_final: 0.5922 (tppt) REVERT: Q 963 LYS cc_start: 0.7603 (pttm) cc_final: 0.6910 (tptt) REVERT: Q 1004 LYS cc_start: 0.7524 (tttp) cc_final: 0.7014 (mptt) outliers start: 9 outliers final: 1 residues processed: 70 average time/residue: 1.4400 time to fit residues: 103.9515 Evaluate side-chains 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1036 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 17 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134979 restraints weight = 4052.596| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.44 r_work: 0.3679 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4640 Z= 0.153 Angle : 0.514 4.731 6248 Z= 0.289 Chirality : 0.044 0.127 646 Planarity : 0.004 0.039 808 Dihedral : 4.905 23.132 640 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.17 % Allowed : 12.17 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.35), residues: 564 helix: 0.46 (0.36), residues: 208 sheet: -0.09 (0.44), residues: 120 loop : -0.42 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP D1006 HIS 0.006 0.001 HIS D 979 PHE 0.014 0.002 PHE D 965 TYR 0.013 0.002 TYR Q 920 ARG 0.003 0.000 ARG D1012 Details of bonding type rmsd hydrogen bonds : bond 0.05056 ( 191) hydrogen bonds : angle 4.93209 ( 519) metal coordination : bond 0.00584 ( 8) metal coordination : angle 0.70427 ( 6) covalent geometry : bond 0.00331 ( 4632) covalent geometry : angle 0.51356 ( 6242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.595 Fit side-chains REVERT: D 1158 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5972 (mpt) REVERT: Q 963 LYS cc_start: 0.7612 (pttm) cc_final: 0.6903 (tptt) REVERT: Q 1004 LYS cc_start: 0.7517 (tttp) cc_final: 0.7005 (mptt) REVERT: Q 1108 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7316 (tm) outliers start: 10 outliers final: 1 residues processed: 70 average time/residue: 1.5900 time to fit residues: 114.7563 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1158 MET Chi-restraints excluded: chain Q residue 1036 VAL Chi-restraints excluded: chain Q residue 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN Q 909 HIS Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135011 restraints weight = 4005.783| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.42 r_work: 0.3680 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4640 Z= 0.143 Angle : 0.508 4.421 6248 Z= 0.285 Chirality : 0.043 0.126 646 Planarity : 0.004 0.039 808 Dihedral : 4.893 22.967 640 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.61 % Allowed : 12.61 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.35), residues: 564 helix: 0.56 (0.37), residues: 204 sheet: 0.09 (0.45), residues: 116 loop : -0.53 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D1006 HIS 0.005 0.001 HIS D 979 PHE 0.013 0.002 PHE D 965 TYR 0.012 0.002 TYR Q 920 ARG 0.002 0.000 ARG D1012 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 191) hydrogen bonds : angle 4.88354 ( 519) metal coordination : bond 0.00560 ( 8) metal coordination : angle 0.74385 ( 6) covalent geometry : bond 0.00311 ( 4632) covalent geometry : angle 0.50771 ( 6242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.543 Fit side-chains REVERT: D 1158 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5991 (mmp) REVERT: Q 1004 LYS cc_start: 0.7504 (tttp) cc_final: 0.6998 (mptt) REVERT: Q 1028 MET cc_start: 0.7921 (mmt) cc_final: 0.7675 (mmt) REVERT: Q 1108 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7305 (tm) outliers start: 12 outliers final: 2 residues processed: 71 average time/residue: 1.5953 time to fit residues: 116.7465 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1028 MET Chi-restraints excluded: chain D residue 1158 MET Chi-restraints excluded: chain Q residue 1036 VAL Chi-restraints excluded: chain Q residue 1108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134109 restraints weight = 4036.246| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.42 r_work: 0.3672 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 4640 Z= 0.167 Angle : 0.557 9.122 6248 Z= 0.303 Chirality : 0.044 0.128 646 Planarity : 0.004 0.041 808 Dihedral : 5.019 23.532 640 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.17 % Allowed : 13.26 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.35), residues: 564 helix: 0.45 (0.37), residues: 206 sheet: -0.11 (0.44), residues: 120 loop : -0.59 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP D1006 HIS 0.010 0.001 HIS D1084 PHE 0.015 0.002 PHE D 965 TYR 0.012 0.002 TYR D1139 ARG 0.002 0.001 ARG Q1047 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 191) hydrogen bonds : angle 4.93788 ( 519) metal coordination : bond 0.05102 ( 8) metal coordination : angle 4.21614 ( 6) covalent geometry : bond 0.00358 ( 4632) covalent geometry : angle 0.54150 ( 6242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.503 Fit side-chains REVERT: D 1158 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.5799 (mpt) REVERT: Q 957 ASP cc_start: 0.7426 (m-30) cc_final: 0.7225 (m-30) REVERT: Q 1004 LYS cc_start: 0.7524 (tttp) cc_final: 0.7000 (mptt) REVERT: Q 1108 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7326 (tm) outliers start: 10 outliers final: 2 residues processed: 66 average time/residue: 1.5994 time to fit residues: 108.8032 Evaluate side-chains 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1028 MET Chi-restraints excluded: chain D residue 1158 MET Chi-restraints excluded: chain Q residue 1036 VAL Chi-restraints excluded: chain Q residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.0030 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.153119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133124 restraints weight = 4068.620| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.43 r_work: 0.3663 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 4640 Z= 0.190 Angle : 0.597 9.514 6248 Z= 0.318 Chirality : 0.045 0.129 646 Planarity : 0.004 0.043 808 Dihedral : 5.144 24.257 640 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.61 % Allowed : 13.48 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.34), residues: 564 helix: 0.35 (0.37), residues: 206 sheet: -0.19 (0.44), residues: 120 loop : -0.71 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D1006 HIS 0.006 0.001 HIS D 979 PHE 0.015 0.002 PHE D 965 TYR 0.013 0.002 TYR D1139 ARG 0.003 0.000 ARG Q1047 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 191) hydrogen bonds : angle 4.99319 ( 519) metal coordination : bond 0.06700 ( 8) metal coordination : angle 5.94791 ( 6) covalent geometry : bond 0.00405 ( 4632) covalent geometry : angle 0.56780 ( 6242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.505 Fit side-chains REVERT: D 1158 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5807 (mpt) REVERT: Q 1004 LYS cc_start: 0.7538 (tttp) cc_final: 0.6998 (mptt) outliers start: 12 outliers final: 3 residues processed: 66 average time/residue: 1.7689 time to fit residues: 120.3063 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1028 MET Chi-restraints excluded: chain D residue 1158 MET Chi-restraints excluded: chain Q residue 1036 VAL Chi-restraints excluded: chain Q residue 1108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN D1064 ASN Q 966 GLN Q1022 ASN Q1156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134884 restraints weight = 4001.066| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.41 r_work: 0.3682 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 4640 Z= 0.157 Angle : 0.574 12.515 6248 Z= 0.298 Chirality : 0.043 0.126 646 Planarity : 0.004 0.040 808 Dihedral : 5.001 23.427 640 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.74 % Allowed : 14.13 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.35), residues: 564 helix: 0.53 (0.37), residues: 202 sheet: -0.03 (0.45), residues: 116 loop : -0.72 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D1006 HIS 0.017 0.001 HIS D1084 PHE 0.013 0.001 PHE D 965 TYR 0.012 0.002 TYR D1139 ARG 0.003 0.000 ARG Q 932 Details of bonding type rmsd hydrogen bonds : bond 0.04864 ( 191) hydrogen bonds : angle 4.88390 ( 519) metal coordination : bond 0.09198 ( 8) metal coordination : angle 7.46574 ( 6) covalent geometry : bond 0.00309 ( 4632) covalent geometry : angle 0.52535 ( 6242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.484 Fit side-chains REVERT: Q 1004 LYS cc_start: 0.7513 (tttp) cc_final: 0.6987 (mptt) REVERT: Q 1108 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7381 (tm) outliers start: 8 outliers final: 2 residues processed: 64 average time/residue: 1.6308 time to fit residues: 107.7354 Evaluate side-chains 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1028 MET Chi-restraints excluded: chain Q residue 1036 VAL Chi-restraints excluded: chain Q residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.2980 chunk 44 optimal weight: 0.1980 chunk 7 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 41 optimal weight: 0.5980 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140533 restraints weight = 4070.989| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.44 r_work: 0.3741 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 4640 Z= 0.106 Angle : 0.504 9.010 6248 Z= 0.262 Chirality : 0.041 0.135 646 Planarity : 0.003 0.034 808 Dihedral : 4.556 20.811 640 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.65 % Allowed : 15.65 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.35), residues: 564 helix: 0.77 (0.36), residues: 202 sheet: 0.06 (0.46), residues: 116 loop : -0.49 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D1006 HIS 0.015 0.001 HIS D1084 PHE 0.009 0.001 PHE D1098 TYR 0.010 0.001 TYR D1050 ARG 0.002 0.000 ARG Q 932 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 191) hydrogen bonds : angle 4.54596 ( 519) metal coordination : bond 0.06527 ( 8) metal coordination : angle 5.77597 ( 6) covalent geometry : bond 0.00198 ( 4632) covalent geometry : angle 0.47136 ( 6242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.535 Fit side-chains REVERT: D 963 LYS cc_start: 0.7215 (pttm) cc_final: 0.6041 (tppt) REVERT: Q 1004 LYS cc_start: 0.7373 (tttp) cc_final: 0.6843 (mptt) REVERT: Q 1022 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7584 (t0) outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 1.6055 time to fit residues: 110.9563 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1028 MET Chi-restraints excluded: chain Q residue 1022 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 947 ASN Q 966 GLN Q1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134182 restraints weight = 4025.394| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.41 r_work: 0.3676 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 4640 Z= 0.192 Angle : 0.621 10.884 6248 Z= 0.322 Chirality : 0.045 0.129 646 Planarity : 0.004 0.042 808 Dihedral : 5.018 23.244 640 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.87 % Allowed : 15.00 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.35), residues: 564 helix: 0.52 (0.37), residues: 206 sheet: -0.08 (0.45), residues: 120 loop : -0.65 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D1006 HIS 0.011 0.001 HIS D1084 PHE 0.017 0.002 PHE D 965 TYR 0.015 0.002 TYR Q 920 ARG 0.003 0.001 ARG D1027 Details of bonding type rmsd hydrogen bonds : bond 0.05223 ( 191) hydrogen bonds : angle 4.82725 ( 519) metal coordination : bond 0.07383 ( 8) metal coordination : angle 6.08817 ( 6) covalent geometry : bond 0.00405 ( 4632) covalent geometry : angle 0.59148 ( 6242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5566.40 seconds wall clock time: 99 minutes 16.98 seconds (5956.98 seconds total)