Starting phenix.real_space_refine on Wed Sep 17 08:47:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w28_43741/09_2025/8w28_43741_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w28_43741/09_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_43741/09_2025/8w28_43741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w28_43741/09_2025/8w28_43741.map" model { file = "/net/cci-nas-00/data/ceres_data/8w28_43741/09_2025/8w28_43741_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w28_43741/09_2025/8w28_43741_neut.cif" } resolution = 2.19 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= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} 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: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} 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: 1.49, per 1000 atoms: 0.33 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: 0.46 Conformation dependent library (CDL) restraints added in 165.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 0.70 Time building geometry restraints manager: 0.54 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: 0.01 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.600 Find NCS groups from input model: 0.090 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:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG Q1100 TYR 0.011 0.001 TYR Q1142 PHE 0.009 0.001 PHE D1098 TRP 0.007 0.002 TRP D1006 HIS 0.003 0.001 HIS D1041 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 4632) covalent geometry : angle 0.48528 ( 6242) hydrogen bonds : bond 0.14863 ( 191) hydrogen bonds : angle 6.43497 ( 519) metal coordination : bond 0.00282 ( 8) metal coordination : angle 0.43170 ( 6) *********************** 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 : 0.221 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: 0.8008 time to fit residues: 87.9674 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 : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 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 898 GLN D1156 GLN Q 889 HIS Q 966 GLN Q1022 ASN Q1156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.159233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139211 restraints weight = 3945.035| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.41 r_work: 0.3716 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4640 Z= 0.157 Angle : 0.551 5.515 6248 Z= 0.306 Chirality : 0.045 0.142 646 Planarity : 0.004 0.037 808 Dihedral : 4.949 23.306 640 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.52 % Allowed : 13.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.35), residues: 564 helix: 0.66 (0.36), residues: 208 sheet: -0.09 (0.45), residues: 120 loop : -0.23 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1128 TYR 0.015 0.002 TYR Q1139 PHE 0.013 0.002 PHE D1055 TRP 0.009 0.003 TRP D1006 HIS 0.006 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4632) covalent geometry : angle 0.55055 ( 6242) hydrogen bonds : bond 0.05181 ( 191) hydrogen bonds : angle 5.08881 ( 519) metal coordination : bond 0.00534 ( 8) metal coordination : angle 0.71289 ( 6) *********************** 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 85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.185 Fit side-chains REVERT: D 963 LYS cc_start: 0.6974 (pttm) cc_final: 0.5703 (tppt) REVERT: D 1115 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7706 (ptm) REVERT: Q 963 LYS cc_start: 0.7591 (pttm) cc_final: 0.6794 (tptt) REVERT: Q 1004 LYS cc_start: 0.7468 (tttp) cc_final: 0.6947 (mptt) outliers start: 7 outliers final: 1 residues processed: 80 average time/residue: 0.7705 time to fit residues: 63.4970 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.158090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137874 restraints weight = 4008.791| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.44 r_work: 0.3704 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4640 Z= 0.127 Angle : 0.492 4.554 6248 Z= 0.276 Chirality : 0.043 0.143 646 Planarity : 0.003 0.038 808 Dihedral : 4.801 22.615 640 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.17 % Allowed : 13.48 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.13 (0.35), residues: 564 helix: 0.71 (0.36), residues: 204 sheet: 0.05 (0.45), residues: 116 loop : -0.31 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q1128 TYR 0.012 0.001 TYR Q 920 PHE 0.013 0.001 PHE D 965 TRP 0.009 0.002 TRP D1006 HIS 0.005 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4632) covalent geometry : angle 0.49227 ( 6242) hydrogen bonds : bond 0.04919 ( 191) hydrogen bonds : angle 4.93017 ( 519) metal coordination : bond 0.00522 ( 8) metal coordination : angle 0.57412 ( 6) *********************** 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 85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.165 Fit side-chains REVERT: D 892 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7312 (p0) REVERT: D 963 LYS cc_start: 0.7024 (pttm) cc_final: 0.5858 (tppt) REVERT: Q 963 LYS cc_start: 0.7618 (pttm) cc_final: 0.6841 (tptt) REVERT: Q 1004 LYS cc_start: 0.7473 (tttp) cc_final: 0.6972 (mptt) outliers start: 10 outliers final: 1 residues processed: 77 average time/residue: 0.7447 time to fit residues: 59.0200 Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain Q residue 1036 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.158815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139144 restraints weight = 3968.722| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.39 r_work: 0.3718 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4640 Z= 0.109 Angle : 0.462 4.471 6248 Z= 0.260 Chirality : 0.042 0.125 646 Planarity : 0.003 0.036 808 Dihedral : 4.622 21.853 640 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.74 % Allowed : 13.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.36), residues: 564 helix: 0.64 (0.36), residues: 208 sheet: 0.13 (0.45), residues: 116 loop : -0.26 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 896 TYR 0.014 0.001 TYR D 943 PHE 0.011 0.001 PHE D 965 TRP 0.008 0.002 TRP D1006 HIS 0.004 0.001 HIS D 909 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4632) covalent geometry : angle 0.46154 ( 6242) hydrogen bonds : bond 0.04355 ( 191) hydrogen bonds : angle 4.75680 ( 519) metal coordination : bond 0.00437 ( 8) metal coordination : angle 0.56995 ( 6) *********************** 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 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.155 Fit side-chains REVERT: D 892 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7356 (p0) REVERT: D 963 LYS cc_start: 0.7068 (pttm) cc_final: 0.5897 (tppt) REVERT: Q 963 LYS cc_start: 0.7597 (pttm) cc_final: 0.6882 (tptt) REVERT: Q 1004 LYS cc_start: 0.7456 (tttp) cc_final: 0.6968 (mptt) REVERT: Q 1108 LEU cc_start: 0.7930 (mm) cc_final: 0.7221 (tm) outliers start: 8 outliers final: 1 residues processed: 73 average time/residue: 0.7497 time to fit residues: 56.3245 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 : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ASP 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 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.0030 chunk 44 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.155626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135439 restraints weight = 3968.895| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.42 r_work: 0.3684 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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= 0.144 Angle : 0.503 4.269 6248 Z= 0.282 Chirality : 0.043 0.128 646 Planarity : 0.004 0.039 808 Dihedral : 4.813 22.784 640 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.74 % Allowed : 13.91 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.07 (0.35), residues: 564 helix: 0.68 (0.37), residues: 204 sheet: 0.16 (0.45), residues: 116 loop : -0.43 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1012 TYR 0.010 0.002 TYR Q1139 PHE 0.015 0.002 PHE D 965 TRP 0.010 0.002 TRP D1006 HIS 0.005 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4632) covalent geometry : angle 0.50310 ( 6242) hydrogen bonds : bond 0.04939 ( 191) hydrogen bonds : angle 4.84931 ( 519) metal coordination : bond 0.00523 ( 8) metal coordination : angle 0.64396 ( 6) *********************** 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 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.194 Fit side-chains REVERT: D 1158 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.5951 (mpt) REVERT: Q 963 LYS cc_start: 0.7561 (pttm) cc_final: 0.6870 (tptt) REVERT: Q 1004 LYS cc_start: 0.7514 (tttp) cc_final: 0.7016 (mptt) outliers start: 8 outliers final: 2 residues processed: 73 average time/residue: 0.8270 time to fit residues: 61.9751 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.155475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135331 restraints weight = 4077.305| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.44 r_work: 0.3682 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2918 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= 0.141 Angle : 0.498 4.529 6248 Z= 0.280 Chirality : 0.043 0.126 646 Planarity : 0.004 0.042 808 Dihedral : 4.818 22.873 640 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 13.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.35), residues: 564 helix: 0.62 (0.37), residues: 204 sheet: 0.12 (0.45), residues: 116 loop : -0.52 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1012 TYR 0.010 0.002 TYR Q1139 PHE 0.014 0.002 PHE D 965 TRP 0.010 0.002 TRP D1006 HIS 0.005 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4632) covalent geometry : angle 0.49753 ( 6242) hydrogen bonds : bond 0.04846 ( 191) hydrogen bonds : angle 4.84863 ( 519) metal coordination : bond 0.00540 ( 8) metal coordination : angle 0.66246 ( 6) *********************** 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: 9 poor density : 69 time to evaluate : 0.194 Fit side-chains REVERT: Q 1004 LYS cc_start: 0.7516 (tttp) cc_final: 0.7005 (mptt) outliers start: 9 outliers final: 2 residues processed: 72 average time/residue: 0.8555 time to fit residues: 63.3227 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 : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1028 MET Chi-restraints excluded: chain Q residue 1036 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.155021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134882 restraints weight = 4025.789| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.43 r_work: 0.3681 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 4640 Z= 0.154 Angle : 0.540 10.039 6248 Z= 0.292 Chirality : 0.044 0.128 646 Planarity : 0.004 0.042 808 Dihedral : 4.924 23.152 640 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 14.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.35), residues: 564 helix: 0.62 (0.37), residues: 202 sheet: 0.07 (0.45), residues: 116 loop : -0.65 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 932 TYR 0.011 0.002 TYR Q 920 PHE 0.014 0.002 PHE D 965 TRP 0.010 0.003 TRP D1006 HIS 0.012 0.001 HIS D1084 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4632) covalent geometry : angle 0.52047 ( 6242) hydrogen bonds : bond 0.04968 ( 191) hydrogen bonds : angle 4.88291 ( 519) metal coordination : bond 0.04616 ( 8) metal coordination : angle 4.71607 ( 6) *********************** 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 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.184 Fit side-chains REVERT: Q 1004 LYS cc_start: 0.7512 (tttp) cc_final: 0.6988 (mptt) REVERT: Q 1108 LEU cc_start: 0.7963 (mm) cc_final: 0.7306 (tm) REVERT: Q 1113 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5591 (pp-130) outliers start: 9 outliers final: 2 residues processed: 66 average time/residue: 0.8553 time to fit residues: 58.0106 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 1113 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 Q1156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.135879 restraints weight = 4093.008| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.41 r_work: 0.3688 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 4640 Z= 0.155 Angle : 0.562 9.914 6248 Z= 0.297 Chirality : 0.043 0.127 646 Planarity : 0.004 0.042 808 Dihedral : 4.933 23.126 640 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.96 % Allowed : 14.57 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.17 (0.35), residues: 564 helix: 0.61 (0.37), residues: 202 sheet: 0.02 (0.45), residues: 116 loop : -0.69 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 932 TYR 0.012 0.002 TYR D1139 PHE 0.014 0.002 PHE D 965 TRP 0.010 0.002 TRP D1006 HIS 0.005 0.001 HIS D 979 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4632) covalent geometry : angle 0.53857 ( 6242) hydrogen bonds : bond 0.04917 ( 191) hydrogen bonds : angle 4.86682 ( 519) metal coordination : bond 0.05782 ( 8) metal coordination : angle 5.17955 ( 6) *********************** 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 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.188 Fit side-chains REVERT: Q 1004 LYS cc_start: 0.7506 (tttp) cc_final: 0.6983 (mptt) REVERT: Q 1108 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7344 (tm) outliers start: 9 outliers final: 2 residues processed: 67 average time/residue: 0.8752 time to fit residues: 60.1829 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 : 0.187 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.155549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135637 restraints weight = 3954.128| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.41 r_work: 0.3692 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 4640 Z= 0.153 Angle : 0.575 12.465 6248 Z= 0.294 Chirality : 0.043 0.126 646 Planarity : 0.004 0.042 808 Dihedral : 4.883 22.948 640 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.52 % Allowed : 15.22 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.15 (0.35), residues: 564 helix: 0.63 (0.37), residues: 202 sheet: -0.02 (0.45), residues: 116 loop : -0.67 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 932 TYR 0.012 0.001 TYR D1139 PHE 0.013 0.001 PHE D 965 TRP 0.010 0.002 TRP D1006 HIS 0.018 0.001 HIS D1084 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4632) covalent geometry : angle 0.52609 ( 6242) hydrogen bonds : bond 0.04724 ( 191) hydrogen bonds : angle 4.80254 ( 519) metal coordination : bond 0.09590 ( 8) metal coordination : angle 7.54580 ( 6) *********************** 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 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.194 Fit side-chains REVERT: Q 1004 LYS cc_start: 0.7492 (tttp) cc_final: 0.6986 (mptt) REVERT: Q 1108 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7333 (tm) REVERT: Q 1113 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5676 (pp-130) outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 0.8467 time to fit residues: 57.4746 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain Q residue 1113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.0030 chunk 16 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.2588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.158441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138693 restraints weight = 4068.253| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.43 r_work: 0.3722 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 4640 Z= 0.114 Angle : 0.523 9.501 6248 Z= 0.269 Chirality : 0.041 0.131 646 Planarity : 0.003 0.039 808 Dihedral : 4.657 21.506 640 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.87 % Allowed : 15.87 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.00 (0.35), residues: 564 helix: 0.76 (0.37), residues: 202 sheet: 0.01 (0.45), residues: 116 loop : -0.54 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 932 TYR 0.008 0.001 TYR Q1050 PHE 0.009 0.001 PHE D 965 TRP 0.007 0.001 TRP D1006 HIS 0.015 0.001 HIS D1084 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 4632) covalent geometry : angle 0.48718 ( 6242) hydrogen bonds : bond 0.04057 ( 191) hydrogen bonds : angle 4.60804 ( 519) metal coordination : bond 0.07119 ( 8) metal coordination : angle 6.13342 ( 6) ********************** 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 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.114 Fit side-chains REVERT: D 963 LYS cc_start: 0.7246 (pttm) cc_final: 0.6054 (tppt) REVERT: Q 1004 LYS cc_start: 0.7411 (tttp) cc_final: 0.6882 (mptt) REVERT: Q 1022 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7666 (t160) REVERT: Q 1108 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7353 (tm) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.8309 time to fit residues: 54.6157 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 : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1028 MET Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain Q residue 1022 ASN 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 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 49 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 overall best weight: 0.2412 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.158031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138226 restraints weight = 4104.793| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.44 r_work: 0.3723 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 4640 Z= 0.109 Angle : 0.511 9.496 6248 Z= 0.265 Chirality : 0.041 0.132 646 Planarity : 0.003 0.040 808 Dihedral : 4.585 21.199 640 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.87 % Allowed : 15.65 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.07 (0.35), residues: 564 helix: 0.80 (0.37), residues: 202 sheet: 0.08 (0.45), residues: 116 loop : -0.50 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 932 TYR 0.008 0.001 TYR D1142 PHE 0.009 0.001 PHE D 965 TRP 0.007 0.001 TRP D1006 HIS 0.014 0.001 HIS D1084 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 4632) covalent geometry : angle 0.48093 ( 6242) hydrogen bonds : bond 0.03982 ( 191) hydrogen bonds : angle 4.53925 ( 519) metal coordination : bond 0.06073 ( 8) metal coordination : angle 5.61412 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2501.29 seconds wall clock time: 43 minutes 17.13 seconds (2597.13 seconds total)