Starting phenix.real_space_refine (version: dev) on Sat Feb 18 06:12:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6w_20265/02_2023/6p6w_20265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6w_20265/02_2023/6p6w_20265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6w_20265/02_2023/6p6w_20265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6w_20265/02_2023/6p6w_20265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6w_20265/02_2023/6p6w_20265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6w_20265/02_2023/6p6w_20265.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.011 sd= 0.279 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1080": "OD1" <-> "OD2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1105": "NH1" <-> "NH2" Residue "A PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1032": "OE1" <-> "OE2" Residue "B ASP 1080": "OD1" <-> "OD2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1102": "NH1" <-> "NH2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1080": "OD1" <-> "OD2" Residue "C ARG 1099": "NH1" <-> "NH2" Residue "C ARG 1102": "NH1" <-> "NH2" Residue "C ARG 1105": "NH1" <-> "NH2" Residue "C PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1032": "OE1" <-> "OE2" Residue "D PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1080": "OD1" <-> "OD2" Residue "D ARG 1099": "NH1" <-> "NH2" Residue "D ARG 1102": "NH1" <-> "NH2" Residue "D ARG 1105": "NH1" <-> "NH2" Residue "D PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7468 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "D" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Time building chain proxies: 4.35, per 1000 atoms: 0.58 Number of scatterers: 7468 At special positions: 0 Unit cell: (102.432, 102.432, 74.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1224 8.00 N 1108 7.00 C 5084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1094 " - pdb=" SG CYS B1150 " distance=2.04 Simple disulfide: pdb=" SG CYS A1150 " - pdb=" SG CYS D1094 " distance=2.03 Simple disulfide: pdb=" SG CYS B1094 " - pdb=" SG CYS C1150 " distance=2.03 Simple disulfide: pdb=" SG CYS C1094 " - pdb=" SG CYS D1150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 1001 through 1010 removed outlier: 4.055A pdb=" N GLU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1032 Processing helix chain 'A' and resid 1034 through 1041 Processing helix chain 'A' and resid 1041 through 1067 Processing helix chain 'A' and resid 1074 through 1087 removed outlier: 3.539A pdb=" N SER A1087 " --> pdb=" O VAL A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1109 removed outlier: 4.129A pdb=" N ILE A1097 " --> pdb=" O CYS A1094 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A1098 " --> pdb=" O PHE A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1126 removed outlier: 4.207A pdb=" N ILE A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1152 removed outlier: 4.705A pdb=" N SER A1132 " --> pdb=" O PRO A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1175 removed outlier: 3.724A pdb=" N SER A1166 " --> pdb=" O THR A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.530A pdb=" N LEU A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1226 removed outlier: 3.670A pdb=" N PHE A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Proline residue: A1200 - end of helix removed outlier: 3.557A pdb=" N PHE A1203 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A1213 " --> pdb=" O MET A1209 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A1223 " --> pdb=" O ASP A1219 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A1224 " --> pdb=" O ALA A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'B' and resid 1002 through 1010 removed outlier: 4.047A pdb=" N GLU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1032 Processing helix chain 'B' and resid 1034 through 1041 Processing helix chain 'B' and resid 1041 through 1067 Processing helix chain 'B' and resid 1074 through 1087 removed outlier: 3.559A pdb=" N SER B1087 " --> pdb=" O VAL B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1109 removed outlier: 4.292A pdb=" N ILE B1097 " --> pdb=" O CYS B1094 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B1098 " --> pdb=" O PHE B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1126 removed outlier: 4.215A pdb=" N ILE B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1152 removed outlier: 4.681A pdb=" N SER B1132 " --> pdb=" O PRO B1128 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1175 removed outlier: 3.733A pdb=" N SER B1166 " --> pdb=" O THR B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1183 through 1188 removed outlier: 3.517A pdb=" N LEU B1187 " --> pdb=" O ILE B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1226 removed outlier: 3.830A pdb=" N PHE B1198 " --> pdb=" O ALA B1194 " (cutoff:3.500A) Proline residue: B1200 - end of helix removed outlier: 3.581A pdb=" N PHE B1203 " --> pdb=" O ILE B1199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B1206 " --> pdb=" O ILE B1202 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B1213 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B1223 " --> pdb=" O ASP B1219 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B1224 " --> pdb=" O ALA B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1227 through 1229 No H-bonds generated for 'chain 'B' and resid 1227 through 1229' Processing helix chain 'C' and resid 1002 through 1010 removed outlier: 4.047A pdb=" N GLU C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1032 Processing helix chain 'C' and resid 1034 through 1041 Processing helix chain 'C' and resid 1041 through 1067 Processing helix chain 'C' and resid 1074 through 1087 removed outlier: 3.574A pdb=" N SER C1087 " --> pdb=" O VAL C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1109 removed outlier: 4.298A pdb=" N ILE C1097 " --> pdb=" O CYS C1094 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C1098 " --> pdb=" O PHE C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1126 removed outlier: 4.242A pdb=" N ILE C1119 " --> pdb=" O GLN C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1152 removed outlier: 4.719A pdb=" N SER C1132 " --> pdb=" O PRO C1128 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1175 removed outlier: 3.753A pdb=" N SER C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) Processing helix chain 'C' and resid 1183 through 1188 removed outlier: 3.520A pdb=" N LEU C1187 " --> pdb=" O ILE C1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1226 removed outlier: 3.671A pdb=" N PHE C1198 " --> pdb=" O ALA C1194 " (cutoff:3.500A) Proline residue: C1200 - end of helix removed outlier: 3.555A pdb=" N PHE C1203 " --> pdb=" O ILE C1199 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C1206 " --> pdb=" O ILE C1202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C1213 " --> pdb=" O MET C1209 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C1223 " --> pdb=" O ASP C1219 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C1224 " --> pdb=" O ALA C1220 " (cutoff:3.500A) Processing helix chain 'C' and resid 1227 through 1229 No H-bonds generated for 'chain 'C' and resid 1227 through 1229' Processing helix chain 'D' and resid 1002 through 1010 removed outlier: 4.040A pdb=" N GLU D1010 " --> pdb=" O THR D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1033 removed outlier: 4.132A pdb=" N THR D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1041 Processing helix chain 'D' and resid 1041 through 1067 Processing helix chain 'D' and resid 1074 through 1087 removed outlier: 3.596A pdb=" N SER D1087 " --> pdb=" O VAL D1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1109 removed outlier: 4.248A pdb=" N ILE D1097 " --> pdb=" O CYS D1094 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D1098 " --> pdb=" O PHE D1095 " (cutoff:3.500A) Processing helix chain 'D' and resid 1115 through 1126 removed outlier: 4.206A pdb=" N ILE D1119 " --> pdb=" O GLN D1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1152 removed outlier: 4.711A pdb=" N SER D1132 " --> pdb=" O PRO D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1162 through 1175 removed outlier: 3.722A pdb=" N SER D1166 " --> pdb=" O THR D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1188 Processing helix chain 'D' and resid 1194 through 1226 removed outlier: 3.881A pdb=" N PHE D1198 " --> pdb=" O ALA D1194 " (cutoff:3.500A) Proline residue: D1200 - end of helix removed outlier: 3.649A pdb=" N PHE D1203 " --> pdb=" O ILE D1199 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D1206 " --> pdb=" O ILE D1202 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D1213 " --> pdb=" O MET D1209 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D1223 " --> pdb=" O ASP D1219 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU D1224 " --> pdb=" O ALA D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1227 through 1229 No H-bonds generated for 'chain 'D' and resid 1227 through 1229' 514 hydrogen bonds defined for protein. 1410 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: 1.85 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2097 1.34 - 1.47: 2167 1.47 - 1.60: 3312 1.60 - 1.73: 0 1.73 - 1.86: 96 Bond restraints: 7672 Sorted by residual: bond pdb=" N CYS A1094 " pdb=" CA CYS A1094 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.41e+00 bond pdb=" CB CYS A1094 " pdb=" SG CYS A1094 " ideal model delta sigma weight residual 1.808 1.858 -0.050 3.30e-02 9.18e+02 2.29e+00 bond pdb=" N CYS C1094 " pdb=" CA CYS C1094 " ideal model delta sigma weight residual 1.459 1.476 -0.017 1.15e-02 7.56e+03 2.29e+00 bond pdb=" CB THR C1028 " pdb=" CG2 THR C1028 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.90e+00 bond pdb=" CB TRP B1179 " pdb=" CG TRP B1179 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.82e+00 ... (remaining 7667 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.45: 174 106.45 - 113.33: 4149 113.33 - 120.21: 3252 120.21 - 127.09: 2791 127.09 - 133.96: 70 Bond angle restraints: 10436 Sorted by residual: angle pdb=" CA CYS A1094 " pdb=" CB CYS A1094 " pdb=" SG CYS A1094 " ideal model delta sigma weight residual 114.40 124.12 -9.72 2.30e+00 1.89e-01 1.79e+01 angle pdb=" N VAL C1113 " pdb=" CA VAL C1113 " pdb=" C VAL C1113 " ideal model delta sigma weight residual 108.88 116.37 -7.49 2.16e+00 2.14e-01 1.20e+01 angle pdb=" N VAL A1113 " pdb=" CA VAL A1113 " pdb=" C VAL A1113 " ideal model delta sigma weight residual 108.88 116.17 -7.29 2.16e+00 2.14e-01 1.14e+01 angle pdb=" N VAL B1113 " pdb=" CA VAL B1113 " pdb=" C VAL B1113 " ideal model delta sigma weight residual 108.88 116.12 -7.24 2.16e+00 2.14e-01 1.12e+01 angle pdb=" C HIS A1067 " pdb=" N ARG A1068 " pdb=" CA ARG A1068 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 ... (remaining 10431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 3853 17.01 - 34.01: 486 34.01 - 51.02: 99 51.02 - 68.02: 5 68.02 - 85.03: 9 Dihedral angle restraints: 4452 sinusoidal: 1740 harmonic: 2712 Sorted by residual: dihedral pdb=" CB CYS A1150 " pdb=" SG CYS A1150 " pdb=" SG CYS D1094 " pdb=" CB CYS D1094 " ideal model delta sinusoidal sigma weight residual -86.00 -171.03 85.03 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS B1094 " pdb=" SG CYS B1094 " pdb=" SG CYS C1150 " pdb=" CB CYS C1150 " ideal model delta sinusoidal sigma weight residual -86.00 -170.13 84.13 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS C1094 " pdb=" SG CYS C1094 " pdb=" SG CYS D1150 " pdb=" CB CYS D1150 " ideal model delta sinusoidal sigma weight residual -86.00 -169.67 83.67 1 1.00e+01 1.00e-02 8.54e+01 ... (remaining 4449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 725 0.041 - 0.082: 363 0.082 - 0.123: 117 0.123 - 0.164: 49 0.164 - 0.205: 10 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CA VAL C1113 " pdb=" N VAL C1113 " pdb=" C VAL C1113 " pdb=" CB VAL C1113 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL D1103 " pdb=" CA VAL D1103 " pdb=" CG1 VAL D1103 " pdb=" CG2 VAL D1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CB VAL D1126 " pdb=" CA VAL D1126 " pdb=" CG1 VAL D1126 " pdb=" CG2 VAL D1126 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 1261 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D1185 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO D1186 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D1186 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D1186 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C1185 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO C1186 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C1186 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C1186 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1185 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO A1186 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A1186 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1186 " -0.037 5.00e-02 4.00e+02 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2040 2.79 - 3.32: 7607 3.32 - 3.85: 12230 3.85 - 4.37: 13209 4.37 - 4.90: 22125 Nonbonded interactions: 57211 Sorted by model distance: nonbonded pdb=" O VAL B1083 " pdb=" OG SER B1087 " model vdw 2.265 2.440 nonbonded pdb=" O PHE B1041 " pdb=" OG1 THR B1045 " model vdw 2.288 2.440 nonbonded pdb=" O ARG D1108 " pdb=" OG1 THR D1111 " model vdw 2.297 2.440 nonbonded pdb=" O PHE C1041 " pdb=" OG1 THR C1045 " model vdw 2.307 2.440 nonbonded pdb=" OG SER B1125 " pdb=" OD1 ASP B1219 " model vdw 2.308 2.440 ... (remaining 57206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5084 2.51 5 N 1108 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.410 Check model and map are aligned: 0.100 Process input model: 21.970 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.005 0.050 7672 Z= 0.349 Angle : 0.998 9.722 10436 Z= 0.562 Chirality : 0.057 0.205 1264 Planarity : 0.008 0.067 1232 Dihedral : 15.271 81.545 2672 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 0.60 % 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: -5.12 (0.20), residues: 908 helix: -2.78 (0.14), residues: 756 sheet: None (None), residues: 0 loop : -5.33 (0.32), residues: 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 280 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 285 average time/residue: 0.2158 time to fit residues: 78.9061 Evaluate side-chains 218 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0642 time to fit residues: 1.4549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 HIS ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 GLN B1067 HIS ** C1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN C1067 HIS ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1050 GLN D1067 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 7672 Z= 0.221 Angle : 0.721 8.353 10436 Z= 0.380 Chirality : 0.043 0.172 1264 Planarity : 0.005 0.050 1232 Dihedral : 5.729 23.012 980 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 4.78 % 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: -2.89 (0.25), residues: 908 helix: -1.24 (0.17), residues: 764 sheet: None (None), residues: 0 loop : -4.84 (0.38), residues: 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 26 residues processed: 267 average time/residue: 0.2288 time to fit residues: 78.5616 Evaluate side-chains 248 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.0726 time to fit residues: 4.5725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7672 Z= 0.219 Angle : 0.735 8.807 10436 Z= 0.383 Chirality : 0.043 0.153 1264 Planarity : 0.005 0.037 1232 Dihedral : 5.434 21.657 980 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 3.23 % 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: -1.86 (0.27), residues: 908 helix: -0.52 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -4.60 (0.39), residues: 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 255 average time/residue: 0.2263 time to fit residues: 73.8176 Evaluate side-chains 222 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 214 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0762 time to fit residues: 2.2839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 8 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7672 Z= 0.195 Angle : 0.717 6.738 10436 Z= 0.374 Chirality : 0.043 0.155 1264 Planarity : 0.004 0.037 1232 Dihedral : 5.182 21.105 980 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 3.47 % 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: -1.19 (0.27), residues: 908 helix: -0.08 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -3.78 (0.41), residues: 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 235 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 251 average time/residue: 0.2289 time to fit residues: 73.7310 Evaluate side-chains 227 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0922 time to fit residues: 3.1475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 GLN ** B1172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1211 ASN ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7672 Z= 0.222 Angle : 0.748 7.719 10436 Z= 0.389 Chirality : 0.044 0.169 1264 Planarity : 0.005 0.050 1232 Dihedral : 5.118 20.124 980 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 3.59 % 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: -1.03 (0.28), residues: 908 helix: 0.01 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -4.19 (0.43), residues: 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 251 average time/residue: 0.2286 time to fit residues: 73.3333 Evaluate side-chains 224 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0709 time to fit residues: 2.6865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.0170 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 ASN B1050 GLN ** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7672 Z= 0.212 Angle : 0.745 8.046 10436 Z= 0.387 Chirality : 0.044 0.147 1264 Planarity : 0.005 0.060 1232 Dihedral : 5.090 19.004 980 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 2.75 % 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: -0.17 (0.29), residues: 908 helix: 0.58 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -2.34 (0.49), residues: 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 248 average time/residue: 0.2273 time to fit residues: 72.0753 Evaluate side-chains 224 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0822 time to fit residues: 2.9159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 ASN B1050 GLN C1025 ASN ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7672 Z= 0.202 Angle : 0.785 7.786 10436 Z= 0.409 Chirality : 0.046 0.206 1264 Planarity : 0.005 0.037 1232 Dihedral : 5.062 17.678 980 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 2.27 % 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 (0.29), residues: 908 helix: 0.69 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -2.20 (0.50), residues: 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 235 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 243 average time/residue: 0.2098 time to fit residues: 65.6224 Evaluate side-chains 223 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1267 time to fit residues: 2.7784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7672 Z= 0.283 Angle : 0.856 10.867 10436 Z= 0.444 Chirality : 0.050 0.221 1264 Planarity : 0.005 0.037 1232 Dihedral : 5.275 19.246 980 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer Outliers : 2.39 % 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: -0.76 (0.28), residues: 908 helix: 0.16 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -3.82 (0.48), residues: 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 238 average time/residue: 0.2511 time to fit residues: 77.5515 Evaluate side-chains 227 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1090 time to fit residues: 3.0642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 83 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7672 Z= 0.234 Angle : 0.919 15.951 10436 Z= 0.466 Chirality : 0.050 0.190 1264 Planarity : 0.005 0.045 1232 Dihedral : 5.325 19.382 980 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.32 % 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: -0.76 (0.28), residues: 908 helix: 0.14 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -3.65 (0.50), residues: 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 234 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 240 average time/residue: 0.2270 time to fit residues: 69.7122 Evaluate side-chains 230 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 222 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1062 time to fit residues: 2.5140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 42 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7672 Z= 0.229 Angle : 0.969 18.059 10436 Z= 0.483 Chirality : 0.050 0.221 1264 Planarity : 0.005 0.035 1232 Dihedral : 5.263 20.303 980 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 0.84 % 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: -0.10 (0.29), residues: 908 helix: 0.59 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -2.18 (0.49), residues: 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 242 average time/residue: 0.2350 time to fit residues: 72.5145 Evaluate side-chains 226 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0864 time to fit residues: 2.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 69 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 3 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: ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1025 ASN D1067 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.135185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.117337 restraints weight = 22528.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120069 restraints weight = 13609.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.122076 restraints weight = 9443.342| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7672 Z= 0.238 Angle : 0.960 15.581 10436 Z= 0.480 Chirality : 0.050 0.241 1264 Planarity : 0.005 0.036 1232 Dihedral : 5.263 19.409 980 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.20 % 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: -0.11 (0.29), residues: 908 helix: 0.59 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 208 =============================================================================== Job complete usr+sys time: 1895.75 seconds wall clock time: 35 minutes 15.44 seconds (2115.44 seconds total)