Starting phenix.real_space_refine on Fri Dec 27 21:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pq5_17820/12_2024/8pq5_17820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pq5_17820/12_2024/8pq5_17820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pq5_17820/12_2024/8pq5_17820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pq5_17820/12_2024/8pq5_17820.map" model { file = "/net/cci-nas-00/data/ceres_data/8pq5_17820/12_2024/8pq5_17820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pq5_17820/12_2024/8pq5_17820.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 413 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 25 5.16 5 C 3991 2.51 5 N 1082 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6300 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2781 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 338} Chain breaks: 1 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2990 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 361} Chain breaks: 2 Chain: "C" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 467 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.68, per 1000 atoms: 0.74 Number of scatterers: 6300 At special positions: 0 Unit cell: (109.021, 81.991, 97.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 6 15.00 O 1196 8.00 N 1082 7.00 C 3991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 971.8 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 44.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.672A pdb=" N MET A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 4.019A pdb=" N VAL A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.867A pdb=" N ARG A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 160 No H-bonds generated for 'chain 'A' and resid 159 through 160' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.560A pdb=" N MET A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1090 removed outlier: 4.968A pdb=" N GLN A1061 " --> pdb=" O GLN A1057 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A1062 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A1069 " --> pdb=" O GLU A1065 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A1072 " --> pdb=" O ASP A1068 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS A1073 " --> pdb=" O ARG A1069 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'A' and resid 1132 through 1147 Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.937A pdb=" N GLY A1168 " --> pdb=" O ASN A1164 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 removed outlier: 3.521A pdb=" N PHE B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.703A pdb=" N ALA B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.512A pdb=" N LEU B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.887A pdb=" N ARG B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 4.399A pdb=" N GLU B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.584A pdb=" N ARG B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1048 removed outlier: 4.382A pdb=" N ARG B1024 " --> pdb=" O VAL B1020 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLN B1035 " --> pdb=" O LEU B1031 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B1040 " --> pdb=" O VAL B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1115 Processing helix chain 'B' and resid 1119 through 1135 Processing helix chain 'B' and resid 1150 through 1165 removed outlier: 3.629A pdb=" N ALA B1156 " --> pdb=" O GLN B1152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B1163 " --> pdb=" O ASP B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1181 removed outlier: 3.592A pdb=" N LEU B1180 " --> pdb=" O ARG B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1210 removed outlier: 4.196A pdb=" N ASP B1208 " --> pdb=" O GLU B1204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B1210 " --> pdb=" O ALA B1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 563 Processing helix chain 'C' and resid 589 through 603 Processing helix chain 'C' and resid 604 through 607 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.552A pdb=" N LEU A 6 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1152 through 1154 removed outlier: 6.047A pdb=" N PHE A1153 " --> pdb=" O ILE A1185 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE A1187 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE A1201 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 29 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL A1203 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1099 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 9 Processing sheet with id=AA5, first strand: chain 'B' and resid 1139 through 1141 removed outlier: 6.415A pdb=" N TYR B1140 " --> pdb=" O ILE B1171 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN B 28 " --> pdb=" O PHE B1170 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS B 27 " --> pdb=" O LYS B1185 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR B1187 " --> pdb=" O HIS B 27 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL B 29 " --> pdb=" O TYR B1187 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL B1189 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 31 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N PHE B1191 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1054 through 1057 258 hydrogen bonds defined for protein. 723 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: 1.86 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2066 1.35 - 1.46: 1357 1.46 - 1.58: 2932 1.58 - 1.69: 10 1.69 - 1.81: 44 Bond restraints: 6409 Sorted by residual: bond pdb=" CA MET B1109 " pdb=" CB MET B1109 " ideal model delta sigma weight residual 1.528 1.588 -0.059 2.61e-02 1.47e+03 5.15e+00 bond pdb=" CA GLU B1108 " pdb=" CB GLU B1108 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.31e-02 5.83e+03 1.52e+00 bond pdb=" CG1 ILE A1174 " pdb=" CD1 ILE A1174 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.20e+00 bond pdb=" CG LEU C 581 " pdb=" CD1 LEU C 581 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CG1 ILE B1128 " pdb=" CD1 ILE B1128 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.04e+00 ... (remaining 6404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8337 1.69 - 3.39: 235 3.39 - 5.08: 38 5.08 - 6.77: 8 6.77 - 8.47: 4 Bond angle restraints: 8622 Sorted by residual: angle pdb=" C ALA A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 121.75 116.65 5.10 1.73e+00 3.34e-01 8.68e+00 angle pdb=" N ALA B 163 " pdb=" CA ALA B 163 " pdb=" C ALA B 163 " ideal model delta sigma weight residual 110.97 107.76 3.21 1.09e+00 8.42e-01 8.67e+00 angle pdb=" N ASN A 11 " pdb=" CA ASN A 11 " pdb=" C ASN A 11 " ideal model delta sigma weight residual 111.28 115.20 -3.92 1.35e+00 5.49e-01 8.43e+00 angle pdb=" N THR B1214 " pdb=" CA THR B1214 " pdb=" C THR B1214 " ideal model delta sigma weight residual 111.30 107.28 4.02 1.43e+00 4.89e-01 7.92e+00 angle pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " ideal model delta sigma weight residual 111.30 117.24 -5.94 2.30e+00 1.89e-01 6.68e+00 ... (remaining 8617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 3484 17.10 - 34.21: 389 34.21 - 51.31: 71 51.31 - 68.41: 13 68.41 - 85.51: 10 Dihedral angle restraints: 3967 sinusoidal: 1694 harmonic: 2273 Sorted by residual: dihedral pdb=" CA GLU B 161 " pdb=" C GLU B 161 " pdb=" N VAL B 162 " pdb=" CA VAL B 162 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LYS A1175 " pdb=" C LYS A1175 " pdb=" N GLU A1176 " pdb=" CA GLU A1176 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TYR A1194 " pdb=" C TYR A1194 " pdb=" N THR A1195 " pdb=" CA THR A1195 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 3964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 595 0.036 - 0.072: 223 0.072 - 0.108: 94 0.108 - 0.143: 26 0.143 - 0.179: 8 Chirality restraints: 946 Sorted by residual: chirality pdb=" CB ILE B 138 " pdb=" CA ILE B 138 " pdb=" CG1 ILE B 138 " pdb=" CG2 ILE B 138 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA GLU B 161 " pdb=" N GLU B 161 " pdb=" C GLU B 161 " pdb=" CB GLU B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA TYR A1194 " pdb=" N TYR A1194 " pdb=" C TYR A1194 " pdb=" CB TYR A1194 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 943 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1154 " -0.231 9.50e-02 1.11e+02 1.04e-01 6.83e+00 pdb=" NE ARG B1154 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B1154 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B1154 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B1154 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 151 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C PRO B 151 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO B 151 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 152 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A1204 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A1205 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1205 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1205 " -0.021 5.00e-02 4.00e+02 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 220 2.69 - 3.24: 6940 3.24 - 3.79: 10805 3.79 - 4.35: 14142 4.35 - 4.90: 21206 Nonbonded interactions: 53313 Sorted by model distance: nonbonded pdb=" O GLU A 156 " pdb=" OG SER A 161 " model vdw 2.133 3.040 nonbonded pdb=" OD1 ASP B 51 " pdb=" OG SER B 54 " model vdw 2.154 3.040 nonbonded pdb=" OG SER A1178 " pdb=" O PHE A1182 " model vdw 2.182 3.040 nonbonded pdb=" OD2 ASP B1150 " pdb=" OH TYR C 598 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A1217 " pdb=" O PRO C 616 " model vdw 2.235 3.040 ... (remaining 53308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.003 0.059 6409 Z= 0.192 Angle : 0.690 8.465 8622 Z= 0.366 Chirality : 0.047 0.179 946 Planarity : 0.005 0.104 1108 Dihedral : 14.875 85.513 2495 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.84 (0.31), residues: 768 helix: -0.74 (0.31), residues: 275 sheet: -1.61 (0.40), residues: 140 loop : -1.32 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A1145 PHE 0.023 0.002 PHE A 12 TYR 0.013 0.002 TYR B1140 ARG 0.008 0.001 ARG B1154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8863 (t80) cc_final: 0.8255 (m-80) REVERT: A 42 MET cc_start: 0.8925 (tmm) cc_final: 0.8617 (tmm) REVERT: A 1084 ILE cc_start: 0.9431 (mm) cc_final: 0.9171 (pt) REVERT: A 1174 ILE cc_start: 0.8999 (mp) cc_final: 0.8726 (mp) REVERT: B 1 MET cc_start: 0.7335 (tmm) cc_final: 0.6939 (tmm) REVERT: B 47 PHE cc_start: 0.9293 (t80) cc_final: 0.8841 (t80) REVERT: B 169 ASP cc_start: 0.8874 (p0) cc_final: 0.8592 (p0) REVERT: B 1057 MET cc_start: 0.5718 (ppp) cc_final: 0.5321 (tmm) REVERT: B 1100 VAL cc_start: 0.8519 (p) cc_final: 0.7819 (p) REVERT: B 1102 PHE cc_start: 0.8853 (p90) cc_final: 0.8198 (p90) REVERT: B 1153 HIS cc_start: 0.8207 (m90) cc_final: 0.7909 (m90) REVERT: B 1193 ASN cc_start: 0.8995 (t0) cc_final: 0.8417 (p0) REVERT: C 592 GLN cc_start: 0.8427 (tp-100) cc_final: 0.8063 (tp-100) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2645 time to fit residues: 35.2674 Evaluate side-chains 90 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 6409 Z= 0.471 Angle : 0.941 17.623 8622 Z= 0.480 Chirality : 0.052 0.200 946 Planarity : 0.007 0.076 1108 Dihedral : 10.779 89.478 912 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 41.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 1.33 % Allowed : 10.21 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.01 (0.29), residues: 768 helix: -1.71 (0.27), residues: 287 sheet: -2.04 (0.42), residues: 135 loop : -2.11 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A1145 PHE 0.032 0.003 PHE A 12 TYR 0.030 0.004 TYR A1194 ARG 0.008 0.001 ARG A1090 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.766 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: A 27 PHE cc_start: 0.9003 (t80) cc_final: 0.8207 (m-10) REVERT: A 174 GLU cc_start: 0.8423 (mp0) cc_final: 0.8128 (mp0) REVERT: A 1185 ILE cc_start: 0.9524 (mm) cc_final: 0.9260 (pt) REVERT: A 1194 TYR cc_start: 0.7594 (p90) cc_final: 0.7264 (p90) REVERT: B 1 MET cc_start: 0.7613 (tmm) cc_final: 0.7342 (tmm) REVERT: B 11 PHE cc_start: 0.8718 (t80) cc_final: 0.8462 (t80) REVERT: B 47 PHE cc_start: 0.9308 (t80) cc_final: 0.8943 (t80) REVERT: B 160 ARG cc_start: 0.8963 (tmt170) cc_final: 0.8572 (tmt170) REVERT: B 1100 VAL cc_start: 0.8716 (p) cc_final: 0.8120 (p) REVERT: B 1102 PHE cc_start: 0.8738 (p90) cc_final: 0.8141 (p90) outliers start: 9 outliers final: 5 residues processed: 127 average time/residue: 0.2577 time to fit residues: 40.5755 Evaluate side-chains 100 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 56 optimal weight: 0.0370 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN A1145 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6409 Z= 0.229 Angle : 0.711 10.125 8622 Z= 0.367 Chirality : 0.048 0.172 946 Planarity : 0.004 0.041 1108 Dihedral : 10.115 88.455 912 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.44 % Allowed : 6.07 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.69 (0.29), residues: 768 helix: -1.35 (0.28), residues: 295 sheet: -1.85 (0.41), residues: 139 loop : -2.03 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A1145 PHE 0.025 0.002 PHE A 12 TYR 0.024 0.002 TYR A1194 ARG 0.009 0.001 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.769 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: A 42 MET cc_start: 0.9000 (tmm) cc_final: 0.8736 (tmm) REVERT: A 175 MET cc_start: 0.8079 (mtt) cc_final: 0.7409 (mtt) REVERT: A 1194 TYR cc_start: 0.7364 (p90) cc_final: 0.7093 (p90) REVERT: B 1 MET cc_start: 0.7437 (tmm) cc_final: 0.7151 (tmm) REVERT: B 160 ARG cc_start: 0.8941 (tmt170) cc_final: 0.8540 (tmt170) REVERT: B 1100 VAL cc_start: 0.8734 (p) cc_final: 0.8157 (p) REVERT: B 1102 PHE cc_start: 0.8698 (p90) cc_final: 0.8106 (p90) REVERT: C 592 GLN cc_start: 0.8474 (tp-100) cc_final: 0.8153 (tp-100) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.2523 time to fit residues: 40.1457 Evaluate side-chains 95 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 0.2980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 GLN ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6409 Z= 0.228 Angle : 0.700 11.720 8622 Z= 0.359 Chirality : 0.047 0.173 946 Planarity : 0.004 0.029 1108 Dihedral : 9.948 87.580 912 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.58 (0.29), residues: 768 helix: -1.33 (0.27), residues: 299 sheet: -1.61 (0.43), residues: 130 loop : -2.00 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 66 PHE 0.033 0.002 PHE A 12 TYR 0.019 0.002 TYR A1194 ARG 0.009 0.001 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.728 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: A 42 MET cc_start: 0.8997 (tmm) cc_final: 0.8760 (tmm) REVERT: A 174 GLU cc_start: 0.8644 (mp0) cc_final: 0.8315 (mp0) REVERT: A 175 MET cc_start: 0.8001 (mtt) cc_final: 0.7642 (mtt) REVERT: B 1 MET cc_start: 0.7430 (tmm) cc_final: 0.7136 (tmm) REVERT: B 47 PHE cc_start: 0.9336 (t80) cc_final: 0.9116 (t80) REVERT: B 1100 VAL cc_start: 0.8776 (p) cc_final: 0.8121 (p) REVERT: B 1102 PHE cc_start: 0.8666 (p90) cc_final: 0.8041 (p90) REVERT: C 592 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8075 (tp-100) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2403 time to fit residues: 37.1333 Evaluate side-chains 94 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6409 Z= 0.277 Angle : 0.752 13.183 8622 Z= 0.385 Chirality : 0.049 0.163 946 Planarity : 0.005 0.036 1108 Dihedral : 9.931 89.712 912 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.15 % Allowed : 4.29 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.60 (0.29), residues: 768 helix: -1.30 (0.28), residues: 293 sheet: -1.81 (0.43), residues: 128 loop : -1.97 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 27 PHE 0.027 0.002 PHE A 12 TYR 0.018 0.002 TYR B1140 ARG 0.010 0.001 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.903 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: A 42 MET cc_start: 0.9028 (tmm) cc_final: 0.8781 (tmm) REVERT: A 175 MET cc_start: 0.7875 (mtt) cc_final: 0.7640 (mtt) REVERT: B 1 MET cc_start: 0.7511 (tmm) cc_final: 0.7221 (tmm) REVERT: B 47 PHE cc_start: 0.9314 (t80) cc_final: 0.9112 (t80) REVERT: B 1057 MET cc_start: 0.6843 (ptt) cc_final: 0.5826 (ppp) REVERT: B 1100 VAL cc_start: 0.8751 (p) cc_final: 0.8103 (p) REVERT: B 1102 PHE cc_start: 0.8667 (p90) cc_final: 0.8082 (p90) REVERT: C 592 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7967 (tp-100) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2518 time to fit residues: 37.3322 Evaluate side-chains 86 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6409 Z= 0.206 Angle : 0.687 10.908 8622 Z= 0.352 Chirality : 0.048 0.178 946 Planarity : 0.004 0.037 1108 Dihedral : 9.871 86.613 912 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.44 (0.29), residues: 768 helix: -1.15 (0.28), residues: 298 sheet: -1.40 (0.44), residues: 130 loop : -2.05 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 66 PHE 0.024 0.002 PHE A 12 TYR 0.016 0.002 TYR B1011 ARG 0.007 0.001 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.667 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: A 42 MET cc_start: 0.8969 (tmm) cc_final: 0.8750 (tmm) REVERT: A 175 MET cc_start: 0.7904 (mtt) cc_final: 0.7648 (mtt) REVERT: A 1064 LYS cc_start: 0.9241 (ptpp) cc_final: 0.8798 (mmmt) REVERT: A 1097 PHE cc_start: 0.8977 (t80) cc_final: 0.8759 (t80) REVERT: B 1 MET cc_start: 0.7474 (tmm) cc_final: 0.7138 (tmm) REVERT: B 47 PHE cc_start: 0.9298 (t80) cc_final: 0.9078 (t80) REVERT: B 109 TYR cc_start: 0.8787 (m-80) cc_final: 0.8478 (m-80) REVERT: B 160 ARG cc_start: 0.9011 (tmt170) cc_final: 0.8792 (tmt170) REVERT: B 1100 VAL cc_start: 0.8783 (p) cc_final: 0.8159 (p) REVERT: B 1102 PHE cc_start: 0.8607 (p90) cc_final: 0.7983 (p90) REVERT: C 592 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8052 (tp-100) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2243 time to fit residues: 36.4786 Evaluate side-chains 100 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B1114 GLN ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6409 Z= 0.257 Angle : 0.735 12.876 8622 Z= 0.376 Chirality : 0.049 0.175 946 Planarity : 0.004 0.030 1108 Dihedral : 9.881 87.926 912 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.15 % Allowed : 2.96 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.56 (0.30), residues: 768 helix: -1.18 (0.28), residues: 294 sheet: -1.86 (0.44), residues: 128 loop : -2.00 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 66 PHE 0.027 0.002 PHE A 12 TYR 0.016 0.002 TYR B1140 ARG 0.009 0.001 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.727 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: A 42 MET cc_start: 0.9012 (tmm) cc_final: 0.8769 (tmm) REVERT: A 174 GLU cc_start: 0.8710 (mp0) cc_final: 0.8402 (mp0) REVERT: A 175 MET cc_start: 0.7985 (mtt) cc_final: 0.7592 (mtt) REVERT: A 1064 LYS cc_start: 0.9234 (ptpp) cc_final: 0.8769 (mmmt) REVERT: B 1 MET cc_start: 0.7483 (tmm) cc_final: 0.7096 (tmm) REVERT: B 109 TYR cc_start: 0.8872 (m-80) cc_final: 0.8599 (m-80) REVERT: B 1057 MET cc_start: 0.6745 (ptm) cc_final: 0.6426 (ppp) REVERT: B 1100 VAL cc_start: 0.8755 (p) cc_final: 0.8119 (p) REVERT: B 1102 PHE cc_start: 0.8618 (p90) cc_final: 0.8023 (p90) REVERT: C 592 GLN cc_start: 0.8418 (tp-100) cc_final: 0.7947 (tp-100) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2369 time to fit residues: 36.9135 Evaluate side-chains 97 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.0030 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6409 Z= 0.191 Angle : 0.683 9.338 8622 Z= 0.351 Chirality : 0.048 0.182 946 Planarity : 0.004 0.038 1108 Dihedral : 9.919 87.468 912 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.15 % Allowed : 2.22 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.22 (0.30), residues: 768 helix: -0.89 (0.29), residues: 296 sheet: -1.33 (0.45), residues: 121 loop : -1.99 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 66 PHE 0.018 0.002 PHE A 79 TYR 0.014 0.002 TYR B1011 ARG 0.004 0.001 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8905 (tmm) cc_final: 0.8687 (tmm) REVERT: A 1064 LYS cc_start: 0.9230 (ptpp) cc_final: 0.8831 (mmmt) REVERT: A 1097 PHE cc_start: 0.9002 (t80) cc_final: 0.8748 (t80) REVERT: B 43 TYR cc_start: 0.7992 (m-80) cc_final: 0.7690 (m-80) REVERT: B 47 PHE cc_start: 0.9272 (t80) cc_final: 0.9059 (t80) REVERT: B 109 TYR cc_start: 0.8763 (m-80) cc_final: 0.8432 (m-10) REVERT: B 1057 MET cc_start: 0.6581 (ptm) cc_final: 0.5401 (tmm) REVERT: B 1100 VAL cc_start: 0.8831 (p) cc_final: 0.7822 (p) REVERT: B 1102 PHE cc_start: 0.8629 (p90) cc_final: 0.8027 (p90) REVERT: B 1112 MET cc_start: 0.7909 (ppp) cc_final: 0.7687 (ppp) REVERT: C 592 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7796 (tp-100) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2329 time to fit residues: 36.6790 Evaluate side-chains 97 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6409 Z= 0.263 Angle : 0.761 12.679 8622 Z= 0.391 Chirality : 0.049 0.176 946 Planarity : 0.005 0.063 1108 Dihedral : 9.892 88.137 912 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.49 (0.29), residues: 768 helix: -1.15 (0.28), residues: 296 sheet: -1.57 (0.51), residues: 99 loop : -2.06 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 66 PHE 0.032 0.003 PHE A 12 TYR 0.033 0.003 TYR B1026 ARG 0.016 0.001 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.721 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: A 42 MET cc_start: 0.9013 (tmm) cc_final: 0.8780 (tmm) REVERT: A 1064 LYS cc_start: 0.9230 (ptpp) cc_final: 0.8761 (mmmt) REVERT: A 1097 PHE cc_start: 0.9005 (t80) cc_final: 0.8773 (t80) REVERT: B 1 MET cc_start: 0.7668 (tmm) cc_final: 0.7292 (tmm) REVERT: B 43 TYR cc_start: 0.7925 (m-80) cc_final: 0.7622 (m-80) REVERT: B 109 TYR cc_start: 0.8752 (m-80) cc_final: 0.8498 (m-10) REVERT: B 160 ARG cc_start: 0.9031 (ttt-90) cc_final: 0.8703 (ttt-90) REVERT: B 1100 VAL cc_start: 0.8584 (p) cc_final: 0.7735 (p) REVERT: B 1102 PHE cc_start: 0.8603 (p90) cc_final: 0.8003 (p90) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2312 time to fit residues: 34.0346 Evaluate side-chains 92 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6409 Z= 0.193 Angle : 0.712 9.210 8622 Z= 0.367 Chirality : 0.048 0.201 946 Planarity : 0.005 0.083 1108 Dihedral : 9.955 88.251 912 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.23 (0.30), residues: 768 helix: -0.98 (0.29), residues: 298 sheet: -1.31 (0.43), residues: 128 loop : -1.91 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 66 PHE 0.027 0.002 PHE A 12 TYR 0.015 0.002 TYR B1011 ARG 0.011 0.001 ARG B 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.765 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: A 175 MET cc_start: 0.8619 (mtm) cc_final: 0.8105 (mtm) REVERT: A 1064 LYS cc_start: 0.9207 (ptpp) cc_final: 0.8812 (mmmt) REVERT: A 1084 ILE cc_start: 0.9431 (mm) cc_final: 0.9222 (pt) REVERT: A 1097 PHE cc_start: 0.9007 (t80) cc_final: 0.8756 (t80) REVERT: A 1125 MET cc_start: 0.7850 (ptt) cc_final: 0.7636 (ptp) REVERT: A 1153 PHE cc_start: 0.8413 (m-10) cc_final: 0.8172 (m-10) REVERT: B 1 MET cc_start: 0.7588 (tmm) cc_final: 0.7195 (tmm) REVERT: B 43 TYR cc_start: 0.7978 (m-80) cc_final: 0.7691 (m-80) REVERT: B 47 PHE cc_start: 0.9284 (t80) cc_final: 0.9079 (t80) REVERT: B 109 TYR cc_start: 0.8644 (m-80) cc_final: 0.8334 (m-10) REVERT: B 160 ARG cc_start: 0.9030 (ttt-90) cc_final: 0.8681 (ttt-90) REVERT: B 1102 PHE cc_start: 0.8627 (p90) cc_final: 0.7988 (p90) REVERT: B 1112 MET cc_start: 0.8025 (ppp) cc_final: 0.7786 (ppp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2447 time to fit residues: 37.5155 Evaluate side-chains 96 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.106309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.083635 restraints weight = 32196.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.085753 restraints weight = 26166.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.087471 restraints weight = 22125.234| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6409 Z= 0.210 Angle : 0.726 11.030 8622 Z= 0.372 Chirality : 0.048 0.187 946 Planarity : 0.005 0.071 1108 Dihedral : 9.894 88.706 912 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.20 (0.30), residues: 768 helix: -0.91 (0.29), residues: 292 sheet: -1.22 (0.49), residues: 106 loop : -1.94 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 66 PHE 0.029 0.002 PHE A 12 TYR 0.032 0.002 TYR B1026 ARG 0.012 0.001 ARG B 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1594.91 seconds wall clock time: 30 minutes 1.25 seconds (1801.25 seconds total)