Starting phenix.real_space_refine on Wed Feb 14 22:14:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c14_7328/02_2024/6c14_7328.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c14_7328/02_2024/6c14_7328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c14_7328/02_2024/6c14_7328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c14_7328/02_2024/6c14_7328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c14_7328/02_2024/6c14_7328.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c14_7328/02_2024/6c14_7328.pdb" } resolution = 4.5 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= 1.000 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 3678 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4406 2.51 5 N 1100 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 1163": "NH1" <-> "NH2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1163": "NH1" <-> "NH2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6746 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2110 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Conformer: "B" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} bond proxies already assigned to first conformer: 2142 Chain: "B" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1263 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain breaks: 2 Chain: "C" Number of atoms: 2110 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Conformer: "B" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} bond proxies already assigned to first conformer: 2142 Chain: "D" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1263 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain breaks: 2 Time building chain proxies: 5.94, per 1000 atoms: 0.88 Number of scatterers: 6746 At special positions: 0 Unit cell: (73.84, 80.08, 139.36, 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 46 16.00 O 1194 8.00 N 1100 7.00 C 4406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 79 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 130 " 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: 2.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 49.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.886A pdb=" N ALA A1183 " --> pdb=" O ASN A1180 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A1184 " --> pdb=" O TYR A1181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1180 through 1184' Processing helix chain 'A' and resid 1193 through 1197 Processing helix chain 'A' and resid 1231 through 1235 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1261 through 1268 Processing helix chain 'A' and resid 1268 through 1280 Processing helix chain 'A' and resid 1327 through 1337 removed outlier: 4.074A pdb=" N LEU A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A1337 " --> pdb=" O LYS A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1344 removed outlier: 3.889A pdb=" N ILE A1342 " --> pdb=" O LYS A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 3.835A pdb=" N LYS A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1372 " --> pdb=" O ILE A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1410 Proline residue: A1395 - end of helix Processing helix chain 'B' and resid 16 through 45 Processing helix chain 'B' and resid 91 through 117 Processing helix chain 'B' and resid 122 through 152 removed outlier: 3.593A pdb=" N LYS B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 176 through 199 removed outlier: 4.125A pdb=" N MET B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1184 removed outlier: 3.882A pdb=" N ALA C1183 " --> pdb=" O ASN C1180 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C1184 " --> pdb=" O TYR C1181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1180 through 1184' Processing helix chain 'C' and resid 1193 through 1197 Processing helix chain 'C' and resid 1231 through 1235 Processing helix chain 'C' and resid 1249 through 1253 Processing helix chain 'C' and resid 1261 through 1268 Processing helix chain 'C' and resid 1268 through 1280 Processing helix chain 'C' and resid 1327 through 1337 removed outlier: 4.073A pdb=" N LEU C1335 " --> pdb=" O LEU C1331 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C1337 " --> pdb=" O LYS C1333 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1344 removed outlier: 3.889A pdb=" N ILE C1342 " --> pdb=" O LYS C1338 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1372 removed outlier: 3.858A pdb=" N LYS C1370 " --> pdb=" O THR C1366 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C1372 " --> pdb=" O ILE C1368 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1410 Proline residue: C1395 - end of helix Processing helix chain 'D' and resid 16 through 45 Processing helix chain 'D' and resid 91 through 117 Processing helix chain 'D' and resid 122 through 152 removed outlier: 3.593A pdb=" N LYS D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 176 through 199 removed outlier: 4.125A pdb=" N MET D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1148 through 1149 Processing sheet with id=AA2, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 3.954A pdb=" N LEU A1244 " --> pdb=" O TYR A1154 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A1239 " --> pdb=" O ALA A1229 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1229 " --> pdb=" O GLY A1239 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1243 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1225 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1158 through 1159 removed outlier: 7.252A pdb=" N VAL A1158 " --> pdb=" O VAL A1248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1202 removed outlier: 3.564A pdb=" N GLY A1199 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1311 through 1315 removed outlier: 3.818A pdb=" N SER A1258 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1315 " --> pdb=" O GLN A1254 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A1254 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA8, first strand: chain 'C' and resid 1148 through 1149 Processing sheet with id=AA9, first strand: chain 'C' and resid 1153 through 1155 removed outlier: 3.955A pdb=" N LEU C1244 " --> pdb=" O TYR C1154 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY C1239 " --> pdb=" O ALA C1229 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1229 " --> pdb=" O GLY C1239 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C1243 " --> pdb=" O PHE C1225 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C1225 " --> pdb=" O VAL C1243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1158 through 1159 removed outlier: 7.252A pdb=" N VAL C1158 " --> pdb=" O VAL C1248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 1199 through 1202 removed outlier: 3.580A pdb=" N GLY C1199 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1311 through 1315 removed outlier: 3.819A pdb=" N SER C1258 " --> pdb=" O CYS C1311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C1315 " --> pdb=" O GLN C1254 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C1254 " --> pdb=" O VAL C1315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1297 through 1299 Processing sheet with id=AB5, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB6, first strand: chain 'D' and resid 59 through 60 344 hydrogen bonds defined for protein. 966 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: 1.88 Time building geometry restraints manager: 2.72 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: 2088 1.35 - 1.47: 1769 1.47 - 1.60: 2967 1.60 - 1.72: 0 1.72 - 1.85: 70 Bond restraints: 6894 Sorted by residual: bond pdb=" CB MET D 28 " pdb=" CG MET D 28 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" CB MET B 28 " pdb=" CG MET B 28 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB TRP B 29 " pdb=" CG TRP B 29 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.82e+00 bond pdb=" CB TRP D 29 " pdb=" CG TRP D 29 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.81e+00 bond pdb=" C ILE C1394 " pdb=" N PRO C1395 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.77e+00 ... (remaining 6889 not shown) Histogram of bond angle deviations from ideal: 97.85 - 106.02: 152 106.02 - 114.19: 3982 114.19 - 122.36: 4198 122.36 - 130.53: 978 130.53 - 138.70: 26 Bond angle restraints: 9336 Sorted by residual: angle pdb=" C ARG C1360 " pdb=" N THR C1361 " pdb=" CA THR C1361 " ideal model delta sigma weight residual 120.94 138.70 -17.76 1.90e+00 2.77e-01 8.73e+01 angle pdb=" C ARG A1360 " pdb=" N THR A1361 " pdb=" CA THR A1361 " ideal model delta sigma weight residual 120.94 138.36 -17.42 1.90e+00 2.77e-01 8.41e+01 angle pdb=" CA ARG B 20 " pdb=" CB ARG B 20 " pdb=" CG ARG B 20 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA ARG D 20 " pdb=" CB ARG D 20 " pdb=" CG ARG D 20 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" N SER C1374 " pdb=" CA SER C1374 " pdb=" C SER C1374 " ideal model delta sigma weight residual 108.34 113.08 -4.74 1.31e+00 5.83e-01 1.31e+01 ... (remaining 9331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.34: 3814 13.34 - 26.69: 200 26.69 - 40.03: 56 40.03 - 53.37: 10 53.37 - 66.71: 2 Dihedral angle restraints: 4082 sinusoidal: 1594 harmonic: 2488 Sorted by residual: dihedral pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " pdb=" SG CYS B 130 " pdb=" CB CYS B 130 " ideal model delta sinusoidal sigma weight residual 93.00 140.28 -47.28 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS D 114 " pdb=" SG CYS D 114 " pdb=" SG CYS D 130 " pdb=" CB CYS D 130 " ideal model delta sinusoidal sigma weight residual 93.00 140.28 -47.28 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CA LYS C1344 " pdb=" C LYS C1344 " pdb=" N ASP C1345 " pdb=" CA ASP C1345 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 819 0.061 - 0.122: 203 0.122 - 0.183: 40 0.183 - 0.243: 9 0.243 - 0.304: 3 Chirality restraints: 1074 Sorted by residual: chirality pdb=" CB ILE D 45 " pdb=" CA ILE D 45 " pdb=" CG1 ILE D 45 " pdb=" CG2 ILE D 45 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB ILE B 45 " pdb=" CA ILE B 45 " pdb=" CG1 ILE B 45 " pdb=" CG2 ILE B 45 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE C1388 " pdb=" CA ILE C1388 " pdb=" CG1 ILE C1388 " pdb=" CG2 ILE C1388 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1071 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 46 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO D 47 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 47 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 47 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 46 " -0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO B 47 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 47 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 47 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C1347 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO C1348 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C1348 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1348 " -0.034 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1611 2.79 - 3.32: 6290 3.32 - 3.84: 11324 3.84 - 4.37: 12852 4.37 - 4.90: 20646 Nonbonded interactions: 52723 Sorted by model distance: nonbonded pdb=" OD2 ASP A1319 " pdb=" OG1 THR A1322 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP C1319 " pdb=" OG1 THR C1322 " model vdw 2.264 2.440 nonbonded pdb=" O TRP D 29 " pdb=" OG1 THR D 33 " model vdw 2.322 2.440 nonbonded pdb=" O TRP B 29 " pdb=" OG1 THR B 33 " model vdw 2.323 2.440 nonbonded pdb=" OE1 GLU A1203 " pdb=" OG1 THR A1206 " model vdw 2.329 2.440 ... (remaining 52718 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' and (resid 1145 through 1245 or resid 1247 through 1410)) selection = (chain 'C' and (resid 1145 through 1245 or resid 1247 through 1410)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 6.120 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 24.270 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.055 6894 Z= 0.332 Angle : 1.036 17.757 9336 Z= 0.585 Chirality : 0.059 0.304 1074 Planarity : 0.008 0.075 1160 Dihedral : 9.458 66.714 2478 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.27 % Allowed : 0.82 % Favored : 98.90 % 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: -4.44 (0.22), residues: 846 helix: -2.47 (0.20), residues: 358 sheet: -3.92 (0.33), residues: 112 loop : -3.00 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP D 49 HIS 0.007 0.002 HIS B 15 PHE 0.031 0.003 PHE B 100 TYR 0.024 0.003 TYR D 148 ARG 0.013 0.001 ARG C1371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1160 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6122 (tp30) REVERT: A 1164 MET cc_start: 0.7863 (mmm) cc_final: 0.7520 (pmm) REVERT: A 1186 TYR cc_start: 0.8119 (m-80) cc_final: 0.7777 (m-80) REVERT: A 1193 ILE cc_start: 0.8771 (mt) cc_final: 0.8554 (mm) REVERT: A 1203 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8312 (tm-30) REVERT: A 1240 LYS cc_start: 0.8913 (pttt) cc_final: 0.8329 (ptmt) REVERT: A 1249 ASN cc_start: 0.7574 (p0) cc_final: 0.6349 (t0) REVERT: A 1270 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8713 (pm20) REVERT: A 1271 ASP cc_start: 0.9388 (m-30) cc_final: 0.9143 (m-30) REVERT: A 1274 GLU cc_start: 0.9370 (tt0) cc_final: 0.8867 (mt-10) REVERT: A 1389 ILE cc_start: 0.9477 (mt) cc_final: 0.9074 (mt) REVERT: A 1393 CYS cc_start: 0.9536 (m) cc_final: 0.9039 (m) REVERT: B 32 LEU cc_start: 0.9692 (mt) cc_final: 0.8587 (mt) REVERT: B 66 SER cc_start: 0.8173 (p) cc_final: 0.7957 (t) REVERT: B 123 THR cc_start: 0.8848 (p) cc_final: 0.8590 (p) REVERT: B 127 TYR cc_start: 0.8937 (m-10) cc_final: 0.8610 (m-80) REVERT: B 133 MET cc_start: 0.9426 (mmp) cc_final: 0.9213 (mmm) REVERT: B 141 LEU cc_start: 0.9413 (mt) cc_final: 0.9210 (mt) REVERT: B 180 MET cc_start: 0.7759 (ttp) cc_final: 0.7143 (tpp) REVERT: C 1149 PHE cc_start: 0.8141 (m-80) cc_final: 0.7937 (m-80) REVERT: C 1160 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6341 (pt0) REVERT: C 1164 MET cc_start: 0.7934 (mmm) cc_final: 0.7540 (pmm) REVERT: C 1186 TYR cc_start: 0.8116 (m-80) cc_final: 0.7820 (m-80) REVERT: C 1203 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8299 (tm-30) REVERT: C 1206 THR cc_start: 0.9144 (p) cc_final: 0.8785 (p) REVERT: C 1240 LYS cc_start: 0.8896 (pttt) cc_final: 0.8317 (ptmt) REVERT: C 1249 ASN cc_start: 0.7522 (p0) cc_final: 0.6558 (p0) REVERT: C 1251 LEU cc_start: 0.9152 (mt) cc_final: 0.8857 (mm) REVERT: C 1267 LYS cc_start: 0.9554 (tttt) cc_final: 0.9321 (ttpp) REVERT: C 1271 ASP cc_start: 0.9390 (m-30) cc_final: 0.9177 (m-30) REVERT: C 1274 GLU cc_start: 0.9359 (tt0) cc_final: 0.8851 (mt-10) REVERT: C 1389 ILE cc_start: 0.9501 (mt) cc_final: 0.9044 (mt) REVERT: C 1393 CYS cc_start: 0.9402 (m) cc_final: 0.8910 (m) REVERT: D 32 LEU cc_start: 0.9607 (mt) cc_final: 0.8255 (mt) REVERT: D 66 SER cc_start: 0.8056 (p) cc_final: 0.7832 (t) REVERT: D 67 TYR cc_start: 0.7263 (p90) cc_final: 0.6333 (p90) REVERT: D 73 LEU cc_start: 0.9200 (mt) cc_final: 0.8992 (mt) REVERT: D 80 LYS cc_start: 0.9065 (mttt) cc_final: 0.8735 (mtpt) REVERT: D 105 MET cc_start: 0.8890 (ttm) cc_final: 0.8674 (ttp) REVERT: D 118 PHE cc_start: 0.7510 (t80) cc_final: 0.6983 (t80) REVERT: D 141 LEU cc_start: 0.9417 (mt) cc_final: 0.9185 (mt) REVERT: D 180 MET cc_start: 0.7893 (ttp) cc_final: 0.7275 (tpp) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1843 time to fit residues: 82.2704 Evaluate side-chains 212 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1254 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1217 ASN C1254 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6894 Z= 0.261 Angle : 0.737 8.345 9336 Z= 0.396 Chirality : 0.048 0.198 1074 Planarity : 0.006 0.053 1160 Dihedral : 6.290 22.163 936 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.96 % Allowed : 1.24 % Favored : 97.80 % 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: -3.40 (0.25), residues: 846 helix: -1.44 (0.22), residues: 368 sheet: -3.32 (0.38), residues: 116 loop : -2.65 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 29 HIS 0.002 0.001 HIS B 15 PHE 0.046 0.002 PHE D 100 TYR 0.021 0.002 TYR B 67 ARG 0.012 0.001 ARG C1278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 255 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1184 MET cc_start: 0.8387 (mmp) cc_final: 0.8009 (mmm) REVERT: A 1186 TYR cc_start: 0.7972 (m-80) cc_final: 0.7730 (m-80) REVERT: A 1203 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8413 (tm-30) REVERT: A 1251 LEU cc_start: 0.9229 (mt) cc_final: 0.9019 (mm) REVERT: A 1271 ASP cc_start: 0.9401 (m-30) cc_final: 0.9040 (m-30) REVERT: A 1275 ILE cc_start: 0.9470 (mm) cc_final: 0.8886 (mm) REVERT: B 32 LEU cc_start: 0.9568 (mt) cc_final: 0.8712 (mt) REVERT: B 73 LEU cc_start: 0.9274 (mt) cc_final: 0.8915 (pp) REVERT: B 98 MET cc_start: 0.8981 (ttp) cc_final: 0.8755 (tmm) REVERT: B 142 MET cc_start: 0.8882 (mtp) cc_final: 0.8680 (mtp) REVERT: B 180 MET cc_start: 0.7900 (ttp) cc_final: 0.7198 (tpp) REVERT: C 1149 PHE cc_start: 0.8271 (m-80) cc_final: 0.8011 (m-80) REVERT: C 1184 MET cc_start: 0.8415 (mmp) cc_final: 0.8019 (mmm) REVERT: C 1203 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8450 (tm-30) REVERT: C 1271 ASP cc_start: 0.9357 (m-30) cc_final: 0.9096 (m-30) REVERT: C 1275 ILE cc_start: 0.9463 (mm) cc_final: 0.8866 (mm) REVERT: D 20 ARG cc_start: 0.7721 (tpp80) cc_final: 0.7520 (tpp80) REVERT: D 32 LEU cc_start: 0.9462 (mt) cc_final: 0.8362 (mt) REVERT: D 80 LYS cc_start: 0.9145 (mttt) cc_final: 0.8817 (mtmt) REVERT: D 98 MET cc_start: 0.9020 (ttp) cc_final: 0.8666 (tmm) REVERT: D 103 LEU cc_start: 0.9293 (tt) cc_final: 0.8931 (mt) REVERT: D 105 MET cc_start: 0.9055 (ttm) cc_final: 0.8639 (tmm) REVERT: D 118 PHE cc_start: 0.7641 (t80) cc_final: 0.7307 (t80) REVERT: D 134 GLN cc_start: 0.9092 (mp-120) cc_final: 0.8766 (mt0) REVERT: D 180 MET cc_start: 0.7939 (ttp) cc_final: 0.7333 (tpp) REVERT: D 183 ILE cc_start: 0.8798 (tt) cc_final: 0.8567 (tt) outliers start: 5 outliers final: 0 residues processed: 258 average time/residue: 0.1732 time to fit residues: 59.1059 Evaluate side-chains 201 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1216 HIS C1281 GLN D 46 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6894 Z= 0.235 Angle : 0.709 8.939 9336 Z= 0.378 Chirality : 0.048 0.219 1074 Planarity : 0.006 0.056 1160 Dihedral : 5.911 22.594 936 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.10 % Allowed : 3.57 % Favored : 95.33 % 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: -2.66 (0.26), residues: 846 helix: -0.79 (0.23), residues: 368 sheet: -2.55 (0.44), residues: 122 loop : -2.45 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 29 HIS 0.003 0.001 HIS C1299 PHE 0.044 0.002 PHE C1165 TYR 0.016 0.002 TYR D 67 ARG 0.012 0.001 ARG A1298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1184 MET cc_start: 0.8297 (mmp) cc_final: 0.7997 (mmm) REVERT: A 1203 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8680 (tm-30) REVERT: A 1211 THR cc_start: 0.8926 (p) cc_final: 0.8336 (t) REVERT: A 1213 MET cc_start: 0.8342 (ptm) cc_final: 0.7470 (ptm) REVERT: A 1225 PHE cc_start: 0.9001 (p90) cc_final: 0.8702 (p90) REVERT: A 1363 GLU cc_start: 0.8164 (tt0) cc_final: 0.7954 (tp30) REVERT: B 32 LEU cc_start: 0.9542 (mt) cc_final: 0.9009 (mt) REVERT: B 98 MET cc_start: 0.8977 (ttp) cc_final: 0.8763 (tmm) REVERT: B 99 PHE cc_start: 0.8874 (t80) cc_final: 0.8629 (t80) REVERT: B 180 MET cc_start: 0.7952 (ttp) cc_final: 0.7264 (tpp) REVERT: C 1149 PHE cc_start: 0.8149 (m-80) cc_final: 0.7920 (m-80) REVERT: C 1184 MET cc_start: 0.8405 (mmp) cc_final: 0.8081 (mmm) REVERT: C 1203 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8690 (tm-30) REVERT: C 1211 THR cc_start: 0.8918 (p) cc_final: 0.8270 (t) REVERT: C 1213 MET cc_start: 0.8422 (ptm) cc_final: 0.7640 (ptm) REVERT: C 1225 PHE cc_start: 0.8955 (p90) cc_final: 0.8531 (p90) REVERT: D 32 LEU cc_start: 0.9482 (mt) cc_final: 0.8738 (mt) REVERT: D 98 MET cc_start: 0.8970 (ttp) cc_final: 0.8655 (tmm) REVERT: D 99 PHE cc_start: 0.8757 (t80) cc_final: 0.8444 (t80) REVERT: D 105 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8588 (tmm) REVERT: D 118 PHE cc_start: 0.7581 (t80) cc_final: 0.7175 (t80) REVERT: D 133 MET cc_start: 0.9333 (mmm) cc_final: 0.9126 (mmm) REVERT: D 134 GLN cc_start: 0.9121 (mp-120) cc_final: 0.8750 (mt0) REVERT: D 141 LEU cc_start: 0.9346 (mt) cc_final: 0.9128 (mt) REVERT: D 180 MET cc_start: 0.7908 (ttp) cc_final: 0.7289 (tpp) REVERT: D 183 ILE cc_start: 0.8779 (tt) cc_final: 0.8564 (tt) outliers start: 6 outliers final: 2 residues processed: 245 average time/residue: 0.1682 time to fit residues: 55.3931 Evaluate side-chains 195 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.0270 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6894 Z= 0.367 Angle : 0.840 11.270 9336 Z= 0.443 Chirality : 0.050 0.224 1074 Planarity : 0.006 0.054 1160 Dihedral : 6.296 23.362 936 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.69 % Allowed : 3.30 % Favored : 96.02 % 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: -2.79 (0.27), residues: 846 helix: -0.83 (0.24), residues: 380 sheet: -2.17 (0.45), residues: 126 loop : -2.86 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 49 HIS 0.006 0.001 HIS C1299 PHE 0.032 0.003 PHE A1165 TYR 0.025 0.003 TYR D 67 ARG 0.008 0.001 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 222 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.7876 (mmt) cc_final: 0.7653 (mmp) REVERT: A 1184 MET cc_start: 0.8342 (mmp) cc_final: 0.8067 (mmm) REVERT: A 1203 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8769 (tm-30) REVERT: A 1225 PHE cc_start: 0.9195 (p90) cc_final: 0.8935 (p90) REVERT: A 1244 LEU cc_start: 0.8949 (tt) cc_final: 0.8740 (tp) REVERT: A 1387 PHE cc_start: 0.9239 (m-80) cc_final: 0.9031 (m-80) REVERT: A 1390 ILE cc_start: 0.8781 (pt) cc_final: 0.8342 (pt) REVERT: B 66 SER cc_start: 0.8485 (p) cc_final: 0.7845 (t) REVERT: B 98 MET cc_start: 0.8993 (ttp) cc_final: 0.8752 (tmm) REVERT: B 99 PHE cc_start: 0.8978 (t80) cc_final: 0.8680 (t80) REVERT: B 180 MET cc_start: 0.7961 (ttp) cc_final: 0.7328 (tpp) REVERT: C 1184 MET cc_start: 0.8224 (mmp) cc_final: 0.7986 (mmm) REVERT: C 1203 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8715 (tm-30) REVERT: D 20 ARG cc_start: 0.8707 (mmt90) cc_final: 0.8255 (tpp80) REVERT: D 32 LEU cc_start: 0.9576 (mt) cc_final: 0.9114 (mt) REVERT: D 66 SER cc_start: 0.8297 (p) cc_final: 0.8058 (t) REVERT: D 98 MET cc_start: 0.8982 (ttp) cc_final: 0.8662 (tmm) REVERT: D 99 PHE cc_start: 0.8970 (t80) cc_final: 0.8615 (t80) REVERT: D 105 MET cc_start: 0.9129 (ttp) cc_final: 0.8760 (tmm) REVERT: D 106 PHE cc_start: 0.8238 (m-80) cc_final: 0.7908 (m-80) REVERT: D 118 PHE cc_start: 0.7633 (t80) cc_final: 0.7154 (t80) REVERT: D 176 ARG cc_start: 0.6814 (mmm160) cc_final: 0.6591 (tpt170) REVERT: D 180 MET cc_start: 0.7719 (ttp) cc_final: 0.7132 (tpp) REVERT: D 183 ILE cc_start: 0.8799 (tt) cc_final: 0.8521 (tt) outliers start: 3 outliers final: 1 residues processed: 224 average time/residue: 0.1786 time to fit residues: 53.6036 Evaluate side-chains 180 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6894 Z= 0.224 Angle : 0.708 8.918 9336 Z= 0.372 Chirality : 0.048 0.260 1074 Planarity : 0.005 0.062 1160 Dihedral : 5.783 20.603 936 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.41 % Allowed : 2.61 % Favored : 96.98 % 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: -2.38 (0.27), residues: 846 helix: -0.45 (0.24), residues: 380 sheet: -2.03 (0.43), residues: 136 loop : -2.65 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 177 HIS 0.003 0.001 HIS C1299 PHE 0.034 0.002 PHE B 100 TYR 0.036 0.002 TYR B 127 ARG 0.011 0.001 ARG C1298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 0.808 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 1164 MET cc_start: 0.7907 (mmt) cc_final: 0.7609 (mmp) REVERT: A 1184 MET cc_start: 0.8295 (mmp) cc_final: 0.8030 (mmm) REVERT: A 1203 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8782 (tm-30) REVERT: A 1211 THR cc_start: 0.8665 (p) cc_final: 0.8136 (t) REVERT: A 1213 MET cc_start: 0.8265 (ptm) cc_final: 0.7538 (ptm) REVERT: A 1215 PHE cc_start: 0.8064 (m-80) cc_final: 0.7381 (m-80) REVERT: A 1363 GLU cc_start: 0.8313 (tt0) cc_final: 0.8010 (tp30) REVERT: A 1387 PHE cc_start: 0.9139 (m-80) cc_final: 0.8856 (m-80) REVERT: B 66 SER cc_start: 0.8488 (p) cc_final: 0.8172 (t) REVERT: B 98 MET cc_start: 0.8982 (ttp) cc_final: 0.8740 (tmm) REVERT: B 99 PHE cc_start: 0.8939 (t80) cc_final: 0.8673 (t80) REVERT: B 118 PHE cc_start: 0.7026 (t80) cc_final: 0.6732 (t80) REVERT: B 123 THR cc_start: 0.8891 (p) cc_final: 0.8643 (p) REVERT: B 127 TYR cc_start: 0.8656 (m-80) cc_final: 0.8404 (m-80) REVERT: B 141 LEU cc_start: 0.9514 (mt) cc_final: 0.9145 (mt) REVERT: B 180 MET cc_start: 0.7913 (ttp) cc_final: 0.7236 (tpp) REVERT: B 183 ILE cc_start: 0.8635 (tt) cc_final: 0.8382 (tt) REVERT: C 1184 MET cc_start: 0.8232 (mmp) cc_final: 0.8014 (mmm) REVERT: C 1211 THR cc_start: 0.8924 (p) cc_final: 0.8476 (t) REVERT: C 1213 MET cc_start: 0.8489 (ptm) cc_final: 0.8078 (ptm) REVERT: C 1225 PHE cc_start: 0.8953 (p90) cc_final: 0.8372 (p90) REVERT: C 1389 ILE cc_start: 0.9388 (mt) cc_final: 0.9135 (tt) REVERT: D 66 SER cc_start: 0.8352 (p) cc_final: 0.8046 (t) REVERT: D 80 LYS cc_start: 0.8485 (pttt) cc_final: 0.7754 (tppt) REVERT: D 98 MET cc_start: 0.8980 (ttp) cc_final: 0.8668 (tmm) REVERT: D 99 PHE cc_start: 0.8908 (t80) cc_final: 0.8635 (t80) REVERT: D 118 PHE cc_start: 0.7575 (t80) cc_final: 0.7222 (t80) REVERT: D 133 MET cc_start: 0.9335 (mmm) cc_final: 0.9129 (mmm) REVERT: D 134 GLN cc_start: 0.9085 (mp10) cc_final: 0.8825 (mt0) REVERT: D 141 LEU cc_start: 0.9446 (mt) cc_final: 0.9242 (mt) REVERT: D 180 MET cc_start: 0.7827 (ttp) cc_final: 0.7225 (tpp) REVERT: D 183 ILE cc_start: 0.8620 (tt) cc_final: 0.8381 (tt) outliers start: 1 outliers final: 1 residues processed: 229 average time/residue: 0.1778 time to fit residues: 55.0274 Evaluate side-chains 188 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6894 Z= 0.213 Angle : 0.692 9.721 9336 Z= 0.361 Chirality : 0.047 0.261 1074 Planarity : 0.005 0.052 1160 Dihedral : 5.492 19.821 936 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.27 % Allowed : 1.92 % Favored : 97.80 % 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: -2.00 (0.28), residues: 846 helix: -0.11 (0.24), residues: 380 sheet: -1.93 (0.44), residues: 138 loop : -2.45 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 132 HIS 0.002 0.000 HIS C1299 PHE 0.032 0.002 PHE B 100 TYR 0.028 0.002 TYR B 127 ARG 0.009 0.001 ARG A1371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.810 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 1164 MET cc_start: 0.7945 (mmt) cc_final: 0.7657 (mmp) REVERT: A 1184 MET cc_start: 0.8332 (mmp) cc_final: 0.8081 (mmm) REVERT: A 1203 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8779 (tm-30) REVERT: A 1211 THR cc_start: 0.8714 (p) cc_final: 0.8202 (t) REVERT: A 1213 MET cc_start: 0.8322 (ptm) cc_final: 0.7571 (ptm) REVERT: A 1215 PHE cc_start: 0.8074 (m-80) cc_final: 0.7587 (m-80) REVERT: A 1225 PHE cc_start: 0.9032 (p90) cc_final: 0.8605 (p90) REVERT: A 1363 GLU cc_start: 0.8213 (tt0) cc_final: 0.7966 (tp30) REVERT: A 1387 PHE cc_start: 0.9137 (m-80) cc_final: 0.8876 (m-80) REVERT: B 20 ARG cc_start: 0.8566 (mmt90) cc_final: 0.8365 (mmt90) REVERT: B 25 VAL cc_start: 0.8312 (m) cc_final: 0.7388 (m) REVERT: B 66 SER cc_start: 0.8458 (p) cc_final: 0.8172 (t) REVERT: B 80 LYS cc_start: 0.8426 (pttt) cc_final: 0.7795 (tppt) REVERT: B 99 PHE cc_start: 0.8921 (t80) cc_final: 0.8721 (t80) REVERT: B 118 PHE cc_start: 0.6940 (t80) cc_final: 0.6575 (t80) REVERT: B 123 THR cc_start: 0.8839 (p) cc_final: 0.8600 (p) REVERT: B 180 MET cc_start: 0.7924 (ttp) cc_final: 0.7246 (tpp) REVERT: B 183 ILE cc_start: 0.8661 (tt) cc_final: 0.8345 (tt) REVERT: C 1184 MET cc_start: 0.8262 (mmp) cc_final: 0.8012 (mmm) REVERT: C 1211 THR cc_start: 0.8903 (p) cc_final: 0.8456 (t) REVERT: C 1225 PHE cc_start: 0.8974 (p90) cc_final: 0.8457 (p90) REVERT: D 20 ARG cc_start: 0.8935 (tpp-160) cc_final: 0.8361 (tpp80) REVERT: D 66 SER cc_start: 0.8434 (p) cc_final: 0.8112 (t) REVERT: D 98 MET cc_start: 0.8940 (ttp) cc_final: 0.8661 (tmm) REVERT: D 99 PHE cc_start: 0.8864 (t80) cc_final: 0.8609 (t80) REVERT: D 118 PHE cc_start: 0.7364 (t80) cc_final: 0.6821 (t80) REVERT: D 133 MET cc_start: 0.9374 (mmm) cc_final: 0.9141 (mmm) REVERT: D 134 GLN cc_start: 0.9246 (mp10) cc_final: 0.8948 (mt0) REVERT: D 142 MET cc_start: 0.8962 (mtp) cc_final: 0.8729 (mtp) REVERT: D 180 MET cc_start: 0.7790 (ttp) cc_final: 0.6963 (tpp) REVERT: D 183 ILE cc_start: 0.8590 (tt) cc_final: 0.8343 (tt) REVERT: D 184 LEU cc_start: 0.9083 (mt) cc_final: 0.8863 (mt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1668 time to fit residues: 51.1603 Evaluate side-chains 182 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.0020 chunk 9 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6894 Z= 0.227 Angle : 0.680 9.483 9336 Z= 0.353 Chirality : 0.047 0.219 1074 Planarity : 0.005 0.051 1160 Dihedral : 5.385 18.453 936 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.27 % Allowed : 2.06 % Favored : 97.66 % 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: -1.77 (0.28), residues: 846 helix: 0.04 (0.24), residues: 382 sheet: -1.86 (0.44), residues: 138 loop : -2.27 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 29 HIS 0.003 0.001 HIS C1299 PHE 0.030 0.002 PHE D 100 TYR 0.014 0.002 TYR B 67 ARG 0.011 0.001 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.7961 (mmt) cc_final: 0.7714 (mmp) REVERT: A 1184 MET cc_start: 0.8305 (mmp) cc_final: 0.8084 (mmm) REVERT: A 1203 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8763 (tm-30) REVERT: A 1211 THR cc_start: 0.8759 (p) cc_final: 0.8268 (t) REVERT: A 1215 PHE cc_start: 0.8163 (m-80) cc_final: 0.7690 (m-80) REVERT: A 1225 PHE cc_start: 0.8973 (p90) cc_final: 0.8563 (p90) REVERT: A 1294 ILE cc_start: 0.8339 (mm) cc_final: 0.7432 (pt) REVERT: A 1363 GLU cc_start: 0.8217 (tt0) cc_final: 0.7869 (tp30) REVERT: A 1387 PHE cc_start: 0.9146 (m-80) cc_final: 0.8895 (m-80) REVERT: B 50 ILE cc_start: 0.8986 (pt) cc_final: 0.8613 (mm) REVERT: B 118 PHE cc_start: 0.6996 (t80) cc_final: 0.6747 (t80) REVERT: B 134 GLN cc_start: 0.9188 (mp10) cc_final: 0.8844 (mt0) REVERT: B 141 LEU cc_start: 0.9396 (mt) cc_final: 0.9061 (mt) REVERT: B 145 CYS cc_start: 0.8049 (t) cc_final: 0.7751 (p) REVERT: B 180 MET cc_start: 0.7912 (ttp) cc_final: 0.7234 (tpp) REVERT: B 183 ILE cc_start: 0.8648 (tt) cc_final: 0.8378 (tt) REVERT: C 1211 THR cc_start: 0.8941 (p) cc_final: 0.8241 (t) REVERT: C 1215 PHE cc_start: 0.8018 (m-80) cc_final: 0.7467 (m-80) REVERT: C 1225 PHE cc_start: 0.8964 (p90) cc_final: 0.8487 (p90) REVERT: C 1387 PHE cc_start: 0.9303 (m-80) cc_final: 0.8726 (m-80) REVERT: D 20 ARG cc_start: 0.8801 (mmt180) cc_final: 0.8431 (tpp80) REVERT: D 32 LEU cc_start: 0.9545 (mt) cc_final: 0.9239 (pp) REVERT: D 50 ILE cc_start: 0.8956 (pt) cc_final: 0.8557 (mm) REVERT: D 66 SER cc_start: 0.8555 (p) cc_final: 0.8251 (t) REVERT: D 98 MET cc_start: 0.8967 (ttp) cc_final: 0.8710 (tmm) REVERT: D 99 PHE cc_start: 0.8891 (t80) cc_final: 0.8638 (t80) REVERT: D 105 MET cc_start: 0.8911 (tmm) cc_final: 0.8589 (tmm) REVERT: D 118 PHE cc_start: 0.7309 (t80) cc_final: 0.6789 (t80) REVERT: D 133 MET cc_start: 0.9370 (mmm) cc_final: 0.9120 (mmm) REVERT: D 134 GLN cc_start: 0.9205 (mp10) cc_final: 0.8907 (mt0) REVERT: D 180 MET cc_start: 0.7795 (ttp) cc_final: 0.6915 (tpp) REVERT: D 183 ILE cc_start: 0.8624 (tt) cc_final: 0.8365 (tt) REVERT: D 184 LEU cc_start: 0.9102 (mt) cc_final: 0.8768 (mt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1659 time to fit residues: 51.0315 Evaluate side-chains 179 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6894 Z= 0.200 Angle : 0.691 9.754 9336 Z= 0.352 Chirality : 0.047 0.212 1074 Planarity : 0.005 0.050 1160 Dihedral : 5.204 16.641 936 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.27 % Allowed : 0.69 % Favored : 99.04 % 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: -1.62 (0.28), residues: 846 helix: 0.28 (0.25), residues: 374 sheet: -1.73 (0.44), residues: 140 loop : -2.32 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 29 HIS 0.002 0.000 HIS C1299 PHE 0.029 0.001 PHE B 100 TYR 0.013 0.001 TYR C1222 ARG 0.008 0.001 ARG C1298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8003 (mmt) cc_final: 0.7505 (mmp) REVERT: A 1184 MET cc_start: 0.8287 (mmp) cc_final: 0.8085 (mmm) REVERT: A 1203 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8801 (tm-30) REVERT: A 1208 LEU cc_start: 0.9113 (tp) cc_final: 0.8910 (tp) REVERT: A 1211 THR cc_start: 0.8780 (p) cc_final: 0.8193 (t) REVERT: A 1213 MET cc_start: 0.8224 (ptm) cc_final: 0.7512 (ptm) REVERT: A 1215 PHE cc_start: 0.8023 (m-80) cc_final: 0.7760 (m-80) REVERT: A 1225 PHE cc_start: 0.8957 (p90) cc_final: 0.8547 (p90) REVERT: A 1294 ILE cc_start: 0.8292 (mm) cc_final: 0.7327 (pt) REVERT: A 1363 GLU cc_start: 0.8167 (tt0) cc_final: 0.7835 (tp30) REVERT: A 1387 PHE cc_start: 0.9100 (m-80) cc_final: 0.8849 (m-80) REVERT: B 134 GLN cc_start: 0.9227 (mp10) cc_final: 0.8898 (mt0) REVERT: B 141 LEU cc_start: 0.9363 (mt) cc_final: 0.9032 (mt) REVERT: B 180 MET cc_start: 0.7825 (ttp) cc_final: 0.7222 (tpp) REVERT: C 1184 MET cc_start: 0.8565 (mmp) cc_final: 0.8234 (mmm) REVERT: C 1211 THR cc_start: 0.8847 (p) cc_final: 0.8355 (t) REVERT: C 1213 MET cc_start: 0.8109 (ptm) cc_final: 0.7281 (ptm) REVERT: C 1215 PHE cc_start: 0.7716 (m-80) cc_final: 0.7405 (m-80) REVERT: C 1225 PHE cc_start: 0.8907 (p90) cc_final: 0.8533 (p90) REVERT: C 1387 PHE cc_start: 0.9264 (m-80) cc_final: 0.8600 (m-80) REVERT: D 50 ILE cc_start: 0.8959 (pt) cc_final: 0.8477 (mm) REVERT: D 66 SER cc_start: 0.8684 (p) cc_final: 0.8406 (t) REVERT: D 99 PHE cc_start: 0.8853 (t80) cc_final: 0.8589 (t80) REVERT: D 118 PHE cc_start: 0.7219 (t80) cc_final: 0.6745 (t80) REVERT: D 133 MET cc_start: 0.9354 (mmm) cc_final: 0.9100 (mmm) REVERT: D 134 GLN cc_start: 0.9285 (mp10) cc_final: 0.8991 (mt0) REVERT: D 141 LEU cc_start: 0.9445 (mt) cc_final: 0.9182 (pp) REVERT: D 180 MET cc_start: 0.7674 (ttp) cc_final: 0.6844 (tpp) REVERT: D 183 ILE cc_start: 0.8578 (tt) cc_final: 0.8322 (tt) REVERT: D 184 LEU cc_start: 0.9088 (mt) cc_final: 0.8758 (mt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1635 time to fit residues: 50.1197 Evaluate side-chains 182 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.0170 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.0020 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6894 Z= 0.199 Angle : 0.678 10.013 9336 Z= 0.340 Chirality : 0.046 0.208 1074 Planarity : 0.005 0.051 1160 Dihedral : 5.044 15.784 936 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.27 % Allowed : 0.69 % Favored : 99.04 % 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: -1.44 (0.28), residues: 846 helix: 0.54 (0.25), residues: 372 sheet: -1.74 (0.43), residues: 140 loop : -2.32 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 29 HIS 0.002 0.000 HIS C1299 PHE 0.028 0.001 PHE B 100 TYR 0.013 0.001 TYR C1222 ARG 0.008 0.001 ARG C1298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8049 (mmt) cc_final: 0.7728 (mmp) REVERT: A 1203 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8782 (tm-30) REVERT: A 1208 LEU cc_start: 0.9094 (tp) cc_final: 0.8871 (tp) REVERT: A 1211 THR cc_start: 0.8727 (p) cc_final: 0.8287 (t) REVERT: A 1213 MET cc_start: 0.8205 (ptm) cc_final: 0.7652 (ptm) REVERT: A 1215 PHE cc_start: 0.8040 (m-80) cc_final: 0.7819 (m-80) REVERT: A 1225 PHE cc_start: 0.8804 (p90) cc_final: 0.8465 (p90) REVERT: A 1294 ILE cc_start: 0.8062 (mm) cc_final: 0.7392 (pt) REVERT: A 1363 GLU cc_start: 0.8184 (tt0) cc_final: 0.7842 (tp30) REVERT: A 1387 PHE cc_start: 0.9089 (m-80) cc_final: 0.8854 (m-80) REVERT: B 123 THR cc_start: 0.8853 (p) cc_final: 0.8160 (t) REVERT: B 127 TYR cc_start: 0.8808 (m-10) cc_final: 0.8604 (m-10) REVERT: B 180 MET cc_start: 0.7971 (ttp) cc_final: 0.7424 (tpt) REVERT: C 1211 THR cc_start: 0.8850 (p) cc_final: 0.8425 (t) REVERT: C 1215 PHE cc_start: 0.7721 (m-80) cc_final: 0.6684 (m-80) REVERT: C 1225 PHE cc_start: 0.8983 (p90) cc_final: 0.8600 (p90) REVERT: C 1387 PHE cc_start: 0.9276 (m-80) cc_final: 0.8504 (m-80) REVERT: D 50 ILE cc_start: 0.8932 (pt) cc_final: 0.8449 (mm) REVERT: D 66 SER cc_start: 0.8597 (p) cc_final: 0.8365 (t) REVERT: D 99 PHE cc_start: 0.8867 (t80) cc_final: 0.8628 (t80) REVERT: D 118 PHE cc_start: 0.7094 (t80) cc_final: 0.6831 (t80) REVERT: D 133 MET cc_start: 0.9327 (mmm) cc_final: 0.9036 (mmm) REVERT: D 134 GLN cc_start: 0.9258 (mp10) cc_final: 0.8957 (mt0) REVERT: D 141 LEU cc_start: 0.9436 (mt) cc_final: 0.9161 (pp) REVERT: D 142 MET cc_start: 0.8715 (mtp) cc_final: 0.8495 (mtm) REVERT: D 180 MET cc_start: 0.7694 (ttp) cc_final: 0.6832 (tpp) REVERT: D 183 ILE cc_start: 0.8551 (tt) cc_final: 0.8321 (tt) REVERT: D 184 LEU cc_start: 0.9101 (mt) cc_final: 0.8725 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1695 time to fit residues: 50.8657 Evaluate side-chains 185 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 83 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6894 Z= 0.210 Angle : 0.698 9.962 9336 Z= 0.351 Chirality : 0.047 0.191 1074 Planarity : 0.005 0.051 1160 Dihedral : 5.009 22.339 936 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.27 % Allowed : 0.69 % Favored : 99.04 % 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: -1.29 (0.28), residues: 846 helix: 0.61 (0.25), residues: 372 sheet: -1.74 (0.45), residues: 130 loop : -2.14 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 29 HIS 0.002 0.000 HIS C1299 PHE 0.030 0.001 PHE D 100 TYR 0.013 0.001 TYR C1222 ARG 0.012 0.001 ARG B 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8008 (mmt) cc_final: 0.7486 (mmp) REVERT: A 1203 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8777 (tm-30) REVERT: A 1208 LEU cc_start: 0.9100 (tp) cc_final: 0.8878 (tp) REVERT: A 1211 THR cc_start: 0.8728 (p) cc_final: 0.8166 (t) REVERT: A 1213 MET cc_start: 0.8242 (ptm) cc_final: 0.8028 (tmm) REVERT: A 1225 PHE cc_start: 0.8817 (p90) cc_final: 0.8446 (p90) REVERT: A 1294 ILE cc_start: 0.8085 (mm) cc_final: 0.7353 (pt) REVERT: A 1387 PHE cc_start: 0.9097 (m-80) cc_final: 0.8863 (m-80) REVERT: B 20 ARG cc_start: 0.8328 (mmt90) cc_final: 0.8103 (mmt-90) REVERT: B 50 ILE cc_start: 0.9011 (pt) cc_final: 0.8592 (mm) REVERT: B 123 THR cc_start: 0.8778 (p) cc_final: 0.8527 (t) REVERT: B 132 TRP cc_start: 0.8190 (m-10) cc_final: 0.7966 (t60) REVERT: B 141 LEU cc_start: 0.9457 (mt) cc_final: 0.9084 (mt) REVERT: B 142 MET cc_start: 0.8919 (mtp) cc_final: 0.8480 (mtm) REVERT: B 145 CYS cc_start: 0.8171 (t) cc_final: 0.7958 (p) REVERT: B 180 MET cc_start: 0.7963 (ttp) cc_final: 0.7229 (tpp) REVERT: C 1160 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7200 (tp30) REVERT: C 1184 MET cc_start: 0.8650 (mmp) cc_final: 0.8297 (mmm) REVERT: C 1211 THR cc_start: 0.8793 (p) cc_final: 0.8394 (t) REVERT: C 1225 PHE cc_start: 0.8949 (p90) cc_final: 0.8557 (p90) REVERT: C 1387 PHE cc_start: 0.9255 (m-80) cc_final: 0.8576 (m-80) REVERT: D 50 ILE cc_start: 0.8923 (pt) cc_final: 0.8440 (mm) REVERT: D 73 LEU cc_start: 0.9169 (mt) cc_final: 0.8960 (mp) REVERT: D 99 PHE cc_start: 0.8882 (t80) cc_final: 0.8620 (t80) REVERT: D 118 PHE cc_start: 0.7205 (t80) cc_final: 0.6834 (t80) REVERT: D 133 MET cc_start: 0.9334 (mmm) cc_final: 0.9061 (mmm) REVERT: D 134 GLN cc_start: 0.9262 (mp10) cc_final: 0.8981 (mt0) REVERT: D 141 LEU cc_start: 0.9422 (mt) cc_final: 0.9156 (pp) REVERT: D 180 MET cc_start: 0.7736 (ttp) cc_final: 0.6938 (tpp) REVERT: D 183 ILE cc_start: 0.8656 (tt) cc_final: 0.8192 (tt) REVERT: D 184 LEU cc_start: 0.9021 (mt) cc_final: 0.8726 (mt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1644 time to fit residues: 48.2020 Evaluate side-chains 176 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 GLN ** C1321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.073781 restraints weight = 48836.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076993 restraints weight = 29980.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079548 restraints weight = 21150.593| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6894 Z= 0.238 Angle : 0.704 10.405 9336 Z= 0.362 Chirality : 0.046 0.182 1074 Planarity : 0.005 0.054 1160 Dihedral : 5.188 22.275 936 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.27 % Allowed : 0.55 % Favored : 99.18 % 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: -1.49 (0.28), residues: 846 helix: 0.45 (0.24), residues: 372 sheet: -2.01 (0.44), residues: 124 loop : -2.17 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 132 HIS 0.004 0.001 HIS C1216 PHE 0.038 0.002 PHE C1215 TYR 0.014 0.002 TYR C1303 ARG 0.009 0.001 ARG C1298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.42 seconds wall clock time: 33 minutes 23.60 seconds (2003.60 seconds total)