Starting phenix.real_space_refine on Fri Feb 14 06:06:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c14_7328/02_2025/6c14_7328.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c14_7328/02_2025/6c14_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/cci-nas-00/data/ceres_data/6c14_7328/02_2025/6c14_7328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c14_7328/02_2025/6c14_7328.map" model { file = "/net/cci-nas-00/data/ceres_data/6c14_7328/02_2025/6c14_7328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c14_7328/02_2025/6c14_7328.cif" } 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. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.86, per 1000 atoms: 0.87 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 - 3.00 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: 1.62 Conformation dependent library (CDL) restraints added in 1.4 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: 0.70 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: 1.81 Time building geometry restraints manager: 1.87 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: 0.00 - 3.55: 9211 3.55 - 7.10: 113 7.10 - 10.65: 10 10.65 - 14.21: 0 14.21 - 17.76: 2 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 3.040 nonbonded pdb=" OD2 ASP C1319 " pdb=" OG1 THR C1322 " model vdw 2.264 3.040 nonbonded pdb=" O TRP D 29 " pdb=" OG1 THR D 33 " model vdw 2.322 3.040 nonbonded pdb=" O TRP B 29 " pdb=" OG1 THR B 33 " model vdw 2.323 3.040 nonbonded pdb=" OE1 GLU A1203 " pdb=" OG1 THR A1206 " model vdw 2.329 3.040 ... (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 Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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: 1.970 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 20.990 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 1149 PHE cc_start: 0.8145 (m-80) cc_final: 0.7934 (m-80) REVERT: A 1160 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6129 (tp30) REVERT: A 1186 TYR cc_start: 0.8093 (m-80) cc_final: 0.7751 (m-80) REVERT: A 1203 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8336 (tm-30) REVERT: A 1240 LYS cc_start: 0.8893 (pttt) cc_final: 0.8337 (ptmt) REVERT: A 1249 ASN cc_start: 0.7586 (p0) cc_final: 0.6409 (t0) REVERT: A 1270 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8697 (pm20) REVERT: A 1271 ASP cc_start: 0.9376 (m-30) cc_final: 0.9134 (m-30) REVERT: A 1274 GLU cc_start: 0.9366 (tt0) cc_final: 0.8850 (mt-10) REVERT: A 1389 ILE cc_start: 0.9392 (mt) cc_final: 0.9080 (tt) REVERT: A 1393 CYS cc_start: 0.9577 (m) cc_final: 0.9117 (m) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1856 time to fit residues: 19.1790 Evaluate side-chains 56 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.253 Evaluate side-chains 76 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 20 ARG cc_start: 0.6497 (mmp80) cc_final: 0.6060 (tpt170) REVERT: B 32 LEU cc_start: 0.9639 (mt) cc_final: 0.9127 (mm) REVERT: B 66 SER cc_start: 0.8171 (p) cc_final: 0.7953 (t) REVERT: B 123 THR cc_start: 0.8842 (p) cc_final: 0.8601 (p) REVERT: B 127 TYR cc_start: 0.8919 (m-10) cc_final: 0.8577 (m-80) REVERT: B 133 MET cc_start: 0.9448 (mmp) cc_final: 0.9235 (mmm) REVERT: B 180 MET cc_start: 0.7823 (ttp) cc_final: 0.7174 (tpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1018 time to fit residues: 8.7501 Evaluate side-chains 52 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.0010 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1254 GLN A1299 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061987 restraints weight = 15813.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064321 restraints weight = 9208.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066093 restraints weight = 6290.012| |-----------------------------------------------------------------------------| r_work (final): 0.3283 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.109094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.093327 restraints weight = 4599.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095748 restraints weight = 3221.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.097678 restraints weight = 2415.963| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3689 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= 0.287 Angle : 0.800 8.199 9336 Z= 0.433 Chirality : 0.050 0.193 1074 Planarity : 0.006 0.049 1160 Dihedral : 6.397 24.226 936 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.37 % Allowed : 1.65 % 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: -3.31 (0.25), residues: 846 helix: -1.29 (0.23), residues: 368 sheet: -3.39 (0.36), residues: 122 loop : -2.63 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 49 HIS 0.002 0.000 HIS A1216 PHE 0.043 0.002 PHE D 100 TYR 0.019 0.003 TYR D 67 ARG 0.008 0.001 ARG A1219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1149 PHE cc_start: 0.8355 (m-80) cc_final: 0.8076 (m-80) REVERT: A 1184 MET cc_start: 0.8317 (mmp) cc_final: 0.8052 (mmm) REVERT: A 1186 TYR cc_start: 0.7950 (m-80) cc_final: 0.7667 (m-80) REVERT: A 1271 ASP cc_start: 0.9372 (m-30) cc_final: 0.9034 (m-30) REVERT: A 1275 ILE cc_start: 0.9519 (mm) cc_final: 0.8937 (mm) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1585 time to fit residues: 11.6638 Evaluate side-chains 52 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.253 Evaluate side-chains 70 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: B 20 ARG cc_start: 0.6559 (mmp80) cc_final: 0.6269 (tpt170) REVERT: B 32 LEU cc_start: 0.9509 (mt) cc_final: 0.9186 (mt) REVERT: B 73 LEU cc_start: 0.9038 (mt) cc_final: 0.8574 (pp) REVERT: B 98 MET cc_start: 0.8984 (ttp) cc_final: 0.8703 (tmm) REVERT: B 100 PHE cc_start: 0.9042 (m-80) cc_final: 0.8842 (m-80) REVERT: B 180 MET cc_start: 0.7849 (ttp) cc_final: 0.7126 (tpp) outliers start: 3 outliers final: 0 residues processed: 68 average time/residue: 0.1012 time to fit residues: 7.8412 Evaluate side-chains 51 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.9074 > 50: distance: 1 - 2: 10.341 distance: 2 - 3: 8.986 distance: 2 - 5: 9.521 distance: 3 - 4: 32.653 distance: 3 - 6: 22.483 distance: 6 - 7: 32.152 distance: 7 - 8: 19.721 distance: 7 - 10: 26.815 distance: 8 - 9: 17.343 distance: 8 - 13: 32.248 distance: 10 - 11: 28.612 distance: 10 - 12: 42.189 distance: 13 - 14: 8.482 distance: 14 - 15: 18.874 distance: 14 - 17: 17.669 distance: 15 - 16: 10.519 distance: 15 - 21: 8.794 distance: 17 - 18: 28.754 distance: 18 - 19: 35.853 distance: 18 - 20: 17.680 distance: 21 - 22: 17.003 distance: 22 - 23: 11.117 distance: 22 - 25: 11.869 distance: 23 - 24: 7.333 distance: 23 - 32: 29.303 distance: 25 - 26: 10.872 distance: 26 - 27: 33.845 distance: 27 - 28: 7.298 distance: 28 - 29: 4.587 distance: 29 - 30: 10.222 distance: 29 - 31: 16.128 distance: 32 - 33: 20.676 distance: 33 - 34: 9.893 distance: 33 - 36: 11.639 distance: 34 - 35: 17.583 distance: 34 - 40: 28.046 distance: 36 - 37: 22.579 distance: 37 - 38: 12.895 distance: 37 - 39: 5.556 distance: 40 - 41: 22.721 distance: 41 - 42: 14.101 distance: 41 - 44: 23.909 distance: 42 - 43: 27.057 distance: 42 - 47: 29.114 distance: 44 - 45: 17.234 distance: 44 - 46: 20.187 distance: 47 - 48: 23.786 distance: 48 - 49: 34.247 distance: 49 - 50: 40.971 distance: 49 - 51: 7.301 distance: 51 - 52: 19.793 distance: 52 - 53: 21.227 distance: 52 - 55: 11.766 distance: 53 - 54: 20.955 distance: 53 - 59: 49.283 distance: 55 - 56: 30.997 distance: 56 - 57: 32.023 distance: 56 - 58: 9.877 distance: 59 - 60: 3.849 distance: 60 - 61: 3.997 distance: 60 - 63: 16.502 distance: 61 - 71: 18.384 distance: 63 - 64: 42.761 distance: 64 - 65: 16.894 distance: 64 - 66: 9.255 distance: 65 - 67: 5.746 distance: 66 - 68: 6.740 distance: 67 - 69: 5.281 distance: 68 - 69: 22.696 distance: 69 - 70: 11.857 distance: 71 - 72: 20.592 distance: 72 - 73: 15.692 distance: 72 - 75: 10.363 distance: 73 - 74: 15.738 distance: 73 - 77: 20.559 distance: 75 - 76: 19.899 distance: 77 - 78: 17.787 distance: 78 - 79: 10.546 distance: 78 - 81: 31.737 distance: 79 - 80: 25.650 distance: 79 - 82: 33.076 distance: 82 - 83: 11.638 distance: 83 - 84: 22.139 distance: 83 - 86: 14.767 distance: 84 - 85: 19.254