Starting phenix.real_space_refine on Sat May 10 03:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9y_44392/05_2025/9b9y_44392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9y_44392/05_2025/9b9y_44392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9y_44392/05_2025/9b9y_44392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9y_44392/05_2025/9b9y_44392.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9y_44392/05_2025/9b9y_44392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9y_44392/05_2025/9b9y_44392.cif" } resolution = 3.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 3095 2.51 5 N 786 2.21 5 O 836 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4753 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3775 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 464} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'7DY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.69 Number of scatterers: 4753 At special positions: 0 Unit cell: (65.27, 88.81, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 32 16.00 F 3 9.00 O 836 8.00 N 786 7.00 C 3095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " 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: 1.24 Conformation dependent library (CDL) restraints added in 577.3 milliseconds 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 5 sheets defined 61.1% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'R' and resid 104 through 109 removed outlier: 3.860A pdb=" N PHE R 108 " --> pdb=" O ASP R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 144 Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 150 through 152 No H-bonds generated for 'chain 'R' and resid 150 through 152' Processing helix chain 'R' and resid 153 through 176 removed outlier: 3.910A pdb=" N GLY R 157 " --> pdb=" O TYR R 153 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER R 167 " --> pdb=" O ASP R 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE R 170 " --> pdb=" O GLY R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 220 Processing helix chain 'R' and resid 220 through 228 removed outlier: 4.667A pdb=" N LYS R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 250 Processing helix chain 'R' and resid 251 through 254 Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.529A pdb=" N LEU R 260 " --> pdb=" O ASN R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 1005 removed outlier: 3.610A pdb=" N LEU R 276 " --> pdb=" O ASP R 272 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE R1002 " --> pdb=" O TRP R 299 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER R1005 " --> pdb=" O GLY R1001 " (cutoff:3.500A) Processing helix chain 'R' and resid 1006 through 1007 No H-bonds generated for 'chain 'R' and resid 1006 through 1007' Processing helix chain 'R' and resid 1008 through 1012 removed outlier: 3.657A pdb=" N TYR R1011 " --> pdb=" O ASN R1008 " (cutoff:3.500A) Processing helix chain 'R' and resid 1015 through 1027 Processing helix chain 'R' and resid 1047 through 1059 Processing helix chain 'R' and resid 1076 through 1090 Processing helix chain 'R' and resid 1101 through 1112 Processing helix chain 'R' and resid 1125 through 1134 removed outlier: 3.585A pdb=" N LEU R1134 " --> pdb=" O GLU R1130 " (cutoff:3.500A) Processing helix chain 'R' and resid 1145 through 1150 removed outlier: 3.834A pdb=" N ILE R1150 " --> pdb=" O LEU R1146 " (cutoff:3.500A) Processing helix chain 'R' and resid 1162 through 1177 Processing helix chain 'R' and resid 1181 through 1195 Processing helix chain 'R' and resid 1196 through 368 removed outlier: 3.779A pdb=" N ARG R 336 " --> pdb=" O SER R1196 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 372 through 383 Processing helix chain 'R' and resid 384 through 401 Proline residue: R 394 - end of helix removed outlier: 3.859A pdb=" N TYR R 397 " --> pdb=" O ASN R 393 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA R 398 " --> pdb=" O PRO R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 412 Processing sheet with id=AA1, first strand: chain 'R' and resid 1093 through 1096 removed outlier: 8.596A pdb=" N LYS R1094 " --> pdb=" O MET R1067 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE R1069 " --> pdb=" O LYS R1094 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE R1096 " --> pdb=" O PHE R1069 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE R1071 " --> pdb=" O ILE R1096 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL R1033 " --> pdb=" O ARG R1068 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE R1070 " --> pdb=" O VAL R1033 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE R1035 " --> pdb=" O ILE R1070 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE R1072 " --> pdb=" O PHE R1035 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE R1037 " --> pdb=" O ILE R1072 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR R1034 " --> pdb=" O PHE R1114 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE R1116 " --> pdb=" O THR R1034 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET R1036 " --> pdb=" O ILE R1116 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL R1115 " --> pdb=" O ILE R1139 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER R1141 " --> pdb=" O VAL R1115 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE R1117 " --> pdb=" O SER R1141 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL R1158 " --> pdb=" O PRO R1138 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA R1140 " --> pdb=" O VAL R1158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 12 through 13 removed outlier: 6.814A pdb=" N VAL N 12 " --> pdb=" O SER N 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.687A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLY N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET N 34 " --> pdb=" O GLY N 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.687A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLY N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET N 34 " --> pdb=" O GLY N 50 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 864 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: 1.42 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 742 1.31 - 1.43: 1334 1.43 - 1.56: 2730 1.56 - 1.69: 0 1.69 - 1.82: 51 Bond restraints: 4857 Sorted by residual: bond pdb=" CBE 7DY R1201 " pdb=" NAI 7DY R1201 " ideal model delta sigma weight residual 1.152 1.455 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" CAQ 7DY R1201 " pdb=" NAG 7DY R1201 " ideal model delta sigma weight residual 1.343 1.457 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" CAX 7DY R1201 " pdb=" CBE 7DY R1201 " ideal model delta sigma weight residual 1.428 1.524 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CBD 7DY R1201 " pdb=" OAE 7DY R1201 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CBC 7DY R1201 " pdb="CLAA 7DY R1201 " ideal model delta sigma weight residual 1.736 1.784 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 4852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.89: 6573 13.89 - 27.78: 0 27.78 - 41.67: 0 41.67 - 55.55: 0 55.55 - 69.44: 1 Bond angle restraints: 6574 Sorted by residual: angle pdb=" CAX 7DY R1201 " pdb=" CBE 7DY R1201 " pdb=" NAI 7DY R1201 " ideal model delta sigma weight residual 180.00 110.56 69.44 3.00e+00 1.11e-01 5.36e+02 angle pdb=" N VAL N 48 " pdb=" CA VAL N 48 " pdb=" C VAL N 48 " ideal model delta sigma weight residual 110.72 115.30 -4.58 1.01e+00 9.80e-01 2.05e+01 angle pdb=" CB MET R1193 " pdb=" CG MET R1193 " pdb=" SD MET R1193 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CAQ 7DY R1201 " pdb=" CAP 7DY R1201 " pdb=" OAE 7DY R1201 " ideal model delta sigma weight residual 101.99 113.29 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N TYR R1109 " pdb=" CA TYR R1109 " pdb=" C TYR R1109 " ideal model delta sigma weight residual 111.28 108.05 3.23 1.09e+00 8.42e-01 8.77e+00 ... (remaining 6569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2570 17.95 - 35.90: 249 35.90 - 53.85: 45 53.85 - 71.79: 7 71.79 - 89.74: 2 Dihedral angle restraints: 2873 sinusoidal: 1135 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual -86.00 -130.51 44.51 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 95 " pdb=" CB CYS N 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.69 37.31 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" C VAL N 48 " pdb=" N VAL N 48 " pdb=" CA VAL N 48 " pdb=" CB VAL N 48 " ideal model delta harmonic sigma weight residual -122.00 -131.44 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 2870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 652 0.069 - 0.137: 94 0.137 - 0.206: 2 0.206 - 0.274: 1 0.274 - 0.343: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CB ILE N 28 " pdb=" CA ILE N 28 " pdb=" CG1 ILE N 28 " pdb=" CG2 ILE N 28 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA VAL N 48 " pdb=" N VAL N 48 " pdb=" C VAL N 48 " pdb=" CB VAL N 48 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA SER R1111 " pdb=" N SER R1111 " pdb=" C SER R1111 " pdb=" CB SER R1111 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 747 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ 7DY R1201 " 0.156 2.00e-02 2.50e+03 2.59e-01 1.51e+03 pdb=" CAM 7DY R1201 " 0.051 2.00e-02 2.50e+03 pdb=" CAR 7DY R1201 " -0.116 2.00e-02 2.50e+03 pdb=" CAS 7DY R1201 " 0.103 2.00e-02 2.50e+03 pdb=" CAX 7DY R1201 " -0.215 2.00e-02 2.50e+03 pdb=" CAY 7DY R1201 " 0.001 2.00e-02 2.50e+03 pdb=" CAZ 7DY R1201 " -0.158 2.00e-02 2.50e+03 pdb=" CBE 7DY R1201 " -0.393 2.00e-02 2.50e+03 pdb=" NAI 7DY R1201 " 0.573 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 112 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO R 113 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 113 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 104 " 0.014 2.00e-02 2.50e+03 1.39e-02 3.38e+00 pdb=" CG PHE N 104 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE N 104 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE N 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE N 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 104 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE N 104 " -0.002 2.00e-02 2.50e+03 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1284 2.81 - 3.33: 4582 3.33 - 3.86: 7769 3.86 - 4.38: 8615 4.38 - 4.90: 15216 Nonbonded interactions: 37466 Sorted by model distance: nonbonded pdb=" OG SER R 265 " pdb=" O PHE R 268 " model vdw 2.288 3.040 nonbonded pdb=" O ARG R 148 " pdb=" NH1 ARG R 230 " model vdw 2.320 3.120 nonbonded pdb=" NH1 ARG R 214 " pdb=" OD1 ASP R 338 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP R 272 " pdb=" OG1 THR R 274 " model vdw 2.331 3.040 nonbonded pdb=" O GLY R 166 " pdb=" NAI 7DY R1201 " model vdw 2.345 3.120 ... (remaining 37461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.006 0.303 4859 Z= 0.306 Angle : 1.158 69.442 6578 Z= 0.479 Chirality : 0.048 0.343 750 Planarity : 0.010 0.259 813 Dihedral : 14.200 89.743 1751 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.20 % Allowed : 0.00 % Favored : 99.80 % 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: 0.65 (0.33), residues: 597 helix: 1.28 (0.27), residues: 312 sheet: 1.76 (0.58), residues: 81 loop : -1.49 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 36 HIS 0.003 0.000 HIS R 219 PHE 0.031 0.002 PHE N 104 TYR 0.012 0.001 TYR N 94 ARG 0.006 0.000 ARG R 145 Details of bonding type rmsd hydrogen bonds : bond 0.14450 ( 287) hydrogen bonds : angle 5.55682 ( 864) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.18744 ( 4) covalent geometry : bond 0.00621 ( 4857) covalent geometry : angle 1.15762 ( 6574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.510 Fit side-chains REVERT: R 135 LEU cc_start: 0.9409 (mm) cc_final: 0.9141 (mm) REVERT: R 139 CYS cc_start: 0.8651 (m) cc_final: 0.8363 (m) REVERT: R 256 ASN cc_start: 0.9270 (p0) cc_final: 0.8637 (p0) REVERT: R 277 MET cc_start: 0.8348 (tmm) cc_final: 0.8001 (tmm) REVERT: R 1168 ASN cc_start: 0.8852 (m110) cc_final: 0.8514 (m110) REVERT: R 1187 ASN cc_start: 0.8991 (m-40) cc_final: 0.8714 (m-40) REVERT: N 36 TRP cc_start: 0.9101 (m100) cc_final: 0.8123 (m100) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1355 time to fit residues: 27.9556 Evaluate side-chains 129 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** 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 = 0.3308 r_free = 0.3308 target = 0.093727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.073078 restraints weight = 9809.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.075883 restraints weight = 5004.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077774 restraints weight = 3279.802| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4859 Z= 0.190 Angle : 0.590 8.483 6578 Z= 0.301 Chirality : 0.043 0.168 750 Planarity : 0.004 0.037 813 Dihedral : 4.902 38.658 670 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.77 % Allowed : 12.38 % Favored : 85.85 % 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: 1.43 (0.34), residues: 597 helix: 2.04 (0.28), residues: 320 sheet: 1.88 (0.56), residues: 82 loop : -1.43 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 299 HIS 0.003 0.001 HIS R 219 PHE 0.015 0.001 PHE N 29 TYR 0.009 0.001 TYR R 215 ARG 0.006 0.001 ARG R 230 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 287) hydrogen bonds : angle 3.96542 ( 864) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.85093 ( 4) covalent geometry : bond 0.00441 ( 4857) covalent geometry : angle 0.59023 ( 6574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.577 Fit side-chains REVERT: R 230 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: R 277 MET cc_start: 0.8398 (tmm) cc_final: 0.8097 (tmm) REVERT: N 36 TRP cc_start: 0.9030 (m100) cc_final: 0.7390 (m100) REVERT: N 82 MET cc_start: 0.8613 (pmm) cc_final: 0.8409 (pmm) outliers start: 9 outliers final: 8 residues processed: 132 average time/residue: 0.1309 time to fit residues: 23.2307 Evaluate side-chains 126 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 83 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.073405 restraints weight = 9845.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076316 restraints weight = 4929.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078279 restraints weight = 3184.487| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4859 Z= 0.145 Angle : 0.563 8.107 6578 Z= 0.286 Chirality : 0.042 0.153 750 Planarity : 0.003 0.027 813 Dihedral : 4.497 33.607 670 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.55 % Allowed : 15.13 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.34), residues: 597 helix: 2.24 (0.28), residues: 321 sheet: 1.74 (0.56), residues: 83 loop : -1.30 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 299 HIS 0.003 0.000 HIS R 219 PHE 0.010 0.001 PHE N 29 TYR 0.009 0.001 TYR R1109 ARG 0.004 0.000 ARG R 230 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 287) hydrogen bonds : angle 3.79855 ( 864) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.16228 ( 4) covalent geometry : bond 0.00336 ( 4857) covalent geometry : angle 0.56196 ( 6574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.505 Fit side-chains REVERT: R 240 MET cc_start: 0.8768 (tmm) cc_final: 0.8056 (ttp) REVERT: R 277 MET cc_start: 0.8304 (tmm) cc_final: 0.7968 (tmm) REVERT: N 36 TRP cc_start: 0.9064 (m100) cc_final: 0.7613 (m100) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.1324 time to fit residues: 23.4566 Evaluate side-chains 126 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.074046 restraints weight = 9879.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.076966 restraints weight = 4971.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078926 restraints weight = 3221.146| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4859 Z= 0.131 Angle : 0.565 8.374 6578 Z= 0.284 Chirality : 0.042 0.167 750 Planarity : 0.003 0.032 813 Dihedral : 4.159 32.704 670 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.54 % Allowed : 15.32 % Favored : 81.14 % 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: 1.78 (0.34), residues: 597 helix: 2.35 (0.28), residues: 321 sheet: 1.86 (0.56), residues: 83 loop : -1.27 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.008 0.001 PHE N 29 TYR 0.007 0.001 TYR R1109 ARG 0.010 0.001 ARG R 230 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 287) hydrogen bonds : angle 3.74875 ( 864) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.68003 ( 4) covalent geometry : bond 0.00304 ( 4857) covalent geometry : angle 0.56491 ( 6574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.546 Fit side-chains REVERT: R 277 MET cc_start: 0.8225 (tmm) cc_final: 0.7880 (tmm) REVERT: N 36 TRP cc_start: 0.9053 (m100) cc_final: 0.7640 (m100) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.1413 time to fit residues: 24.3975 Evaluate side-chains 128 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.074494 restraints weight = 10001.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077434 restraints weight = 4982.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.079416 restraints weight = 3186.882| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4859 Z= 0.119 Angle : 0.574 8.323 6578 Z= 0.291 Chirality : 0.042 0.177 750 Planarity : 0.003 0.035 813 Dihedral : 3.930 32.286 670 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.14 % Allowed : 16.50 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.34), residues: 597 helix: 2.45 (0.28), residues: 319 sheet: 2.00 (0.57), residues: 83 loop : -1.27 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.007 0.001 PHE R 268 TYR 0.008 0.001 TYR R1109 ARG 0.009 0.000 ARG R 230 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 287) hydrogen bonds : angle 3.75166 ( 864) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.61104 ( 4) covalent geometry : bond 0.00271 ( 4857) covalent geometry : angle 0.57374 ( 6574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.522 Fit side-chains REVERT: R 230 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7855 (mmt180) REVERT: R 277 MET cc_start: 0.8264 (tmm) cc_final: 0.7902 (tmm) REVERT: R 1195 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8853 (t80) REVERT: R 371 MET cc_start: 0.7166 (tpt) cc_final: 0.6963 (tpp) REVERT: N 36 TRP cc_start: 0.9035 (m100) cc_final: 0.7615 (m100) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.1328 time to fit residues: 23.3305 Evaluate side-chains 133 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 0.0030 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.072474 restraints weight = 9941.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075336 restraints weight = 4986.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.077287 restraints weight = 3218.282| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4859 Z= 0.161 Angle : 0.602 8.727 6578 Z= 0.303 Chirality : 0.044 0.191 750 Planarity : 0.003 0.035 813 Dihedral : 3.909 32.327 670 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.13 % Allowed : 17.49 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.35), residues: 597 helix: 2.46 (0.28), residues: 319 sheet: 1.99 (0.56), residues: 83 loop : -1.30 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R1082 HIS 0.002 0.000 HIS R 219 PHE 0.011 0.001 PHE N 29 TYR 0.007 0.001 TYR R 215 ARG 0.008 0.000 ARG R 230 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 287) hydrogen bonds : angle 3.79770 ( 864) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.62331 ( 4) covalent geometry : bond 0.00375 ( 4857) covalent geometry : angle 0.60201 ( 6574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: R 277 MET cc_start: 0.8263 (tmm) cc_final: 0.7900 (tmm) REVERT: R 1195 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8875 (t80) REVERT: N 36 TRP cc_start: 0.9090 (m100) cc_final: 0.7645 (m100) REVERT: N 82 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8347 (pmm) outliers start: 21 outliers final: 16 residues processed: 127 average time/residue: 0.1339 time to fit residues: 22.6791 Evaluate side-chains 134 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 1119 SER Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.072187 restraints weight = 9860.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.074971 restraints weight = 4992.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.076866 restraints weight = 3248.429| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4859 Z= 0.164 Angle : 0.613 9.037 6578 Z= 0.308 Chirality : 0.043 0.193 750 Planarity : 0.003 0.033 813 Dihedral : 3.953 32.236 670 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.32 % Allowed : 18.47 % Favored : 77.21 % 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: 1.78 (0.34), residues: 597 helix: 2.43 (0.28), residues: 319 sheet: 1.45 (0.51), residues: 98 loop : -1.41 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP R1082 HIS 0.002 0.000 HIS R 219 PHE 0.008 0.001 PHE N 29 TYR 0.007 0.001 TYR R 215 ARG 0.004 0.000 ARG R 226 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 287) hydrogen bonds : angle 3.82542 ( 864) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.71445 ( 4) covalent geometry : bond 0.00383 ( 4857) covalent geometry : angle 0.61266 ( 6574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.580 Fit side-chains REVERT: R 277 MET cc_start: 0.8247 (tmm) cc_final: 0.7940 (tmm) REVERT: R 1107 GLU cc_start: 0.8782 (pm20) cc_final: 0.8450 (pm20) REVERT: R 1195 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.8898 (t80) REVERT: N 36 TRP cc_start: 0.9082 (m100) cc_final: 0.7657 (m100) REVERT: N 77 THR cc_start: 0.8548 (p) cc_final: 0.8257 (p) REVERT: N 82 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8400 (pmm) REVERT: N 117 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8522 (tp-100) outliers start: 22 outliers final: 17 residues processed: 129 average time/residue: 0.1314 time to fit residues: 22.8059 Evaluate side-chains 136 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.0060 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073254 restraints weight = 9901.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076111 restraints weight = 5006.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078029 restraints weight = 3237.491| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4859 Z= 0.131 Angle : 0.607 8.809 6578 Z= 0.300 Chirality : 0.043 0.197 750 Planarity : 0.003 0.031 813 Dihedral : 3.970 32.259 670 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.32 % Allowed : 18.86 % Favored : 76.82 % 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: 1.78 (0.34), residues: 597 helix: 2.45 (0.28), residues: 319 sheet: 1.47 (0.52), residues: 98 loop : -1.47 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.007 0.001 PHE N 29 TYR 0.005 0.001 TYR R 172 ARG 0.004 0.000 ARG R 226 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 287) hydrogen bonds : angle 3.77166 ( 864) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.57742 ( 4) covalent geometry : bond 0.00307 ( 4857) covalent geometry : angle 0.60681 ( 6574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: R 135 LEU cc_start: 0.9515 (mm) cc_final: 0.9280 (mm) REVERT: R 176 ASP cc_start: 0.8202 (t70) cc_final: 0.7338 (t0) REVERT: R 277 MET cc_start: 0.8245 (tmm) cc_final: 0.7856 (tmm) REVERT: R 1195 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.8946 (t80) REVERT: R 371 MET cc_start: 0.7193 (tpt) cc_final: 0.6919 (tpp) REVERT: N 36 TRP cc_start: 0.9070 (m100) cc_final: 0.7623 (m100) REVERT: N 82 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8397 (pmm) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.1262 time to fit residues: 22.6207 Evaluate side-chains 141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 1119 SER Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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: 59.2532 > 50: distance: 19 - 95: 27.057 distance: 22 - 92: 6.105 distance: 67 - 86: 19.620 distance: 70 - 83: 4.813 distance: 83 - 84: 5.939 distance: 84 - 85: 5.535 distance: 84 - 87: 6.157 distance: 85 - 86: 11.407 distance: 85 - 92: 7.977 distance: 87 - 88: 7.543 distance: 88 - 89: 5.886 distance: 89 - 90: 6.415 distance: 89 - 91: 5.366 distance: 92 - 93: 8.499 distance: 93 - 94: 8.082 distance: 93 - 96: 7.411 distance: 94 - 95: 12.701 distance: 94 - 100: 4.070 distance: 96 - 97: 6.683 distance: 97 - 98: 9.825 distance: 98 - 99: 3.800 distance: 100 - 101: 4.573 distance: 101 - 102: 6.214 distance: 101 - 104: 12.989 distance: 102 - 103: 14.565 distance: 102 - 108: 18.318 distance: 104 - 105: 11.829 distance: 105 - 106: 9.861 distance: 105 - 107: 12.322 distance: 108 - 109: 17.225 distance: 109 - 110: 26.240 distance: 109 - 112: 23.603 distance: 110 - 111: 9.769 distance: 110 - 114: 38.883 distance: 112 - 113: 5.841 distance: 115 - 116: 55.497 distance: 115 - 118: 18.980 distance: 116 - 117: 24.385 distance: 116 - 122: 12.305 distance: 118 - 119: 24.223 distance: 119 - 120: 22.594 distance: 119 - 121: 18.375 distance: 122 - 123: 5.282 distance: 123 - 124: 44.237 distance: 123 - 126: 30.548 distance: 124 - 125: 8.313 distance: 124 - 131: 20.980 distance: 126 - 127: 25.536 distance: 127 - 128: 40.388 distance: 128 - 129: 28.019 distance: 129 - 130: 38.520 distance: 131 - 132: 19.871 distance: 131 - 137: 28.392 distance: 132 - 133: 10.410 distance: 132 - 135: 8.524 distance: 133 - 134: 26.813 distance: 133 - 138: 15.285 distance: 135 - 136: 14.685 distance: 136 - 137: 13.823 distance: 138 - 139: 15.606 distance: 139 - 140: 5.080 distance: 139 - 142: 8.797 distance: 140 - 141: 20.078 distance: 140 - 147: 27.729 distance: 142 - 143: 15.907 distance: 143 - 144: 7.673 distance: 144 - 145: 25.756 distance: 144 - 146: 10.217 distance: 147 - 148: 16.101 distance: 148 - 149: 15.179 distance: 148 - 151: 28.032 distance: 149 - 150: 26.511 distance: 149 - 155: 14.386 distance: 151 - 152: 17.494 distance: 152 - 153: 4.881 distance: 152 - 154: 15.877 distance: 155 - 156: 19.285 distance: 156 - 157: 17.872 distance: 156 - 159: 27.468 distance: 157 - 158: 15.185 distance: 157 - 162: 10.698 distance: 159 - 160: 20.936 distance: 159 - 161: 37.352