Starting phenix.real_space_refine on Sun Jun 15 19:05:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lmv_0921/06_2025/6lmv_0921.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmv_0921/06_2025/6lmv_0921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lmv_0921/06_2025/6lmv_0921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmv_0921/06_2025/6lmv_0921.map" model { file = "/net/cci-nas-00/data/ceres_data/6lmv_0921/06_2025/6lmv_0921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmv_0921/06_2025/6lmv_0921.cif" } resolution = 3.6 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 11538 2.51 5 N 2943 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17766 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: C, B, E, D, G, F, I, H Time building chain proxies: 5.55, per 1000 atoms: 0.31 Number of scatterers: 17766 At special positions: 0 Unit cell: (138.084, 136.631, 103.2, 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 117 16.00 O 3168 8.00 N 2943 7.00 C 11538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 176 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 176 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 176 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 174 " 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: 4.19 Conformation dependent library (CDL) restraints added in 2.2 seconds 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 215 Processing helix chain 'A' and resid 219 through 258 Processing helix chain 'A' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'B' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 96 through 112 Processing helix chain 'B' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 179 through 215 Processing helix chain 'B' and resid 219 through 258 Processing helix chain 'B' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'C' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA C 66 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 96 through 112 Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 179 through 215 Processing helix chain 'C' and resid 219 through 258 Processing helix chain 'C' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'D' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR D 55 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 96 through 112 Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 179 through 215 Processing helix chain 'D' and resid 219 through 258 Processing helix chain 'D' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'E' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.979A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 96 through 112 Processing helix chain 'E' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 171 through 177 Processing helix chain 'E' and resid 179 through 215 Processing helix chain 'E' and resid 219 through 258 Processing helix chain 'E' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 Processing helix chain 'F' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN F 76 " --> pdb=" O GLY F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 96 through 112 Processing helix chain 'F' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'F' and resid 157 through 162 Processing helix chain 'F' and resid 171 through 177 Processing helix chain 'F' and resid 179 through 215 Processing helix chain 'F' and resid 219 through 258 Processing helix chain 'F' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP F 267 " --> pdb=" O THR F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 Processing helix chain 'G' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR G 55 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 96 through 112 Processing helix chain 'G' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 134 Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 149 through 154 Processing helix chain 'G' and resid 157 through 162 Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 179 through 215 Processing helix chain 'G' and resid 219 through 258 Processing helix chain 'G' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP G 267 " --> pdb=" O THR G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 Processing helix chain 'H' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR H 55 " --> pdb=" O PRO H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 96 through 112 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 134 Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 149 through 154 Processing helix chain 'H' and resid 157 through 162 Processing helix chain 'H' and resid 171 through 177 Processing helix chain 'H' and resid 179 through 215 Processing helix chain 'H' and resid 219 through 258 Processing helix chain 'H' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP H 267 " --> pdb=" O THR H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 306 Processing helix chain 'I' and resid 51 through 62 removed outlier: 4.021A pdb=" N TYR I 55 " --> pdb=" O PRO I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA I 66 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 76 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 removed outlier: 3.981A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 96 through 112 Processing helix chain 'I' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 134 Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing helix chain 'I' and resid 149 through 154 Processing helix chain 'I' and resid 157 through 162 Processing helix chain 'I' and resid 171 through 177 Processing helix chain 'I' and resid 179 through 215 Processing helix chain 'I' and resid 219 through 258 Processing helix chain 'I' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP I 267 " --> pdb=" O THR I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 306 1206 hydrogen bonds defined for protein. 3564 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: 5.13 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5274 1.34 - 1.45: 3669 1.45 - 1.57: 9228 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 18306 Sorted by residual: bond pdb=" CA PRO I 51 " pdb=" C PRO I 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" CA PRO B 51 " pdb=" C PRO B 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA PRO D 51 " pdb=" C PRO D 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA PRO G 51 " pdb=" C PRO G 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CA PRO C 51 " pdb=" C PRO C 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 18301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 23827 2.04 - 4.07: 948 4.07 - 6.11: 128 6.11 - 8.15: 36 8.15 - 10.18: 27 Bond angle restraints: 24966 Sorted by residual: angle pdb=" N SER F 141 " pdb=" CA SER F 141 " pdb=" C SER F 141 " ideal model delta sigma weight residual 114.62 106.09 8.53 1.14e+00 7.69e-01 5.60e+01 angle pdb=" N SER H 141 " pdb=" CA SER H 141 " pdb=" C SER H 141 " ideal model delta sigma weight residual 114.62 106.10 8.52 1.14e+00 7.69e-01 5.59e+01 angle pdb=" N SER C 141 " pdb=" CA SER C 141 " pdb=" C SER C 141 " ideal model delta sigma weight residual 114.62 106.10 8.52 1.14e+00 7.69e-01 5.58e+01 angle pdb=" N SER E 141 " pdb=" CA SER E 141 " pdb=" C SER E 141 " ideal model delta sigma weight residual 114.62 106.11 8.51 1.14e+00 7.69e-01 5.57e+01 angle pdb=" N SER A 141 " pdb=" CA SER A 141 " pdb=" C SER A 141 " ideal model delta sigma weight residual 114.62 106.11 8.51 1.14e+00 7.69e-01 5.57e+01 ... (remaining 24961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9581 17.92 - 35.83: 832 35.83 - 53.75: 171 53.75 - 71.67: 18 71.67 - 89.59: 18 Dihedral angle restraints: 10620 sinusoidal: 4032 harmonic: 6588 Sorted by residual: dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 131 " pdb=" CB CYS C 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.41 -89.59 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS I 46 " pdb=" SG CYS I 46 " pdb=" SG CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.42 -89.58 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS E 46 " pdb=" SG CYS E 46 " pdb=" SG CYS E 131 " pdb=" CB CYS E 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.42 -89.58 1 1.00e+01 1.00e-02 9.53e+01 ... (remaining 10617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1174 0.032 - 0.065: 997 0.065 - 0.097: 360 0.097 - 0.130: 102 0.130 - 0.162: 103 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA PRO A 64 " pdb=" N PRO A 64 " pdb=" C PRO A 64 " pdb=" CB PRO A 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO H 64 " pdb=" N PRO H 64 " pdb=" C PRO H 64 " pdb=" CB PRO H 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA PRO G 64 " pdb=" N PRO G 64 " pdb=" C PRO G 64 " pdb=" CB PRO G 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2733 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 63 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO F 64 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 63 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO C 64 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 63 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO G 64 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " -0.039 5.00e-02 4.00e+02 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6452 2.85 - 3.37: 17082 3.37 - 3.88: 28066 3.88 - 4.39: 32115 4.39 - 4.90: 55564 Nonbonded interactions: 139279 Sorted by model distance: nonbonded pdb=" O ALA I 143 " pdb=" NZ LYS I 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA A 143 " pdb=" NZ LYS A 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA H 143 " pdb=" NZ LYS H 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA E 143 " pdb=" NZ LYS E 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA F 143 " pdb=" NZ LYS F 147 " model vdw 2.342 3.120 ... (remaining 139274 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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: 0.600 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 34.500 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.009 0.076 18333 Z= 0.360 Angle : 1.011 10.185 25020 Z= 0.600 Chirality : 0.055 0.162 2736 Planarity : 0.008 0.070 3105 Dihedral : 14.135 88.921 6273 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.94 % Allowed : 4.72 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.49 (0.11), residues: 2187 helix: -3.69 (0.07), residues: 1629 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 262 HIS 0.007 0.002 HIS D 56 PHE 0.016 0.002 PHE I 237 TYR 0.027 0.002 TYR E 155 ARG 0.003 0.001 ARG C 265 Details of bonding type rmsd hydrogen bonds : bond 0.26146 ( 1206) hydrogen bonds : angle 8.74460 ( 3564) SS BOND : bond 0.00305 ( 27) SS BOND : angle 3.05965 ( 54) covalent geometry : bond 0.00869 (18306) covalent geometry : angle 1.00208 (24966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 448 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8692 (p) cc_final: 0.8414 (p) REVERT: A 95 HIS cc_start: 0.6952 (m90) cc_final: 0.6689 (m-70) REVERT: A 125 ASP cc_start: 0.8127 (t0) cc_final: 0.7923 (t70) REVERT: A 200 PHE cc_start: 0.7494 (t80) cc_final: 0.7201 (m-10) REVERT: A 236 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8410 (mmmm) REVERT: A 238 ASP cc_start: 0.8462 (m-30) cc_final: 0.8040 (t0) REVERT: A 269 TRP cc_start: 0.7846 (t-100) cc_final: 0.7473 (t-100) REVERT: A 307 LYS cc_start: 0.5497 (mmtt) cc_final: 0.5268 (tmtt) REVERT: B 125 ASP cc_start: 0.8114 (t0) cc_final: 0.7881 (t70) REVERT: B 200 PHE cc_start: 0.7793 (t80) cc_final: 0.7437 (m-10) REVERT: B 227 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8065 (mm-30) REVERT: B 230 LYS cc_start: 0.8189 (mttt) cc_final: 0.7745 (mttm) REVERT: B 235 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 236 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8288 (mmmt) REVERT: B 251 HIS cc_start: 0.7765 (m90) cc_final: 0.7544 (t-90) REVERT: B 260 LYS cc_start: 0.5995 (mmtt) cc_final: 0.5650 (mmtt) REVERT: B 261 ASP cc_start: 0.8226 (t70) cc_final: 0.8000 (t70) REVERT: C 236 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8429 (tppt) REVERT: C 269 TRP cc_start: 0.7761 (t-100) cc_final: 0.7458 (t-100) REVERT: C 297 TYR cc_start: 0.5609 (m-80) cc_final: 0.5251 (m-80) REVERT: D 110 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8135 (tp-100) REVERT: D 222 GLN cc_start: 0.8795 (tt0) cc_final: 0.8466 (tt0) REVERT: D 236 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8307 (tppt) REVERT: D 250 GLU cc_start: 0.7976 (tp30) cc_final: 0.7509 (tm-30) REVERT: E 222 GLN cc_start: 0.8892 (tt0) cc_final: 0.8639 (tt0) REVERT: E 227 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7728 (mm-30) REVERT: E 230 LYS cc_start: 0.8197 (mttt) cc_final: 0.7745 (mtmt) REVERT: E 235 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8354 (tm-30) REVERT: E 236 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8219 (mmmm) REVERT: E 250 GLU cc_start: 0.8026 (tp30) cc_final: 0.7144 (tp30) REVERT: E 269 TRP cc_start: 0.7748 (t-100) cc_final: 0.7533 (t-100) REVERT: E 297 TYR cc_start: 0.5632 (m-80) cc_final: 0.5152 (m-80) REVERT: F 200 PHE cc_start: 0.7944 (t80) cc_final: 0.7391 (m-10) REVERT: F 250 GLU cc_start: 0.7900 (tp30) cc_final: 0.7529 (tm-30) REVERT: F 254 ARG cc_start: 0.8385 (mmt180) cc_final: 0.8012 (mmt-90) REVERT: F 306 ASN cc_start: 0.8354 (m110) cc_final: 0.7921 (p0) REVERT: G 61 MET cc_start: 0.8051 (mtp) cc_final: 0.7706 (mtp) REVERT: G 200 PHE cc_start: 0.7689 (t80) cc_final: 0.7304 (m-10) REVERT: G 222 GLN cc_start: 0.8755 (tt0) cc_final: 0.8444 (tt0) REVERT: G 223 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7835 (tpp-160) REVERT: G 232 VAL cc_start: 0.8693 (t) cc_final: 0.8438 (p) REVERT: G 235 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8159 (tm-30) REVERT: G 250 GLU cc_start: 0.8181 (tp30) cc_final: 0.7619 (tp30) REVERT: G 251 HIS cc_start: 0.7960 (m90) cc_final: 0.7538 (t-170) REVERT: G 269 TRP cc_start: 0.7912 (t-100) cc_final: 0.7696 (t-100) REVERT: G 297 TYR cc_start: 0.5592 (m-80) cc_final: 0.5030 (m-10) REVERT: H 110 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8391 (tp-100) REVERT: H 177 VAL cc_start: 0.8579 (t) cc_final: 0.8292 (p) REVERT: H 200 PHE cc_start: 0.7844 (t80) cc_final: 0.7279 (m-10) REVERT: H 222 GLN cc_start: 0.8875 (tt0) cc_final: 0.8674 (tt0) REVERT: H 227 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7733 (mm-30) REVERT: H 250 GLU cc_start: 0.8195 (tp30) cc_final: 0.7667 (tm-30) REVERT: H 254 ARG cc_start: 0.7862 (mmt180) cc_final: 0.7330 (mmt-90) REVERT: H 269 TRP cc_start: 0.7771 (t-100) cc_final: 0.7545 (t-100) REVERT: I 125 ASP cc_start: 0.8319 (t0) cc_final: 0.8084 (t70) REVERT: I 251 HIS cc_start: 0.7964 (m90) cc_final: 0.7606 (t-170) outliers start: 18 outliers final: 18 residues processed: 466 average time/residue: 0.4058 time to fit residues: 257.0399 Evaluate side-chains 367 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 349 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 176 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 0.0000 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 HIS A 110 GLN A 135 HIS A 162 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 135 HIS B 162 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 110 GLN C 135 HIS C 162 ASN C 251 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 110 GLN D 135 HIS D 162 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 110 GLN E 135 HIS E 162 ASN E 231 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS F 110 GLN F 135 HIS F 162 ASN F 251 HIS ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS G 135 HIS G 162 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS H 110 GLN H 135 HIS H 162 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS I 110 GLN I 135 HIS I 162 ASN I 222 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113898 restraints weight = 24835.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117239 restraints weight = 13925.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119357 restraints weight = 9884.654| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18333 Z= 0.136 Angle : 0.579 6.763 25020 Z= 0.314 Chirality : 0.038 0.148 2736 Planarity : 0.006 0.065 3105 Dihedral : 6.563 54.614 2421 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.88 % Allowed : 11.37 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.41 (0.16), residues: 2187 helix: -0.46 (0.11), residues: 1647 sheet: None (None), residues: 0 loop : -2.04 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 262 HIS 0.007 0.001 HIS C 251 PHE 0.016 0.001 PHE E 200 TYR 0.009 0.001 TYR A 297 ARG 0.013 0.001 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 1206) hydrogen bonds : angle 4.34295 ( 3564) SS BOND : bond 0.00079 ( 27) SS BOND : angle 1.27066 ( 54) covalent geometry : bond 0.00262 (18306) covalent geometry : angle 0.57704 (24966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 456 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7207 (m) REVERT: A 176 CYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5666 (m) REVERT: A 220 LEU cc_start: 0.8145 (tp) cc_final: 0.7852 (tp) REVERT: A 236 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8348 (mmtp) REVERT: B 176 CYS cc_start: 0.6585 (OUTLIER) cc_final: 0.5898 (m) REVERT: B 200 PHE cc_start: 0.8004 (t80) cc_final: 0.7666 (m-10) REVERT: B 210 THR cc_start: 0.8689 (m) cc_final: 0.8447 (m) REVERT: B 222 GLN cc_start: 0.8951 (tt0) cc_final: 0.8565 (tt0) REVERT: B 230 LYS cc_start: 0.8142 (mttt) cc_final: 0.7911 (mttm) REVERT: B 235 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8544 (tm-30) REVERT: B 250 GLU cc_start: 0.8155 (tp30) cc_final: 0.7614 (tm-30) REVERT: B 254 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7904 (mmt-90) REVERT: B 260 LYS cc_start: 0.5774 (mmtt) cc_final: 0.5325 (mmtp) REVERT: C 130 ARG cc_start: 0.8416 (ttm170) cc_final: 0.8167 (ttm170) REVERT: C 176 CYS cc_start: 0.5429 (OUTLIER) cc_final: 0.4858 (m) REVERT: C 213 ARG cc_start: 0.8237 (mmt90) cc_final: 0.7920 (mmt90) REVERT: C 222 GLN cc_start: 0.8737 (tt0) cc_final: 0.8369 (tt0) REVERT: C 265 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7510 (ttt90) REVERT: D 48 CYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6872 (m) REVERT: D 82 LEU cc_start: 0.9277 (mt) cc_final: 0.9072 (mt) REVERT: D 110 GLN cc_start: 0.8035 (tp40) cc_final: 0.7790 (tp-100) REVERT: D 163 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7424 (ttmt) REVERT: D 176 CYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6233 (m) REVERT: D 210 THR cc_start: 0.8655 (m) cc_final: 0.8383 (m) REVERT: D 222 GLN cc_start: 0.8678 (tt0) cc_final: 0.8354 (tt0) REVERT: D 236 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8604 (mmmm) REVERT: D 238 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8172 (t0) REVERT: D 250 GLU cc_start: 0.8250 (tp30) cc_final: 0.7160 (tp30) REVERT: E 176 CYS cc_start: 0.6499 (OUTLIER) cc_final: 0.5905 (m) REVERT: E 213 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7886 (mmt-90) REVERT: E 230 LYS cc_start: 0.8201 (mttt) cc_final: 0.7935 (mtmt) REVERT: E 235 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7962 (tm-30) REVERT: E 236 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8138 (mmmm) REVERT: E 297 TYR cc_start: 0.5673 (m-80) cc_final: 0.5161 (m-10) REVERT: F 48 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7201 (m) REVERT: F 176 CYS cc_start: 0.5721 (OUTLIER) cc_final: 0.5037 (m) REVERT: F 222 GLN cc_start: 0.8757 (tt0) cc_final: 0.8468 (tt0) REVERT: F 235 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8135 (tm-30) REVERT: F 236 LYS cc_start: 0.9202 (tppt) cc_final: 0.8122 (mmmt) REVERT: F 250 GLU cc_start: 0.8042 (tp30) cc_final: 0.7059 (tp30) REVERT: G 48 CYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7102 (m) REVERT: G 176 CYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5767 (m) REVERT: G 213 ARG cc_start: 0.8279 (mmt90) cc_final: 0.8014 (mmt90) REVERT: G 222 GLN cc_start: 0.8698 (tt0) cc_final: 0.8480 (tt0) REVERT: G 265 ARG cc_start: 0.8056 (ptm-80) cc_final: 0.7645 (ttt90) REVERT: G 297 TYR cc_start: 0.6035 (m-80) cc_final: 0.5467 (m-10) REVERT: H 110 GLN cc_start: 0.8411 (tp40) cc_final: 0.8198 (tp-100) REVERT: H 176 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5369 (m) REVERT: H 177 VAL cc_start: 0.8448 (t) cc_final: 0.8208 (p) REVERT: H 250 GLU cc_start: 0.8113 (tp30) cc_final: 0.7636 (tm-30) REVERT: I 48 CYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6792 (m) REVERT: I 176 CYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5937 (m) REVERT: I 222 GLN cc_start: 0.8626 (tt0) cc_final: 0.8348 (tt0) REVERT: I 269 TRP cc_start: 0.8042 (t-100) cc_final: 0.7789 (t-100) outliers start: 55 outliers final: 27 residues processed: 491 average time/residue: 0.3611 time to fit residues: 248.4460 Evaluate side-chains 400 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 358 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 214 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 152 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 90 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN C 110 GLN C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN E 191 GLN F 110 GLN G 251 HIS ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109595 restraints weight = 25734.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112573 restraints weight = 14909.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114486 restraints weight = 10895.507| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18333 Z= 0.169 Angle : 0.584 6.196 25020 Z= 0.309 Chirality : 0.041 0.140 2736 Planarity : 0.005 0.046 3105 Dihedral : 5.822 59.783 2417 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.93 % Allowed : 13.36 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.53 (0.17), residues: 2187 helix: 1.11 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -2.07 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 195 HIS 0.006 0.001 HIS G 251 PHE 0.017 0.001 PHE H 200 TYR 0.011 0.001 TYR G 297 ARG 0.006 0.001 ARG C 265 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 1206) hydrogen bonds : angle 3.98822 ( 3564) SS BOND : bond 0.00116 ( 27) SS BOND : angle 0.97474 ( 54) covalent geometry : bond 0.00389 (18306) covalent geometry : angle 0.58284 (24966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 374 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5835 (m) REVERT: A 197 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 236 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8448 (mmtp) REVERT: A 238 ASP cc_start: 0.8337 (m-30) cc_final: 0.8066 (t0) REVERT: B 176 CYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6382 (m) REVERT: B 197 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8068 (tp) REVERT: B 200 PHE cc_start: 0.7965 (t80) cc_final: 0.7718 (m-10) REVERT: B 210 THR cc_start: 0.8678 (m) cc_final: 0.8413 (m) REVERT: B 222 GLN cc_start: 0.8950 (tt0) cc_final: 0.8679 (tt0) REVERT: B 250 GLU cc_start: 0.8258 (tp30) cc_final: 0.7573 (tm-30) REVERT: B 254 ARG cc_start: 0.8294 (mmt90) cc_final: 0.7815 (mmt90) REVERT: B 260 LYS cc_start: 0.5888 (mmtt) cc_final: 0.5551 (mmtp) REVERT: C 130 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8130 (ttm170) REVERT: C 176 CYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6087 (m) REVERT: C 197 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 222 GLN cc_start: 0.8647 (tt0) cc_final: 0.8304 (tt0) REVERT: C 238 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7880 (t0) REVERT: D 94 ARG cc_start: 0.8291 (mmt90) cc_final: 0.7880 (mtt90) REVERT: D 110 GLN cc_start: 0.8072 (tp40) cc_final: 0.7854 (tp-100) REVERT: D 163 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7623 (ttmt) REVERT: D 176 CYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6023 (m) REVERT: D 222 GLN cc_start: 0.8638 (tt0) cc_final: 0.8322 (tt0) REVERT: D 250 GLU cc_start: 0.8398 (tp30) cc_final: 0.7988 (tp30) REVERT: E 176 CYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6153 (m) REVERT: E 230 LYS cc_start: 0.8402 (mttt) cc_final: 0.8170 (mtmt) REVERT: E 235 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8446 (tm-30) REVERT: E 236 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8315 (mmmm) REVERT: E 250 GLU cc_start: 0.8060 (tp30) cc_final: 0.7690 (tp30) REVERT: E 297 TYR cc_start: 0.5771 (m-80) cc_final: 0.5484 (m-80) REVERT: F 176 CYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5909 (m) REVERT: F 222 GLN cc_start: 0.8770 (tt0) cc_final: 0.8556 (tt0) REVERT: F 250 GLU cc_start: 0.7862 (tp30) cc_final: 0.7267 (tp30) REVERT: G 104 TRP cc_start: 0.7226 (t-100) cc_final: 0.7007 (t-100) REVERT: G 176 CYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5903 (m) REVERT: G 269 TRP cc_start: 0.8154 (t-100) cc_final: 0.7765 (t-100) REVERT: G 297 TYR cc_start: 0.5548 (m-80) cc_final: 0.5101 (m-10) REVERT: H 176 CYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6074 (m) REVERT: H 199 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7751 (tt) REVERT: H 269 TRP cc_start: 0.8140 (t-100) cc_final: 0.7901 (t-100) REVERT: H 306 ASN cc_start: 0.7667 (m-40) cc_final: 0.7305 (t0) REVERT: I 97 TRP cc_start: 0.5665 (OUTLIER) cc_final: 0.5413 (m-10) REVERT: I 176 CYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6624 (m) outliers start: 94 outliers final: 56 residues processed: 437 average time/residue: 0.3780 time to fit residues: 227.1156 Evaluate side-chains 406 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 335 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 57.8152 > 50: distance: 70 - 74: 11.455 distance: 71 - 102: 17.364 distance: 74 - 75: 7.945 distance: 75 - 76: 20.819 distance: 75 - 78: 16.971 distance: 76 - 77: 11.652 distance: 76 - 81: 5.663 distance: 77 - 111: 44.235 distance: 78 - 79: 12.941 distance: 78 - 80: 34.030 distance: 81 - 82: 16.261 distance: 82 - 83: 5.021 distance: 82 - 85: 15.651 distance: 83 - 84: 17.700 distance: 83 - 88: 17.159 distance: 84 - 119: 24.356 distance: 85 - 86: 24.265 distance: 85 - 87: 29.695 distance: 88 - 89: 4.122 distance: 89 - 90: 7.097 distance: 89 - 92: 17.234 distance: 90 - 91: 17.403 distance: 90 - 102: 12.214 distance: 91 - 124: 21.283 distance: 92 - 93: 9.047 distance: 93 - 94: 9.899 distance: 93 - 95: 9.915 distance: 94 - 96: 10.479 distance: 95 - 97: 10.634 distance: 95 - 98: 5.967 distance: 97 - 99: 7.499 distance: 98 - 100: 8.578 distance: 100 - 101: 10.808 distance: 102 - 103: 16.031 distance: 103 - 104: 33.532 distance: 103 - 106: 27.307 distance: 104 - 105: 37.631 distance: 104 - 111: 40.037 distance: 106 - 107: 8.788 distance: 107 - 108: 10.013 distance: 108 - 109: 18.018 distance: 109 - 110: 14.690 distance: 111 - 112: 24.956 distance: 112 - 113: 28.879 distance: 112 - 115: 41.022 distance: 113 - 114: 14.661 distance: 113 - 119: 28.144 distance: 115 - 116: 14.598 distance: 116 - 117: 28.244 distance: 116 - 118: 23.047 distance: 119 - 120: 18.245 distance: 120 - 121: 5.919 distance: 120 - 123: 6.845 distance: 121 - 122: 15.805 distance: 124 - 125: 12.972 distance: 125 - 126: 3.995 distance: 125 - 128: 7.936 distance: 126 - 127: 30.506 distance: 126 - 134: 17.305 distance: 128 - 129: 16.795 distance: 129 - 130: 8.933 distance: 129 - 131: 6.406 distance: 130 - 132: 8.825 distance: 131 - 133: 9.449 distance: 132 - 133: 10.784 distance: 134 - 135: 37.568 distance: 135 - 136: 37.795 distance: 136 - 137: 19.580 distance: 136 - 138: 14.676 distance: 138 - 139: 27.254 distance: 139 - 140: 19.745 distance: 139 - 142: 16.415 distance: 140 - 141: 30.198 distance: 140 - 149: 18.454 distance: 142 - 143: 26.134 distance: 143 - 144: 20.188 distance: 143 - 145: 25.619 distance: 144 - 146: 33.375 distance: 145 - 147: 33.727 distance: 146 - 148: 15.899 distance: 147 - 148: 21.202 distance: 149 - 150: 10.981 distance: 150 - 151: 7.817 distance: 150 - 153: 22.291 distance: 151 - 152: 7.909 distance: 151 - 160: 23.256 distance: 153 - 154: 23.953 distance: 154 - 155: 32.291 distance: 154 - 156: 11.869 distance: 155 - 157: 12.497 distance: 156 - 158: 16.398 distance: 157 - 159: 11.160 distance: 158 - 159: 21.515