Starting phenix.real_space_refine on Fri Feb 14 18:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x2c_32964/02_2025/7x2c_32964.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2c_32964/02_2025/7x2c_32964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x2c_32964/02_2025/7x2c_32964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2c_32964/02_2025/7x2c_32964.map" model { file = "/net/cci-nas-00/data/ceres_data/7x2c_32964/02_2025/7x2c_32964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2c_32964/02_2025/7x2c_32964.cif" } resolution = 3.2 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= -0.005 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2939 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 2 4.86 5 C 5071 2.51 5 N 1341 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7953 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 279, 2156 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 279, 2156 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 2197 Chain: "A" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1824 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 2538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2526 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Conformer: "B" Number of residues, atoms: 339, 2526 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 bond proxies already assigned to first conformer: 2559 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 953 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'CLR': 1, 'G3C': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 6.80, per 1000 atoms: 0.86 Number of scatterers: 7953 At special positions: 0 Unit cell: (77.177, 101.091, 123.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 56 16.00 O 1483 8.00 N 1341 7.00 C 5071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 2.20 Conformation dependent library (CDL) restraints added in 1.5 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 44.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 removed outlier: 3.522A pdb=" N VAL F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 removed outlier: 3.620A pdb=" N LYS F 57 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 88 removed outlier: 3.815A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.444A pdb=" N ILE F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 136 through 161 removed outlier: 3.527A pdb=" N SER F 155 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 203 through 241 Processing helix chain 'F' and resid 265 through 298 removed outlier: 3.883A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 309 through 332 removed outlier: 3.637A pdb=" N PHE F 313 " --> pdb=" O ASP F 309 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 334 through 344 removed outlier: 3.580A pdb=" N LYS F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.675A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.879A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.556A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.862A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.636A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.559A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.635A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.552A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.595A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.159A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.241A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.394A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.821A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.028A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.595A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.526A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.983A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.055A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1232 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: 2.35 Time building geometry restraints manager: 2.49 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: 2575 1.34 - 1.46: 2028 1.46 - 1.58: 3444 1.58 - 1.70: 6 1.70 - 1.82: 77 Bond restraints: 8130 Sorted by residual: bond pdb=" C06 G3C F 503 " pdb=" C07 G3C F 503 " ideal model delta sigma weight residual 1.523 1.650 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C07 G3C F 502 " pdb=" C08 G3C F 502 " ideal model delta sigma weight residual 1.510 1.637 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C07 G3C F 503 " pdb=" C08 G3C F 503 " ideal model delta sigma weight residual 1.510 1.632 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C06 G3C F 502 " pdb=" C07 G3C F 502 " ideal model delta sigma weight residual 1.523 1.639 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C13 CLR F 501 " pdb=" C17 CLR F 501 " ideal model delta sigma weight residual 1.550 1.438 0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 8125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 10910 2.40 - 4.80: 136 4.80 - 7.20: 26 7.20 - 9.59: 6 9.59 - 11.99: 2 Bond angle restraints: 11080 Sorted by residual: angle pdb=" C23 CLR F 501 " pdb=" C24 CLR F 501 " pdb=" C25 CLR F 501 " ideal model delta sigma weight residual 115.14 103.15 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 122.61 128.39 -5.78 1.56e+00 4.11e-01 1.37e+01 angle pdb=" N GLY B 319 " pdb=" CA GLY B 319 " pdb=" C GLY B 319 " ideal model delta sigma weight residual 110.87 116.55 -5.68 1.54e+00 4.22e-01 1.36e+01 angle pdb=" C TYR F 204 " pdb=" N ILE F 205 " pdb=" CA ILE F 205 " ideal model delta sigma weight residual 122.13 116.03 6.10 1.85e+00 2.92e-01 1.09e+01 angle pdb=" C17 CLR F 501 " pdb=" C20 CLR F 501 " pdb=" C22 CLR F 501 " ideal model delta sigma weight residual 109.45 99.78 9.67 3.00e+00 1.11e-01 1.04e+01 ... (remaining 11075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4409 17.95 - 35.90: 350 35.90 - 53.85: 62 53.85 - 71.80: 13 71.80 - 89.75: 3 Dihedral angle restraints: 4837 sinusoidal: 1820 harmonic: 3017 Sorted by residual: dihedral pdb=" CB CYS F 96 " pdb=" SG CYS F 96 " pdb=" SG CYS F 186 " pdb=" CB CYS F 186 " ideal model delta sinusoidal sigma weight residual 93.00 139.20 -46.20 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CA ILE F 201 " pdb=" C ILE F 201 " pdb=" N SER F 202 " pdb=" CA SER F 202 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA MET F 135 " pdb=" C MET F 135 " pdb=" N THR F 136 " pdb=" CA THR F 136 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1271 0.135 - 0.270: 2 0.270 - 0.405: 2 0.405 - 0.540: 0 0.540 - 0.675: 2 Chirality restraints: 1277 Sorted by residual: chirality pdb=" C13 CLR F 501 " pdb=" C12 CLR F 501 " pdb=" C14 CLR F 501 " pdb=" C17 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.93 -2.26 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C10 CLR F 501 " pdb=" C1 CLR F 501 " pdb=" C5 CLR F 501 " pdb=" C9 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.85 -2.23 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" C07 G3C F 502 " pdb=" C06 G3C F 502 " pdb=" C08 G3C F 502 " pdb=" C15 G3C F 502 " both_signs ideal model delta sigma weight residual False -2.44 -2.75 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1274 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 205 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.92e+00 pdb=" N PRO F 206 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 206 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 206 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 201 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C ILE F 201 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE F 201 " -0.019 2.00e-02 2.50e+03 pdb=" N SER F 202 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 327 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO F 328 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 328 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 328 " 0.040 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 122 2.66 - 3.22: 7579 3.22 - 3.78: 12542 3.78 - 4.34: 16750 4.34 - 4.90: 28139 Nonbonded interactions: 65132 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.102 3.040 nonbonded pdb=" OD1 ASP A 229 " pdb=" OG1 THR E 111 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" N GLY B 324 " model vdw 2.222 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 3.040 nonbonded pdb=" OG SER F 198 " pdb=" O01 G3C F 503 " model vdw 2.255 3.040 ... (remaining 65127 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 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 0.127 8130 Z= 0.394 Angle : 0.705 11.992 11080 Z= 0.358 Chirality : 0.051 0.675 1277 Planarity : 0.005 0.079 1403 Dihedral : 13.490 89.746 2870 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.48 % Allowed : 0.24 % Favored : 99.27 % 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: 0.97 (0.26), residues: 1020 helix: 1.81 (0.26), residues: 406 sheet: 0.52 (0.33), residues: 224 loop : -0.48 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.020 0.001 PHE A 212 TYR 0.021 0.001 TYR B 59 ARG 0.005 0.000 ARG F 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 29 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7120 (tm-30) REVERT: A 386 MET cc_start: 0.7988 (ttm) cc_final: 0.7455 (tpp) REVERT: B 137 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7337 (mmm160) REVERT: B 148 CYS cc_start: 0.8391 (t) cc_final: 0.8171 (t) REVERT: B 217 MET cc_start: 0.6838 (tmm) cc_final: 0.6290 (tmm) REVERT: D 41 CYS cc_start: 0.7902 (m) cc_final: 0.7668 (m) REVERT: D 47 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6891 (mp0) REVERT: E 82 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1881 time to fit residues: 40.7792 Evaluate side-chains 139 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN A 213 GLN B 119 ASN B 237 ASN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112810 restraints weight = 29002.475| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 5.35 r_work: 0.3270 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8130 Z= 0.362 Angle : 0.631 6.714 11080 Z= 0.343 Chirality : 0.045 0.153 1277 Planarity : 0.005 0.077 1403 Dihedral : 4.635 28.194 1203 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.57 % Allowed : 8.95 % Favored : 89.48 % 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: 1.03 (0.26), residues: 1020 helix: 1.94 (0.25), residues: 405 sheet: 0.43 (0.35), residues: 198 loop : -0.40 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 63 HIS 0.006 0.002 HIS A 220 PHE 0.016 0.002 PHE F 289 TYR 0.031 0.002 TYR B 59 ARG 0.004 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7782 (tpt-90) REVERT: A 294 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7766 (mm-40) REVERT: A 386 MET cc_start: 0.8557 (ttm) cc_final: 0.7815 (tpp) REVERT: B 68 ARG cc_start: 0.8344 (mtp180) cc_final: 0.7494 (mtp180) REVERT: B 137 ARG cc_start: 0.7606 (mmm160) cc_final: 0.7128 (mmm160) REVERT: B 217 MET cc_start: 0.6450 (tmm) cc_final: 0.5966 (tmm) REVERT: B 220 GLN cc_start: 0.7716 (tt0) cc_final: 0.7456 (tt0) REVERT: B 254 ASP cc_start: 0.7844 (t70) cc_final: 0.7597 (t70) REVERT: D 47 GLU cc_start: 0.7739 (mt-10) cc_final: 0.6919 (mp0) outliers start: 9 outliers final: 7 residues processed: 150 average time/residue: 0.2010 time to fit residues: 40.9329 Evaluate side-chains 143 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/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-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1629 > 50: distance: 73 - 153: 33.984 distance: 76 - 150: 36.122 distance: 86 - 140: 33.270 distance: 89 - 137: 30.279 distance: 95 - 99: 10.499 distance: 99 - 100: 37.409 distance: 100 - 101: 49.705 distance: 100 - 103: 8.686 distance: 101 - 102: 40.093 distance: 101 - 105: 22.839 distance: 103 - 104: 40.598 distance: 105 - 106: 19.944 distance: 106 - 107: 18.657 distance: 107 - 108: 11.110 distance: 107 - 109: 13.799 distance: 109 - 110: 13.467 distance: 110 - 111: 51.435 distance: 110 - 113: 26.612 distance: 111 - 112: 9.816 distance: 111 - 117: 10.282 distance: 113 - 114: 29.737 distance: 114 - 115: 17.586 distance: 114 - 116: 53.820 distance: 117 - 118: 40.355 distance: 118 - 119: 21.847 distance: 118 - 121: 39.342 distance: 119 - 120: 17.436 distance: 119 - 124: 18.116 distance: 121 - 122: 39.905 distance: 121 - 123: 40.617 distance: 125 - 126: 17.150 distance: 125 - 128: 56.843 distance: 126 - 127: 21.470 distance: 126 - 131: 17.602 distance: 128 - 129: 40.543 distance: 131 - 132: 7.678 distance: 131 - 230: 35.957 distance: 132 - 133: 9.049 distance: 132 - 135: 8.710 distance: 133 - 134: 16.851 distance: 133 - 137: 41.534 distance: 134 - 227: 33.459 distance: 135 - 136: 40.190 distance: 137 - 138: 54.685 distance: 138 - 139: 33.606 distance: 138 - 141: 27.742 distance: 139 - 140: 14.817 distance: 139 - 142: 22.254 distance: 142 - 143: 30.998 distance: 142 - 217: 29.184 distance: 143 - 144: 37.214 distance: 143 - 146: 3.976 distance: 145 - 214: 32.744 distance: 146 - 147: 28.513 distance: 147 - 148: 40.584 distance: 147 - 149: 39.517 distance: 150 - 151: 40.292 distance: 151 - 152: 39.855 distance: 151 - 154: 16.767 distance: 152 - 153: 37.737 distance: 152 - 164: 53.212 distance: 154 - 155: 23.538 distance: 156 - 158: 8.381 distance: 157 - 160: 6.175 distance: 158 - 159: 8.287 distance: 160 - 162: 7.888 distance: 165 - 166: 39.297 distance: 166 - 167: 38.821 distance: 166 - 172: 35.216 distance: 168 - 169: 28.993 distance: 169 - 170: 28.115 distance: 169 - 171: 32.306