Starting phenix.real_space_refine on Fri Dec 8 08:07:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kng_0731/12_2023/6kng_0731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kng_0731/12_2023/6kng_0731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kng_0731/12_2023/6kng_0731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kng_0731/12_2023/6kng_0731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kng_0731/12_2023/6kng_0731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kng_0731/12_2023/6kng_0731.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 30 5.16 5 C 4935 2.51 5 N 1326 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1005 SG CYS A 136 24.373 25.147 33.465 1.00 55.95 S ATOM 3586 SG CYS B 136 39.793 66.348 33.485 1.00 56.25 S ATOM 6167 SG CYS C 136 67.736 32.396 33.517 1.00 56.75 S Time building chain proxies: 4.97, per 1000 atoms: 0.64 Number of scatterers: 7749 At special positions: 0 Unit cell: (92.4, 93.28, 77.44, 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) Cu 6 28.99 S 30 16.00 O 1452 8.00 N 1326 7.00 C 4935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 12.9% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.945A pdb=" N THR A 11 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.678A pdb=" N ALA A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.076A pdb=" N HIS A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.944A pdb=" N THR B 11 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 141 through 147 Processing helix chain 'B' and resid 198 through 211 removed outlier: 3.678A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 4.075A pdb=" N HIS B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.945A pdb=" N THR C 11 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.679A pdb=" N ALA C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 4.076A pdb=" N HIS C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 removed outlier: 6.899A pdb=" N VAL A 15 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N THR A 42 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 6.899A pdb=" N VAL A 15 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N THR A 42 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL A 39 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ARG A 84 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE A 41 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE A 86 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET A 43 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N THR A 121 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS C 336 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ARG A 123 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 334 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS A 125 " --> pdb=" O THR C 332 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N THR C 332 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.517A pdb=" N MET A 73 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU A 157 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 75 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 163 removed outlier: 4.215A pdb=" N LEU A 162 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.727A pdb=" N LYS A 174 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL A 244 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR A 176 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER A 246 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 178 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR A 294 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N GLY A 261 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP A 262 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 277 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.960A pdb=" N ALA A 302 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 338 removed outlier: 9.133A pdb=" N THR A 332 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS B 125 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 334 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG B 123 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS A 336 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR B 121 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 15 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B 42 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 331 through 338 removed outlier: 9.133A pdb=" N THR A 332 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS B 125 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 334 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG B 123 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS A 336 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR B 121 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.519A pdb=" N MET B 73 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 157 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 75 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 163 removed outlier: 4.216A pdb=" N LEU B 162 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.726A pdb=" N LYS B 174 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 244 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR B 176 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER B 246 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 178 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR B 294 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLY B 261 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP B 262 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 277 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 233 through 236 removed outlier: 3.962A pdb=" N ALA B 302 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 338 removed outlier: 9.112A pdb=" N THR B 332 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LYS C 125 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL B 334 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG C 123 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS B 336 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR C 121 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C 15 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR C 42 " --> pdb=" O VAL C 15 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 338 removed outlier: 9.112A pdb=" N THR B 332 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LYS C 125 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL B 334 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG C 123 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS B 336 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR C 121 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.517A pdb=" N MET C 73 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU C 157 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL C 75 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 162 through 163 removed outlier: 4.216A pdb=" N LEU C 162 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 217 through 220 removed outlier: 6.726A pdb=" N LYS C 174 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL C 244 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR C 176 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER C 246 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 178 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR C 294 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N GLY C 261 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP C 262 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 277 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 233 through 236 removed outlier: 3.960A pdb=" N ALA C 302 " --> pdb=" O ILE C 257 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 594 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: 2.40 Time building geometry restraints manager: 3.58 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: 2554 1.34 - 1.45: 1241 1.45 - 1.57: 4101 1.57 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 7953 Sorted by residual: bond pdb=" CB ILE B 9 " pdb=" CG1 ILE B 9 " ideal model delta sigma weight residual 1.530 1.559 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" CB ILE A 9 " pdb=" CG1 ILE A 9 " ideal model delta sigma weight residual 1.530 1.559 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" CB ILE C 9 " pdb=" CG1 ILE C 9 " ideal model delta sigma weight residual 1.530 1.559 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" CG LYS C 166 " pdb=" CD LYS C 166 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.79e-01 bond pdb=" CG LYS B 166 " pdb=" CD LYS B 166 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.28e-01 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.63: 351 106.63 - 113.48: 4299 113.48 - 120.33: 2770 120.33 - 127.18: 3297 127.18 - 134.03: 128 Bond angle restraints: 10845 Sorted by residual: angle pdb=" CA ILE B 9 " pdb=" CB ILE B 9 " pdb=" CG1 ILE B 9 " ideal model delta sigma weight residual 110.40 119.20 -8.80 1.70e+00 3.46e-01 2.68e+01 angle pdb=" CA ILE C 9 " pdb=" CB ILE C 9 " pdb=" CG1 ILE C 9 " ideal model delta sigma weight residual 110.40 119.19 -8.79 1.70e+00 3.46e-01 2.67e+01 angle pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " pdb=" CG1 ILE A 9 " ideal model delta sigma weight residual 110.40 119.18 -8.78 1.70e+00 3.46e-01 2.67e+01 angle pdb=" CB ILE A 9 " pdb=" CG1 ILE A 9 " pdb=" CD1 ILE A 9 " ideal model delta sigma weight residual 113.80 124.32 -10.52 2.10e+00 2.27e-01 2.51e+01 angle pdb=" CB ILE C 9 " pdb=" CG1 ILE C 9 " pdb=" CD1 ILE C 9 " ideal model delta sigma weight residual 113.80 124.31 -10.51 2.10e+00 2.27e-01 2.50e+01 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4205 16.73 - 33.45: 328 33.45 - 50.18: 81 50.18 - 66.90: 33 66.90 - 83.63: 9 Dihedral angle restraints: 4656 sinusoidal: 1812 harmonic: 2844 Sorted by residual: dihedral pdb=" CA HIS C 306 " pdb=" C HIS C 306 " pdb=" N ASN C 307 " pdb=" CA ASN C 307 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA HIS A 306 " pdb=" C HIS A 306 " pdb=" N ASN A 307 " pdb=" CA ASN A 307 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA HIS B 306 " pdb=" C HIS B 306 " pdb=" N ASN B 307 " pdb=" CA ASN B 307 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 690 0.032 - 0.063: 289 0.063 - 0.094: 142 0.094 - 0.126: 65 0.126 - 0.157: 11 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CB ILE A 9 " pdb=" CA ILE A 9 " pdb=" CG1 ILE A 9 " pdb=" CG2 ILE A 9 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CB ILE B 9 " pdb=" CA ILE B 9 " pdb=" CG1 ILE B 9 " pdb=" CG2 ILE B 9 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB ILE C 9 " pdb=" CA ILE C 9 " pdb=" CG1 ILE C 9 " pdb=" CG2 ILE C 9 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1194 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 198 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 199 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 198 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 199 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 199 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 199 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 115 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO C 116 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " -0.017 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 134 2.65 - 3.22: 6625 3.22 - 3.78: 11078 3.78 - 4.34: 16985 4.34 - 4.90: 28331 Nonbonded interactions: 63153 Sorted by model distance: nonbonded pdb=" NE2 HIS C 306 " pdb="CU CU A 501 " model vdw 2.093 2.320 nonbonded pdb=" NE2 HIS A 100 " pdb="CU CU A 501 " model vdw 2.113 2.320 nonbonded pdb=" NE2 HIS B 100 " pdb="CU CU B 501 " model vdw 2.114 2.320 nonbonded pdb=" NE2 HIS C 100 " pdb="CU CU C 501 " model vdw 2.114 2.320 nonbonded pdb=" NE2 HIS B 306 " pdb="CU CU C 501 " model vdw 2.115 2.320 ... (remaining 63148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 5.780 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: 0.010 Extract box with map and model: 24.690 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.250 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7953 Z= 0.304 Angle : 0.653 10.523 10845 Z= 0.353 Chirality : 0.048 0.157 1197 Planarity : 0.004 0.031 1422 Dihedral : 14.335 83.626 2850 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.68 % Allowed : 11.03 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.21), residues: 996 helix: -2.51 (0.47), residues: 69 sheet: -0.28 (0.28), residues: 282 loop : -2.13 (0.18), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 265 HIS 0.006 0.001 HIS B 306 PHE 0.012 0.002 PHE C 320 TYR 0.010 0.001 TYR A 134 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 0.921 Fit side-chains outliers start: 30 outliers final: 5 residues processed: 102 average time/residue: 1.3781 time to fit residues: 148.3968 Evaluate side-chains 59 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.1879 > 50: distance: 52 - 239: 8.513 distance: 55 - 236: 10.378 distance: 97 - 281: 28.630 distance: 100 - 278: 8.282 distance: 113 - 262: 21.797 distance: 116 - 259: 18.531 distance: 129 - 248: 31.195 distance: 132 - 245: 20.636 distance: 143 - 230: 33.715 distance: 146 - 227: 33.501 distance: 210 - 216: 21.670 distance: 216 - 217: 17.243 distance: 216 - 222: 13.280 distance: 217 - 218: 42.366 distance: 217 - 220: 22.568 distance: 218 - 219: 8.022 distance: 218 - 223: 52.041 distance: 220 - 221: 16.871 distance: 221 - 222: 51.993 distance: 225 - 227: 37.815 distance: 227 - 228: 20.923 distance: 228 - 229: 20.217 distance: 228 - 231: 14.267 distance: 229 - 230: 3.166 distance: 229 - 236: 24.193 distance: 231 - 232: 16.643 distance: 232 - 233: 25.209 distance: 233 - 234: 11.336 distance: 233 - 235: 8.857 distance: 236 - 237: 6.611 distance: 237 - 238: 17.507 distance: 237 - 240: 10.923 distance: 238 - 239: 12.580 distance: 238 - 245: 6.177 distance: 240 - 241: 16.682 distance: 241 - 242: 25.465 distance: 242 - 243: 12.104 distance: 242 - 244: 18.157 distance: 245 - 246: 12.597 distance: 246 - 247: 15.176 distance: 246 - 249: 9.681 distance: 247 - 248: 21.789 distance: 247 - 252: 17.907 distance: 249 - 251: 12.825 distance: 252 - 253: 18.301 distance: 253 - 254: 11.518 distance: 253 - 256: 6.206 distance: 254 - 255: 10.007 distance: 254 - 259: 8.972 distance: 256 - 257: 5.373 distance: 256 - 258: 9.424 distance: 259 - 260: 14.019 distance: 260 - 261: 13.983 distance: 260 - 263: 12.270 distance: 261 - 262: 17.295 distance: 261 - 267: 5.007 distance: 263 - 264: 4.535 distance: 264 - 265: 6.040 distance: 264 - 266: 6.077 distance: 267 - 268: 7.370 distance: 268 - 269: 9.998 distance: 268 - 271: 13.300 distance: 269 - 270: 4.708 distance: 269 - 278: 7.778 distance: 271 - 272: 40.256 distance: 272 - 273: 11.453 distance: 273 - 274: 40.565 distance: 274 - 275: 26.082 distance: 275 - 276: 41.070 distance: 275 - 277: 36.668 distance: 278 - 279: 12.759 distance: 279 - 280: 13.860 distance: 279 - 282: 11.678 distance: 280 - 281: 4.316 distance: 280 - 289: 3.979 distance: 282 - 283: 14.331 distance: 283 - 284: 9.330 distance: 283 - 285: 10.029 distance: 284 - 286: 12.131 distance: 285 - 287: 12.866 distance: 286 - 288: 5.771 distance: 287 - 288: 10.453 distance: 289 - 290: 6.812 distance: 290 - 291: 12.931 distance: 290 - 293: 20.258 distance: 291 - 292: 11.697 distance: 291 - 298: 7.753 distance: 293 - 294: 8.635 distance: 294 - 295: 22.138 distance: 295 - 296: 11.438 distance: 296 - 297: 12.339