Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:57:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199_updated_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199_updated_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199_updated_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/12_2022/6hcy_0199_updated_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 11007 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "B" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.75, per 1000 atoms: 0.61 Number of scatterers: 11007 At special positions: 0 Unit cell: (92.6478, 95.0859, 116.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 51 16.00 P 18 15.00 O 1926 8.00 N 1800 7.00 C 7209 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=3, symmetry=0 Links applied NAG-ASN " NAG A 504 " - " ASN A 323 " " NAG B 504 " - " ASN B 323 " " NAG C 504 " - " ASN C 323 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 6 sheets defined 55.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'C' and resid 29 through 41 removed outlier: 3.532A pdb=" N GLN C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.848A pdb=" N LYS C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.641A pdb=" N THR C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 160 through 172 removed outlier: 3.509A pdb=" N ARG C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 removed outlier: 3.822A pdb=" N LYS C 187 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 188 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 189 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 201 through 222 removed outlier: 3.708A pdb=" N PHE C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 221 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 228 No H-bonds generated for 'chain 'C' and resid 225 through 228' Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 243 through 256 Proline residue: C 248 - end of helix Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.516A pdb=" N ALA C 266 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 315 through 330 Processing helix chain 'C' and resid 339 through 365 removed outlier: 4.078A pdb=" N VAL C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 385 through 403 removed outlier: 3.554A pdb=" N LEU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 398 " --> pdb=" O CYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.593A pdb=" N ASN C 444 " --> pdb=" O PRO C 440 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 41 removed outlier: 3.532A pdb=" N GLN A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.849A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.641A pdb=" N THR A 90 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 160 through 172 removed outlier: 3.509A pdb=" N ARG A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.822A pdb=" N LYS A 187 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 189 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 190 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 201 through 222 removed outlier: 3.707A pdb=" N PHE A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 243 through 256 Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.516A pdb=" N ALA A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'A' and resid 339 through 365 removed outlier: 4.078A pdb=" N VAL A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 385 through 403 removed outlier: 3.555A pdb=" N LEU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 438 Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.593A pdb=" N ASN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.532A pdb=" N GLN B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.849A pdb=" N LYS B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.641A pdb=" N THR B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 160 through 172 removed outlier: 3.509A pdb=" N ARG B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.822A pdb=" N LYS B 187 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 188 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 190 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 201 through 222 removed outlier: 3.709A pdb=" N PHE B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 243 through 256 Proline residue: B 248 - end of helix Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.516A pdb=" N ALA B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 290 through 308 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 339 through 365 removed outlier: 4.077A pdb=" N VAL B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 385 through 403 removed outlier: 3.554A pdb=" N LEU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 398 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 438 Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.593A pdb=" N ASN B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.253A pdb=" N ILE C 76 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE C 25 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 78 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE C 100 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 79 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 102 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS C 129 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP C 103 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 131 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 152 through 155 removed outlier: 6.272A pdb=" N THR C 176 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 155 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET C 178 " --> pdb=" O VAL C 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.253A pdb=" N ILE A 76 " --> pdb=" O CYS A 23 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE A 25 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 78 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE A 100 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 79 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 102 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS A 129 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP A 103 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 131 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 152 through 155 removed outlier: 6.272A pdb=" N THR A 176 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 155 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET A 178 " --> pdb=" O VAL A 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.253A pdb=" N ILE B 76 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 25 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 78 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE B 100 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 79 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 102 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS B 129 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 103 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 131 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 152 through 155 removed outlier: 6.272A pdb=" N THR B 176 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 155 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET B 178 " --> pdb=" O VAL B 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 411 hydrogen bonds defined for protein. 1188 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: 3.21 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3496 1.36 - 1.55: 7702 1.55 - 1.73: 40 1.73 - 1.91: 78 1.91 - 2.10: 9 Bond restraints: 11325 Sorted by residual: bond pdb=" C1D NAP B 501 " pdb=" C2D NAP B 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP A 501 " pdb=" C2D NAP A 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP C 501 " pdb=" C2D NAP C 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP B 501 " pdb=" O4D NAP B 501 " ideal model delta sigma weight residual 1.375 1.611 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1D NAP C 501 " pdb=" O4D NAP C 501 " ideal model delta sigma weight residual 1.375 1.610 -0.235 2.00e-02 2.50e+03 1.39e+02 ... (remaining 11320 not shown) Histogram of bond angle deviations from ideal: 86.47 - 104.87: 226 104.87 - 123.26: 14706 123.26 - 141.66: 560 141.66 - 160.05: 0 160.05 - 178.45: 6 Bond angle restraints: 15498 Sorted by residual: angle pdb=" CB ARG A 290 " pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " ideal model delta sigma weight residual 111.30 100.17 11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" CB ARG C 290 " pdb=" CG ARG C 290 " pdb=" CD ARG C 290 " ideal model delta sigma weight residual 111.30 100.18 11.12 2.30e+00 1.89e-01 2.34e+01 angle pdb=" CB ARG B 290 " pdb=" CG ARG B 290 " pdb=" CD ARG B 290 " ideal model delta sigma weight residual 111.30 100.20 11.10 2.30e+00 1.89e-01 2.33e+01 angle pdb=" O1N NAP B 501 " pdb=" PN NAP B 501 " pdb=" O2N NAP B 501 " ideal model delta sigma weight residual 122.51 109.02 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" O1N NAP C 501 " pdb=" PN NAP C 501 " pdb=" O2N NAP C 501 " ideal model delta sigma weight residual 122.51 109.03 13.48 3.00e+00 1.11e-01 2.02e+01 ... (remaining 15493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 6357 34.81 - 69.63: 78 69.63 - 104.44: 21 104.44 - 139.25: 0 139.25 - 174.06: 3 Dihedral angle restraints: 6459 sinusoidal: 2634 harmonic: 3825 Sorted by residual: dihedral pdb=" C2C HEM A 502 " pdb=" C3C HEM A 502 " pdb=" CAC HEM A 502 " pdb=" CBC HEM A 502 " ideal model delta sinusoidal sigma weight residual -0.00 -80.33 80.33 2 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" C2C HEM C 502 " pdb=" C3C HEM C 502 " pdb=" CAC HEM C 502 " pdb=" CBC HEM C 502 " ideal model delta sinusoidal sigma weight residual 0.00 -80.30 80.30 2 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" C2C HEM B 502 " pdb=" C3C HEM B 502 " pdb=" CAC HEM B 502 " pdb=" CBC HEM B 502 " ideal model delta sinusoidal sigma weight residual 0.00 -80.25 80.25 2 1.00e+01 1.00e-02 4.66e+01 ... (remaining 6456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1387 0.071 - 0.142: 297 0.142 - 0.214: 50 0.214 - 0.285: 3 0.285 - 0.356: 6 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C2B NAP B 501 " pdb=" C1B NAP B 501 " pdb=" C3B NAP B 501 " pdb=" O2B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C2B NAP C 501 " pdb=" C1B NAP C 501 " pdb=" C3B NAP C 501 " pdb=" O2B NAP C 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1740 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 286 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP B 286 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 286 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 286 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 286 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 286 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 286 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 286 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 286 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 286 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP C 286 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 286 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 286 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 286 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 286 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 286 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 286 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 286 " -0.004 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 49 2.59 - 3.17: 8727 3.17 - 3.75: 16777 3.75 - 4.32: 24605 4.32 - 4.90: 39678 Nonbonded interactions: 89836 Sorted by model distance: nonbonded pdb=" NE2 HIS A 304 " pdb="FE HEM A 502 " model vdw 2.017 3.080 nonbonded pdb=" NE2 HIS C 304 " pdb="FE HEM C 502 " model vdw 2.018 3.080 nonbonded pdb=" NE2 HIS B 304 " pdb="FE HEM B 502 " model vdw 2.018 3.080 nonbonded pdb=" O3' FAD B 503 " pdb=" O5' FAD B 503 " model vdw 2.260 2.440 nonbonded pdb=" O3' FAD C 503 " pdb=" O5' FAD C 503 " model vdw 2.260 2.440 ... (remaining 89831 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 18 5.49 5 S 51 5.16 5 C 7209 2.51 5 N 1800 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.740 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: 6.230 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.110 Process input model: 29.700 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 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 : 0.015 0.237 11325 Z= 0.905 Angle : 1.260 13.491 15498 Z= 0.590 Chirality : 0.065 0.356 1743 Planarity : 0.008 0.058 1839 Dihedral : 13.936 174.064 4005 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 0.79 % 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: -6.30 (0.15), residues: 1302 helix: -4.31 (0.07), residues: 846 sheet: -1.97 (0.42), residues: 141 loop : -3.85 (0.29), residues: 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 222 time to evaluate : 1.161 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 231 average time/residue: 0.2830 time to fit residues: 86.3218 Evaluate side-chains 107 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN C 143 GLN C 234 ASN C 372 ASN A 234 ASN A 372 ASN B 111 ASN B 234 ASN B 372 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11325 Z= 0.208 Angle : 0.669 11.599 15498 Z= 0.310 Chirality : 0.042 0.142 1743 Planarity : 0.006 0.043 1839 Dihedral : 13.416 168.663 1590 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.20), residues: 1302 helix: -2.00 (0.15), residues: 828 sheet: -1.51 (0.43), residues: 141 loop : -3.14 (0.32), residues: 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 1.222 Fit side-chains outliers start: 37 outliers final: 19 residues processed: 155 average time/residue: 0.2507 time to fit residues: 53.9827 Evaluate side-chains 119 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1090 time to fit residues: 5.4643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN A 372 ASN B 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11325 Z= 0.214 Angle : 0.613 8.366 15498 Z= 0.280 Chirality : 0.042 0.125 1743 Planarity : 0.004 0.039 1839 Dihedral : 12.710 164.759 1590 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.67 % 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: -1.95 (0.23), residues: 1302 helix: -0.57 (0.17), residues: 831 sheet: -1.24 (0.43), residues: 135 loop : -2.84 (0.33), residues: 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.258 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 127 average time/residue: 0.2661 time to fit residues: 46.9162 Evaluate side-chains 103 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1210 time to fit residues: 3.4292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 0.0060 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN C 372 ASN A 111 ASN B 111 ASN B 372 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 11325 Z= 0.254 Angle : 0.608 8.286 15498 Z= 0.278 Chirality : 0.042 0.123 1743 Planarity : 0.004 0.041 1839 Dihedral : 12.504 164.751 1590 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 2.20 % 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: -1.09 (0.24), residues: 1302 helix: 0.14 (0.18), residues: 825 sheet: -0.96 (0.44), residues: 135 loop : -2.57 (0.34), residues: 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.258 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 119 average time/residue: 0.2785 time to fit residues: 45.6774 Evaluate side-chains 106 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0990 time to fit residues: 3.0172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 11325 Z= 0.275 Angle : 0.623 11.757 15498 Z= 0.280 Chirality : 0.043 0.212 1743 Planarity : 0.004 0.037 1839 Dihedral : 12.050 162.988 1590 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.23 % 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: -0.56 (0.24), residues: 1302 helix: 0.54 (0.19), residues: 825 sheet: -0.49 (0.47), residues: 117 loop : -2.40 (0.33), residues: 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 108 average time/residue: 0.2932 time to fit residues: 42.9917 Evaluate side-chains 95 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1204 time to fit residues: 2.7983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11325 Z= 0.189 Angle : 0.578 9.140 15498 Z= 0.261 Chirality : 0.041 0.146 1743 Planarity : 0.004 0.035 1839 Dihedral : 11.806 163.931 1590 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.88 % 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: -0.21 (0.25), residues: 1302 helix: 0.83 (0.19), residues: 828 sheet: -0.34 (0.47), residues: 117 loop : -2.36 (0.33), residues: 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 105 average time/residue: 0.2700 time to fit residues: 39.5686 Evaluate side-chains 96 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0985 time to fit residues: 2.4962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11325 Z= 0.188 Angle : 0.568 8.071 15498 Z= 0.259 Chirality : 0.041 0.127 1743 Planarity : 0.004 0.035 1839 Dihedral : 11.674 164.162 1590 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 1.23 % 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: 0.09 (0.25), residues: 1302 helix: 1.10 (0.19), residues: 828 sheet: -0.24 (0.48), residues: 117 loop : -2.30 (0.34), residues: 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 106 average time/residue: 0.2814 time to fit residues: 41.2356 Evaluate side-chains 94 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1065 time to fit residues: 2.4453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11325 Z= 0.236 Angle : 0.591 7.922 15498 Z= 0.268 Chirality : 0.042 0.142 1743 Planarity : 0.004 0.033 1839 Dihedral : 11.632 163.406 1590 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.88 % 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: 0.18 (0.25), residues: 1302 helix: 1.14 (0.19), residues: 828 sheet: -0.15 (0.48), residues: 117 loop : -2.25 (0.34), residues: 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 96 average time/residue: 0.2908 time to fit residues: 38.1894 Evaluate side-chains 92 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1160 time to fit residues: 2.4488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-dev-4807/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-dev-4807/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: 69.4042 > 50: distance: 65 - 73: 29.215 distance: 73 - 74: 14.900 distance: 74 - 75: 11.365 distance: 74 - 77: 5.076 distance: 75 - 76: 3.815 distance: 75 - 81: 38.929 distance: 77 - 78: 39.751 distance: 78 - 79: 40.739 distance: 79 - 80: 13.940 distance: 81 - 82: 41.165 distance: 82 - 83: 36.679 distance: 82 - 85: 11.323 distance: 83 - 84: 39.861 distance: 83 - 86: 10.355 distance: 86 - 87: 30.673 distance: 87 - 90: 10.514 distance: 88 - 89: 32.379 distance: 88 - 94: 13.021 distance: 90 - 91: 26.511 distance: 90 - 92: 14.856 distance: 94 - 95: 32.912 distance: 95 - 96: 13.767 distance: 96 - 100: 38.969 distance: 98 - 99: 14.776 distance: 100 - 101: 32.246 distance: 101 - 102: 41.691 distance: 101 - 104: 7.483 distance: 102 - 103: 22.564 distance: 102 - 108: 50.600 distance: 109 - 112: 26.528 distance: 111 - 142: 53.510 distance: 112 - 113: 12.133 distance: 113 - 114: 40.317 distance: 116 - 119: 3.006 distance: 117 - 118: 35.295 distance: 117 - 123: 33.665 distance: 119 - 120: 38.191 distance: 123 - 124: 7.894 distance: 124 - 125: 3.172 distance: 124 - 127: 18.045 distance: 125 - 126: 8.014 distance: 125 - 134: 44.480 distance: 127 - 128: 6.108 distance: 130 - 131: 34.060 distance: 131 - 132: 10.456 distance: 131 - 133: 35.103 distance: 134 - 135: 21.092 distance: 135 - 136: 18.638 distance: 135 - 138: 18.760 distance: 136 - 137: 4.554 distance: 136 - 142: 5.809 distance: 138 - 139: 37.536 distance: 138 - 140: 19.064 distance: 139 - 141: 56.567 distance: 142 - 143: 38.484 distance: 143 - 144: 12.514 distance: 143 - 146: 9.796 distance: 144 - 145: 21.008 distance: 144 - 153: 24.225 distance: 145 - 175: 32.756 distance: 146 - 147: 26.341 distance: 147 - 149: 69.234 distance: 150 - 152: 56.114 distance: 151 - 152: 38.077