Starting phenix.real_space_refine on Thu Jan 16 12:16:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eyi_50054/01_2025/9eyi_50054.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eyi_50054/01_2025/9eyi_50054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eyi_50054/01_2025/9eyi_50054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eyi_50054/01_2025/9eyi_50054.map" model { file = "/net/cci-nas-00/data/ceres_data/9eyi_50054/01_2025/9eyi_50054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eyi_50054/01_2025/9eyi_50054.cif" } resolution = 2.75 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= 1.000 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 P 8 5.49 5 S 27 5.16 5 C 6129 2.51 5 N 1614 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9453 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3594 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 469} Chain breaks: 4 Unresolved non-hydrogen bonds: 399 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 25, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 250 Chain: "B" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3416 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 15, 'TRANS': 456} Chain breaks: 6 Unresolved non-hydrogen bonds: 451 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 24, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 275 Chain: "C" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2265 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 16, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {'A3P': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 3} Link IDs: {'rna2p': 2, None: 1} Not linked: pdbres=" A D 3 " pdbres="A3P D 4 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {'A3P': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 3} Link IDs: {'rna2p': 2, None: 1} Not linked: pdbres=" A E 3 " pdbres="A3P E 4 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.09, per 1000 atoms: 0.64 Number of scatterers: 9453 At special positions: 0 Unit cell: (72.6, 126.5, 117.7, 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) S 27 16.00 P 8 15.00 O 1675 8.00 N 1614 7.00 C 6129 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 13 sheets defined 45.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.553A pdb=" N GLN A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 49 through 64 removed outlier: 3.594A pdb=" N LYS A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.874A pdb=" N LEU A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.708A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.905A pdb=" N ALA A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.596A pdb=" N VAL A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 208 through 218 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.871A pdb=" N LYS A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.531A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.918A pdb=" N LEU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 433 through 451 removed outlier: 3.578A pdb=" N LEU A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.777A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.939A pdb=" N LYS B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.649A pdb=" N TRP B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.532A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.679A pdb=" N GLN B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 433 through 451 removed outlier: 3.541A pdb=" N LEU B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 475 Processing helix chain 'B' and resid 501 through 505 removed outlier: 4.138A pdb=" N LEU B 504 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 231 through 250 removed outlier: 3.761A pdb=" N LYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 291 through 303 removed outlier: 4.209A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.512A pdb=" N GLN C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 433 through 451 removed outlier: 3.522A pdb=" N ARG C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 4.137A pdb=" N ASN A 141 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 6.724A pdb=" N ALA A 175 " --> pdb=" O VAL A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 274 removed outlier: 7.935A pdb=" N ILE A 271 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE A 226 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY A 273 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 228 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER A 334 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP A 310 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A 336 " --> pdb=" O TRP A 310 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 312 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET A 338 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL A 333 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 350 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 335 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 378 removed outlier: 5.125A pdb=" N GLN A 460 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 485 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 498 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS A 484 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N CYS A 496 " --> pdb=" O HIS A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.746A pdb=" N LEU B 121 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE B 146 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 176 removed outlier: 6.789A pdb=" N ALA B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.696A pdb=" N GLU B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 270 through 271 removed outlier: 8.036A pdb=" N ILE B 271 " --> pdb=" O PRO B 224 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 226 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N SER B 334 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP B 310 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU B 336 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR B 312 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 333 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE B 350 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 335 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 346 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 373 through 378 removed outlier: 7.828A pdb=" N LEU B 416 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY B 388 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 418 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 390 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ALA B 420 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N TYR B 392 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 456 " --> pdb=" O ASP B 481 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR B 483 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 458 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR B 485 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLN B 460 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS B 484 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N CYS B 496 " --> pdb=" O HIS B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 270 through 273 removed outlier: 7.803A pdb=" N ILE C 271 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE C 226 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY C 273 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 228 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER C 334 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP C 310 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 336 " --> pdb=" O TRP C 310 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR C 312 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N MET C 338 " --> pdb=" O TYR C 312 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 335 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 373 through 379 removed outlier: 4.321A pdb=" N ASN C 414 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 387 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE C 459 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE C 389 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N THR C 461 " --> pdb=" O PHE C 389 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 391 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 456 " --> pdb=" O ASP C 481 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR C 483 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 458 " --> pdb=" O TYR C 483 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR C 485 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N GLN C 460 " --> pdb=" O TYR C 485 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 498 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS C 484 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N CYS C 496 " --> pdb=" O HIS C 484 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1269 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: 3.09 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1507 1.31 - 1.43: 2677 1.43 - 1.56: 5437 1.56 - 1.69: 14 1.69 - 1.82: 43 Bond restraints: 9678 Sorted by residual: bond pdb=" CA LEU A 319 " pdb=" C LEU A 319 " ideal model delta sigma weight residual 1.523 1.406 0.117 1.41e-02 5.03e+03 6.85e+01 bond pdb=" C GLN C 409 " pdb=" N LEU C 410 " ideal model delta sigma weight residual 1.332 1.442 -0.110 1.53e-02 4.27e+03 5.17e+01 bond pdb=" O2P A3P D 4 " pdb=" P1 A3P D 4 " ideal model delta sigma weight residual 1.610 1.470 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O3P A3P E 4 " pdb=" P1 A3P E 4 " ideal model delta sigma weight residual 1.610 1.476 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" O2P A3P E 4 " pdb=" P1 A3P E 4 " ideal model delta sigma weight residual 1.610 1.478 0.132 2.00e-02 2.50e+03 4.34e+01 ... (remaining 9673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 13157 3.08 - 6.16: 46 6.16 - 9.24: 10 9.24 - 12.31: 5 12.31 - 15.39: 4 Bond angle restraints: 13222 Sorted by residual: angle pdb=" C3' A3P D 4 " pdb=" O3' A3P D 4 " pdb=" P1 A3P D 4 " ideal model delta sigma weight residual 106.84 122.23 -15.39 3.00e+00 1.11e-01 2.63e+01 angle pdb=" N LEU A 321 " pdb=" CA LEU A 321 " pdb=" C LEU A 321 " ideal model delta sigma weight residual 111.28 106.10 5.18 1.09e+00 8.42e-01 2.26e+01 angle pdb=" C5' A3P D 4 " pdb=" O5' A3P D 4 " pdb=" P2 A3P D 4 " ideal model delta sigma weight residual 106.77 120.86 -14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C5' A3P E 4 " pdb=" O5' A3P E 4 " pdb=" P2 A3P E 4 " ideal model delta sigma weight residual 106.77 120.79 -14.02 3.00e+00 1.11e-01 2.19e+01 angle pdb=" N LEU A 319 " pdb=" CA LEU A 319 " pdb=" C LEU A 319 " ideal model delta sigma weight residual 113.20 107.55 5.65 1.21e+00 6.83e-01 2.18e+01 ... (remaining 13217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5084 17.96 - 35.92: 429 35.92 - 53.88: 131 53.88 - 71.83: 27 71.83 - 89.79: 9 Dihedral angle restraints: 5680 sinusoidal: 2019 harmonic: 3661 Sorted by residual: dihedral pdb=" CA GLN A 460 " pdb=" C GLN A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" C LEU A 319 " pdb=" N LEU A 319 " pdb=" CA LEU A 319 " pdb=" CB LEU A 319 " ideal model delta harmonic sigma weight residual -122.60 -114.29 -8.31 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CA GLU C 339 " pdb=" C GLU C 339 " pdb=" N PHE C 340 " pdb=" CA PHE C 340 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1140 0.044 - 0.088: 276 0.088 - 0.133: 104 0.133 - 0.177: 4 0.177 - 0.221: 3 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C2' A3P D 4 " pdb=" C3' A3P D 4 " pdb=" O2' A3P D 4 " pdb=" C1' A3P D 4 " both_signs ideal model delta sigma weight residual False -2.72 -2.50 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE C 350 " pdb=" CA ILE C 350 " pdb=" CG1 ILE C 350 " pdb=" CG2 ILE C 350 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C2' A3P E 4 " pdb=" C3' A3P E 4 " pdb=" O2' A3P E 4 " pdb=" C1' A3P E 4 " both_signs ideal model delta sigma weight residual False -2.72 -2.51 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1524 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 318 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C THR A 318 " 0.050 2.00e-02 2.50e+03 pdb=" O THR A 318 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 319 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 381 " 0.032 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO C 382 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 260 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP A 260 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 260 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 260 " 0.010 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1026 2.75 - 3.29: 9241 3.29 - 3.82: 16885 3.82 - 4.36: 20233 4.36 - 4.90: 34056 Nonbonded interactions: 81441 Sorted by model distance: nonbonded pdb=" NE2 GLN B 285 " pdb=" O VAL B 497 " model vdw 2.211 3.120 nonbonded pdb=" OG SER C 395 " pdb=" O1P A3P E 4 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 312 " pdb=" OE1 GLN B 320 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR C 312 " pdb=" OE1 GLN C 320 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR C 345 " pdb=" N7 A E 3 " model vdw 2.244 3.120 ... (remaining 81436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 through 23 and (name N or name CA or name C or name O o \ r name CB )) or resid 24 through 26 or (resid 27 through 30 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 62 or resid 66 through \ 85 or (resid 86 through 88 and (name N or name CA or name C or name O or name CB \ )) or resid 89 through 92 or (resid 93 and (name N or name CA or name C or name \ O or name CB )) or resid 94 through 96 or (resid 104 through 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 127 or (resid 12 \ 8 through 130 and (name N or name CA or name C or name O or name CB )) or resid \ 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or re \ sid 133 through 152 or (resid 153 through 154 and (name N or name CA or name C o \ r name O or name CB )) or resid 155 through 165 or (resid 166 through 173 and (n \ ame N or name CA or name C or name O or name CB )) or resid 174 through 182 or ( \ resid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 \ through 189 or resid 201 through 212 or (resid 213 through 214 and (name N or na \ me CA or name C or name O or name CB )) or resid 215 through 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 275 or (resid 276 and (name N or name CA or name C or name O or nam \ e CB )) or resid 277 through 293 or (resid 294 and (name N or name CA or name C \ or name O or name CB )) or resid 295 through 300 or (resid 301 and (name N or na \ me CA or name C or name O or name CB )) or resid 302 through 303 or (resid 304 a \ nd (name N or name CA or name C or name O or name CB )) or resid 305 through 339 \ or (resid 340 through 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 or (resid 344 and (name N or name CA or name C or name O or nam \ e CB )) or resid 345 through 366 or (resid 367 through 369 and (name N or name C \ A or name C or name O or name CB )) or resid 370 or (resid 371 and (name N or na \ me CA or name C or name O or name CB )) or resid 372 through 375 or (resid 376 a \ nd (name N or name CA or name C or name O or name CB )) or resid 377 through 380 \ or (resid 381 and (name N or name CA or name C or name O or name CB )) or resid \ 382 through 395 or (resid 396 and (name N or name CA or name C or name O or nam \ e CB )) or resid 397 through 421 or (resid 422 and (name N or name CA or name C \ or name O or name CB )) or (resid 426 and (name N or name CA or name C or name O \ or name CB )) or resid 427 or (resid 428 and (name N or name CA or name C or na \ me O or name CB )) or resid 429 through 430 or (resid 431 and (name N or name CA \ or name C or name O or name CB )) or resid 432 through 486 or (resid 487 throug \ h 489 and (name N or name CA or name C or name O or name CB )) or resid 492 thro \ ugh 503 or (resid 504 through 505 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'B' and (resid 4 through 13 or resid 18 through 39 or (resid 40 through 4 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 49 through 6 \ 7 or (resid 68 through 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 106 or (resid 107 and (name N or name CA or name C or nam \ e O or name CB )) or resid 108 through 146 or (resid 147 through 149 and (name N \ or name CA or name C or name O or name CB )) or resid 150 through 166 or resid \ 171 through 296 or (resid 297 and (name N or name CA or name C or name O or name \ CB )) or resid 298 through 338 or (resid 339 through 342 and (name N or name CA \ or name C or name O or name CB )) or resid 343 through 368 or (resid 369 and (n \ ame N or name CA or name C or name O or name CB )) or resid 370 through 505)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.720 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.570 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.140 9678 Z= 0.397 Angle : 0.633 15.392 13222 Z= 0.305 Chirality : 0.044 0.221 1527 Planarity : 0.003 0.050 1651 Dihedral : 15.674 89.791 3304 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.15 % Allowed : 19.59 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.12 (0.25), residues: 1220 helix: 1.43 (0.24), residues: 484 sheet: -0.45 (0.34), residues: 258 loop : -0.97 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 215 HIS 0.006 0.001 HIS C 476 PHE 0.016 0.001 PHE B 498 TYR 0.010 0.001 TYR A 436 ARG 0.007 0.000 ARG C 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7938 (mp10) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.9852 time to fit residues: 111.0259 Evaluate side-chains 96 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.117605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.095451 restraints weight = 19424.208| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.27 r_work: 0.3389 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9678 Z= 0.225 Angle : 0.543 8.448 13222 Z= 0.281 Chirality : 0.044 0.207 1527 Planarity : 0.004 0.036 1651 Dihedral : 10.231 71.846 1459 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.35 % Allowed : 17.44 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.26 (0.25), residues: 1220 helix: 1.51 (0.24), residues: 512 sheet: -0.39 (0.34), residues: 257 loop : -0.99 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 433 HIS 0.004 0.001 HIS C 476 PHE 0.018 0.001 PHE B 498 TYR 0.012 0.001 TYR A 436 ARG 0.005 0.001 ARG C 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8466 (mm-40) REVERT: B 49 ASN cc_start: 0.8176 (t0) cc_final: 0.7810 (t0) REVERT: B 205 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7788 (mpp80) REVERT: B 240 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7886 (ttpp) REVERT: C 252 TRP cc_start: 0.7716 (p-90) cc_final: 0.7405 (p-90) REVERT: C 455 ARG cc_start: 0.8554 (tpp-160) cc_final: 0.8085 (tpp-160) outliers start: 28 outliers final: 9 residues processed: 118 average time/residue: 0.9025 time to fit residues: 117.7829 Evaluate side-chains 95 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.0040 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.119182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.098547 restraints weight = 19937.288| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.19 r_work: 0.3430 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9678 Z= 0.207 Angle : 0.527 7.818 13222 Z= 0.269 Chirality : 0.043 0.183 1527 Planarity : 0.003 0.034 1651 Dihedral : 9.704 69.009 1441 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.46 % Allowed : 18.52 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.34 (0.25), residues: 1220 helix: 1.66 (0.24), residues: 511 sheet: -0.39 (0.34), residues: 257 loop : -1.04 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 433 HIS 0.004 0.001 HIS C 476 PHE 0.016 0.001 PHE B 498 TYR 0.011 0.001 TYR A 436 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8183 (t0) cc_final: 0.7791 (t0) REVERT: B 205 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7839 (mpp80) REVERT: B 240 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7866 (ttpp) REVERT: B 268 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7926 (t0) REVERT: C 252 TRP cc_start: 0.7866 (p-90) cc_final: 0.7622 (p-90) REVERT: C 407 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: C 449 GLN cc_start: 0.7734 (mm110) cc_final: 0.7521 (mm110) REVERT: C 455 ARG cc_start: 0.8409 (tpp-160) cc_final: 0.8130 (tpp-160) outliers start: 29 outliers final: 13 residues processed: 114 average time/residue: 0.9913 time to fit residues: 123.7314 Evaluate side-chains 103 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 0.0010 chunk 122 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN B 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.119143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097948 restraints weight = 19152.021| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.21 r_work: 0.3466 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9678 Z= 0.156 Angle : 0.486 7.346 13222 Z= 0.250 Chirality : 0.042 0.154 1527 Planarity : 0.003 0.039 1651 Dihedral : 9.190 66.774 1438 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.99 % Allowed : 19.24 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.38 (0.25), residues: 1220 helix: 1.69 (0.24), residues: 523 sheet: -0.44 (0.34), residues: 263 loop : -1.04 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 433 HIS 0.005 0.001 HIS C 476 PHE 0.015 0.001 PHE B 498 TYR 0.011 0.001 TYR A 436 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8878 (p) cc_final: 0.8669 (p) REVERT: B 49 ASN cc_start: 0.8115 (t0) cc_final: 0.7734 (t0) REVERT: B 205 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7776 (mpp80) REVERT: B 268 ASP cc_start: 0.8432 (t70) cc_final: 0.7784 (t0) REVERT: C 339 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8462 (tm-30) REVERT: C 407 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: C 455 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.7737 (tpm170) outliers start: 25 outliers final: 9 residues processed: 124 average time/residue: 0.9529 time to fit residues: 129.6740 Evaluate side-chains 102 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6406 > 50: distance: 91 - 96: 29.462 distance: 96 - 97: 42.362 distance: 97 - 98: 20.103 distance: 97 - 100: 18.983 distance: 98 - 108: 20.441 distance: 101 - 102: 56.598 distance: 102 - 104: 13.525 distance: 104 - 106: 24.929 distance: 105 - 106: 40.476 distance: 109 - 110: 31.203 distance: 109 - 112: 19.749 distance: 110 - 111: 21.994 distance: 110 - 118: 21.593 distance: 113 - 115: 46.257 distance: 115 - 117: 26.445 distance: 116 - 117: 30.496 distance: 118 - 119: 12.659 distance: 119 - 120: 33.424 distance: 119 - 122: 44.227 distance: 120 - 121: 15.425 distance: 120 - 130: 44.834 distance: 122 - 123: 3.752 distance: 123 - 124: 7.089 distance: 123 - 125: 21.171 distance: 124 - 126: 14.706 distance: 125 - 127: 16.234 distance: 127 - 128: 14.061 distance: 128 - 129: 40.750 distance: 130 - 131: 28.541 distance: 131 - 134: 30.128 distance: 132 - 139: 40.004 distance: 134 - 135: 29.444 distance: 135 - 136: 15.311 distance: 136 - 137: 10.248 distance: 136 - 138: 24.553 distance: 140 - 141: 39.291 distance: 140 - 143: 37.525 distance: 141 - 150: 40.054 distance: 143 - 144: 3.689 distance: 144 - 145: 14.615 distance: 145 - 147: 31.247 distance: 146 - 148: 12.324 distance: 148 - 149: 27.757 distance: 150 - 151: 3.737 distance: 151 - 152: 33.291 distance: 151 - 154: 37.605 distance: 152 - 153: 8.115 distance: 152 - 158: 7.942 distance: 154 - 155: 56.308 distance: 155 - 157: 40.641 distance: 159 - 160: 40.210 distance: 159 - 162: 24.198 distance: 163 - 164: 40.683 distance: 164 - 167: 39.521 distance: 165 - 166: 39.620 distance: 168 - 169: 33.930 distance: 169 - 170: 38.573 distance: 169 - 172: 6.343 distance: 170 - 171: 43.994 distance: 170 - 173: 19.692 distance: 173 - 174: 46.927 distance: 173 - 179: 32.234 distance: 174 - 175: 3.566 distance: 175 - 176: 53.895 distance: 175 - 180: 33.489 distance: 177 - 178: 56.613 distance: 178 - 179: 39.788