Starting phenix.real_space_refine on Fri Oct 11 08:11:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eyi_50054/10_2024/9eyi_50054.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eyi_50054/10_2024/9eyi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eyi_50054/10_2024/9eyi_50054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eyi_50054/10_2024/9eyi_50054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eyi_50054/10_2024/9eyi_50054.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eyi_50054/10_2024/9eyi_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-5477/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: 5.77, per 1000 atoms: 0.61 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: 2.68 Conformation dependent library (CDL) restraints added in 1.2 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: 1.17 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: 3.02 Time building geometry restraints manager: 3.00 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: 0.610 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.370 Find NCS groups from input model: 0.340 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.079 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: 0.9588 time to fit residues: 108.1004 Evaluate side-chains 96 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8420 (mm-40) REVERT: B 49 ASN cc_start: 0.8078 (t0) cc_final: 0.7754 (t0) REVERT: B 205 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7682 (mpp80) REVERT: B 240 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7845 (ttpp) REVERT: C 252 TRP cc_start: 0.7696 (p-90) cc_final: 0.7413 (p-90) REVERT: C 455 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.8122 (tpp-160) outliers start: 28 outliers final: 9 residues processed: 118 average time/residue: 0.8993 time to fit residues: 116.8650 Evaluate side-chains 95 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9678 Z= 0.184 Angle : 0.520 8.015 13222 Z= 0.265 Chirality : 0.043 0.182 1527 Planarity : 0.003 0.034 1651 Dihedral : 9.676 68.170 1441 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.35 % Allowed : 18.64 % 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: 0.27 (0.25), residues: 1220 helix: 1.57 (0.24), residues: 521 sheet: -0.41 (0.34), residues: 261 loop : -1.09 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8114 (t0) cc_final: 0.7772 (t0) REVERT: B 205 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7774 (mpp80) REVERT: B 268 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7913 (t0) REVERT: C 407 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: C 455 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.8071 (tpp-160) outliers start: 28 outliers final: 12 residues processed: 114 average time/residue: 0.9740 time to fit residues: 121.7055 Evaluate side-chains 100 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 111 optimal weight: 0.9990 chunk 84 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9678 Z= 0.156 Angle : 0.490 7.439 13222 Z= 0.251 Chirality : 0.042 0.153 1527 Planarity : 0.003 0.039 1651 Dihedral : 9.274 66.905 1438 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.11 % Allowed : 19.35 % Favored : 77.54 % 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: 1.71 (0.24), residues: 521 sheet: -0.39 (0.34), residues: 261 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 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 125 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8051 (t0) cc_final: 0.7717 (t0) REVERT: B 205 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7726 (mpp80) REVERT: B 268 ASP cc_start: 0.8295 (t70) cc_final: 0.7717 (t0) REVERT: C 455 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.7727 (tpm170) outliers start: 26 outliers final: 11 residues processed: 119 average time/residue: 0.9225 time to fit residues: 120.8108 Evaluate side-chains 98 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 285 GLN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9678 Z= 0.195 Angle : 0.518 7.820 13222 Z= 0.263 Chirality : 0.043 0.152 1527 Planarity : 0.004 0.058 1651 Dihedral : 9.036 68.311 1436 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.11 % Allowed : 19.95 % Favored : 76.94 % 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: 0.44 (0.25), residues: 1220 helix: 1.73 (0.24), residues: 522 sheet: -0.30 (0.34), residues: 256 loop : -1.07 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 252 HIS 0.005 0.001 HIS C 476 PHE 0.015 0.001 PHE B 498 TYR 0.010 0.001 TYR A 436 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 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 122 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 409 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: B 49 ASN cc_start: 0.8054 (t0) cc_final: 0.7489 (t0) REVERT: B 237 ARG cc_start: 0.7480 (ptp90) cc_final: 0.7187 (ptp90) REVERT: B 268 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7721 (t0) REVERT: C 455 ARG cc_start: 0.8299 (tpp-160) cc_final: 0.7537 (tpt170) REVERT: C 481 ASP cc_start: 0.8047 (m-30) cc_final: 0.7706 (m-30) outliers start: 26 outliers final: 13 residues processed: 115 average time/residue: 0.9559 time to fit residues: 120.7610 Evaluate side-chains 105 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 256 GLU 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 165 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 500 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 413 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.0000 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9678 Z= 0.153 Angle : 0.500 8.332 13222 Z= 0.255 Chirality : 0.042 0.149 1527 Planarity : 0.003 0.051 1651 Dihedral : 8.673 66.702 1432 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.99 % Allowed : 21.15 % Favored : 75.87 % 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: 0.52 (0.25), residues: 1220 helix: 1.81 (0.24), residues: 523 sheet: -0.30 (0.34), residues: 261 loop : -1.03 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 252 HIS 0.006 0.001 HIS C 476 PHE 0.014 0.001 PHE B 498 TYR 0.011 0.001 TYR A 436 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 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 120 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: B 49 ASN cc_start: 0.7991 (t0) cc_final: 0.7418 (t0) REVERT: B 237 ARG cc_start: 0.7471 (ptp90) cc_final: 0.7166 (ptp90) REVERT: B 268 ASP cc_start: 0.8288 (t70) cc_final: 0.7754 (t0) REVERT: C 252 TRP cc_start: 0.7500 (p-90) cc_final: 0.7190 (p-90) REVERT: C 339 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8284 (tm-30) REVERT: C 455 ARG cc_start: 0.8270 (tpp-160) cc_final: 0.7523 (tpt170) REVERT: C 481 ASP cc_start: 0.7883 (m-30) cc_final: 0.7575 (m-30) outliers start: 25 outliers final: 10 residues processed: 114 average time/residue: 0.9377 time to fit residues: 117.0381 Evaluate side-chains 100 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 0.0970 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9678 Z= 0.200 Angle : 0.532 8.447 13222 Z= 0.270 Chirality : 0.043 0.203 1527 Planarity : 0.004 0.046 1651 Dihedral : 8.488 68.634 1431 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.39 % Allowed : 22.46 % Favored : 75.15 % 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: 0.52 (0.25), residues: 1220 helix: 1.80 (0.24), residues: 522 sheet: -0.21 (0.35), residues: 256 loop : -1.05 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 252 HIS 0.006 0.001 HIS C 476 PHE 0.016 0.001 PHE B 498 TYR 0.013 0.001 TYR C 451 ARG 0.004 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 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 110 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: A 409 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: B 49 ASN cc_start: 0.7993 (t0) cc_final: 0.7421 (t0) REVERT: B 237 ARG cc_start: 0.7553 (ptp90) cc_final: 0.7241 (ptp90) REVERT: B 268 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7767 (t0) REVERT: C 455 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7529 (tpt170) REVERT: C 470 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8833 (tp) REVERT: C 481 ASP cc_start: 0.8006 (m-30) cc_final: 0.7655 (m-30) outliers start: 20 outliers final: 11 residues processed: 106 average time/residue: 0.9423 time to fit residues: 109.4765 Evaluate side-chains 102 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 256 GLU 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 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 500 LEU 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 470 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9678 Z= 0.168 Angle : 0.523 8.795 13222 Z= 0.264 Chirality : 0.043 0.215 1527 Planarity : 0.003 0.044 1651 Dihedral : 8.220 67.276 1431 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.91 % Allowed : 22.58 % Favored : 75.51 % 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: 0.55 (0.25), residues: 1220 helix: 1.83 (0.24), residues: 523 sheet: -0.22 (0.35), residues: 256 loop : -1.05 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 238 HIS 0.006 0.001 HIS C 476 PHE 0.015 0.001 PHE B 498 TYR 0.013 0.001 TYR C 451 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 8 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 108 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: B 49 ASN cc_start: 0.7975 (t0) cc_final: 0.7402 (t0) REVERT: B 205 ARG cc_start: 0.7899 (mpp80) cc_final: 0.7691 (mpp80) REVERT: B 237 ARG cc_start: 0.7554 (ptp90) cc_final: 0.7249 (ptp90) REVERT: B 268 ASP cc_start: 0.8305 (t70) cc_final: 0.7772 (t0) REVERT: C 455 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7623 (tpt170) REVERT: C 503 MET cc_start: 0.7986 (mpt) cc_final: 0.7688 (mpt) outliers start: 16 outliers final: 10 residues processed: 105 average time/residue: 0.9985 time to fit residues: 114.5530 Evaluate side-chains 97 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 256 GLU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 48 optimal weight: 40.0000 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9678 Z= 0.182 Angle : 0.530 8.769 13222 Z= 0.268 Chirality : 0.044 0.212 1527 Planarity : 0.003 0.043 1651 Dihedral : 8.063 67.969 1431 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.91 % Allowed : 22.34 % Favored : 75.75 % 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: 0.53 (0.25), residues: 1220 helix: 1.81 (0.24), residues: 524 sheet: -0.26 (0.34), residues: 261 loop : -1.05 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 252 HIS 0.007 0.001 HIS C 476 PHE 0.016 0.001 PHE B 498 TYR 0.013 0.001 TYR C 451 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 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 105 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.7978 (t0) cc_final: 0.7407 (t0) REVERT: B 237 ARG cc_start: 0.7606 (ptp90) cc_final: 0.7297 (ptp90) REVERT: B 268 ASP cc_start: 0.8318 (t70) cc_final: 0.7801 (t0) REVERT: C 455 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7577 (tpt170) REVERT: C 481 ASP cc_start: 0.7862 (m-30) cc_final: 0.7591 (m-30) REVERT: C 503 MET cc_start: 0.8018 (mpt) cc_final: 0.7738 (mpt) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.9329 time to fit residues: 105.7601 Evaluate side-chains 96 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 395 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 265 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9678 Z= 0.259 Angle : 0.579 8.665 13222 Z= 0.291 Chirality : 0.046 0.315 1527 Planarity : 0.004 0.043 1651 Dihedral : 8.212 70.687 1431 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.67 % Allowed : 22.58 % Favored : 75.75 % 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: 0.43 (0.25), residues: 1220 helix: 1.73 (0.24), residues: 523 sheet: -0.29 (0.35), residues: 261 loop : -1.11 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 252 HIS 0.007 0.001 HIS C 476 PHE 0.017 0.001 PHE B 498 TYR 0.014 0.002 TYR C 451 ARG 0.008 0.001 ARG B 205 ********************** REFINEMENT MACRO_CYCLE 10 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 103 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8066 (t0) cc_final: 0.7499 (t0) REVERT: B 237 ARG cc_start: 0.7636 (ptp90) cc_final: 0.7427 (mtm110) REVERT: B 240 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7870 (ttpp) REVERT: B 268 ASP cc_start: 0.8345 (t70) cc_final: 0.7790 (t0) REVERT: C 503 MET cc_start: 0.8017 (mpt) cc_final: 0.7739 (mpt) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.8984 time to fit residues: 99.4134 Evaluate side-chains 96 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 395 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN C 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.119445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098115 restraints weight = 19069.246| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.24 r_work: 0.3457 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9678 Z= 0.181 Angle : 0.544 9.017 13222 Z= 0.274 Chirality : 0.044 0.266 1527 Planarity : 0.003 0.042 1651 Dihedral : 8.001 68.126 1431 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.84 % Allowed : 23.89 % Favored : 75.27 % 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: 0.49 (0.25), residues: 1220 helix: 1.82 (0.24), residues: 522 sheet: -0.30 (0.35), residues: 261 loop : -1.10 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 252 HIS 0.004 0.001 HIS C 476 PHE 0.016 0.001 PHE B 498 TYR 0.016 0.001 TYR C 312 ARG 0.006 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.88 seconds wall clock time: 55 minutes 22.38 seconds (3322.38 seconds total)