Starting phenix.real_space_refine on Mon Aug 5 23:44:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/08_2024/5wpv_8883.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/08_2024/5wpv_8883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/08_2024/5wpv_8883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/08_2024/5wpv_8883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/08_2024/5wpv_8883.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/08_2024/5wpv_8883.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 S 96 5.16 5 Na 1 4.78 5 C 9772 2.51 5 N 2444 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 419": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14889 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "C" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.78, per 1000 atoms: 0.52 Number of scatterers: 14889 At special positions: 0 Unit cell: (110.21, 110.21, 116.63, 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 96 16.00 Na 1 11.00 O 2576 8.00 N 2444 7.00 C 9772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.4 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 61.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 67 through 85 removed outlier: 4.137A pdb=" N ILE A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.070A pdb=" N ILE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 337 removed outlier: 3.730A pdb=" N PHE A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 378 removed outlier: 3.635A pdb=" N LEU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 4.337A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.860A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'A' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 447 removed outlier: 4.937A pdb=" N ARG A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.654A pdb=" N ILE A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.676A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 526 removed outlier: 4.098A pdb=" N TRP A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 67 through 85 removed outlier: 4.138A pdb=" N ILE B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.071A pdb=" N ILE B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 337 removed outlier: 3.731A pdb=" N PHE B 301 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 378 removed outlier: 3.635A pdb=" N LEU B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 4.338A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.859A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 406' Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 447 removed outlier: 4.937A pdb=" N ARG B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.655A pdb=" N ILE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.676A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 526 removed outlier: 4.098A pdb=" N TRP B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 510 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 67 through 85 removed outlier: 4.138A pdb=" N ILE C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.071A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 337 removed outlier: 3.731A pdb=" N PHE C 301 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 378 removed outlier: 3.635A pdb=" N LEU C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 364 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 378 " --> pdb=" O GLY C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 400 removed outlier: 4.338A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 392 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.859A pdb=" N LEU C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 406' Processing helix chain 'C' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 447 removed outlier: 4.936A pdb=" N ARG C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 446 " --> pdb=" O CYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.655A pdb=" N ILE C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 482 removed outlier: 3.675A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 526 removed outlier: 4.098A pdb=" N TRP C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C 510 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS C 526 " --> pdb=" O ASP C 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 67 through 85 removed outlier: 4.137A pdb=" N ILE D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 242 through 247 removed outlier: 4.071A pdb=" N ILE D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 337 removed outlier: 3.731A pdb=" N PHE D 301 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 317 " --> pdb=" O PHE D 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 378 removed outlier: 3.636A pdb=" N LEU D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D 364 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 378 " --> pdb=" O GLY D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 400 removed outlier: 4.337A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 392 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.859A pdb=" N LEU D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 406' Processing helix chain 'D' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 447 removed outlier: 4.937A pdb=" N ARG D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 446 " --> pdb=" O CYS D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.656A pdb=" N ILE D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.675A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 526 removed outlier: 4.099A pdb=" N TRP D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL D 509 " --> pdb=" O PHE D 505 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU D 510 " --> pdb=" O ILE D 506 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 512 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS D 526 " --> pdb=" O ASP D 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.548A pdb=" N GLU A 276 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 230 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 167 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.527A pdb=" N LYS A 238 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.549A pdb=" N GLU B 276 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 230 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 167 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.528A pdb=" N LYS B 238 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.548A pdb=" N GLU C 276 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN C 230 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 167 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.527A pdb=" N LYS C 238 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.548A pdb=" N GLU D 276 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN D 230 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 167 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.527A pdb=" N LYS D 238 " --> pdb=" O ALA D 148 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2451 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: 3.95 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4536 1.34 - 1.46: 3605 1.46 - 1.58: 6963 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15236 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.45e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.82: 215 105.82 - 112.86: 8145 112.86 - 119.90: 5442 119.90 - 126.94: 6710 126.94 - 133.98: 140 Bond angle restraints: 20652 Sorted by residual: angle pdb=" N ILE B 306 " pdb=" CA ILE B 306 " pdb=" C ILE B 306 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" N ILE D 306 " pdb=" CA ILE D 306 " pdb=" C ILE D 306 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" N ILE C 306 " pdb=" CA ILE C 306 " pdb=" C ILE C 306 " ideal model delta sigma weight residual 112.96 108.36 4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" N ILE A 306 " pdb=" CA ILE A 306 " pdb=" C ILE A 306 " ideal model delta sigma weight residual 112.96 108.37 4.59 1.00e+00 1.00e+00 2.10e+01 angle pdb=" C ILE A 514 " pdb=" N ALA A 515 " pdb=" CA ALA A 515 " ideal model delta sigma weight residual 120.28 125.02 -4.74 1.34e+00 5.57e-01 1.25e+01 ... (remaining 20647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 8492 15.64 - 31.27: 399 31.27 - 46.91: 141 46.91 - 62.55: 12 62.55 - 78.18: 12 Dihedral angle restraints: 9056 sinusoidal: 3692 harmonic: 5364 Sorted by residual: dihedral pdb=" CA THR C 360 " pdb=" C THR C 360 " pdb=" N SER C 361 " pdb=" CA SER C 361 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THR A 360 " pdb=" C THR A 360 " pdb=" N SER A 361 " pdb=" CA SER A 361 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THR D 360 " pdb=" C THR D 360 " pdb=" N SER D 361 " pdb=" CA SER D 361 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 9053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1450 0.038 - 0.076: 648 0.076 - 0.114: 230 0.114 - 0.152: 71 0.152 - 0.190: 21 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CB VAL A 452 " pdb=" CA VAL A 452 " pdb=" CG1 VAL A 452 " pdb=" CG2 VAL A 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CB VAL D 452 " pdb=" CA VAL D 452 " pdb=" CG1 VAL D 452 " pdb=" CG2 VAL D 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CB VAL B 452 " pdb=" CA VAL B 452 " pdb=" CG1 VAL B 452 " pdb=" CG2 VAL B 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2417 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 526 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 527 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 526 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 527 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 526 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO A 527 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.034 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4735 2.84 - 3.36: 13526 3.36 - 3.87: 22475 3.87 - 4.39: 25323 4.39 - 4.90: 44296 Nonbonded interactions: 110355 Sorted by model distance: nonbonded pdb=" N PHE A 474 " pdb=" OD2 ASP B 471 " model vdw 2.329 3.120 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.372 3.040 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.373 3.040 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.373 3.040 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.373 3.040 ... (remaining 110350 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 38 through 527) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.630 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.060 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.007 0.056 15236 Z= 0.414 Angle : 0.909 9.418 20652 Z= 0.479 Chirality : 0.051 0.190 2420 Planarity : 0.007 0.057 2516 Dihedral : 11.021 78.184 5584 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.18 % Allowed : 4.93 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.15), residues: 1784 helix: -3.23 (0.10), residues: 1024 sheet: -1.30 (0.32), residues: 252 loop : -3.03 (0.22), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 491 HIS 0.005 0.001 HIS A 103 PHE 0.025 0.003 PHE A 474 TYR 0.025 0.003 TYR A 254 ARG 0.012 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 455 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9101 (tp) cc_final: 0.8479 (mp) REVERT: A 350 PHE cc_start: 0.6714 (t80) cc_final: 0.6029 (t80) REVERT: A 423 PRO cc_start: 0.7803 (Cg_endo) cc_final: 0.7581 (Cg_exo) REVERT: B 74 LEU cc_start: 0.9047 (tp) cc_final: 0.8398 (mp) REVERT: B 245 LEU cc_start: 0.5930 (mm) cc_final: 0.5701 (pp) REVERT: B 350 PHE cc_start: 0.6656 (t80) cc_final: 0.5995 (t80) REVERT: C 74 LEU cc_start: 0.9140 (tp) cc_final: 0.8532 (mp) REVERT: C 175 VAL cc_start: 0.8041 (t) cc_final: 0.7830 (p) REVERT: C 245 LEU cc_start: 0.6118 (mm) cc_final: 0.5912 (pp) REVERT: C 350 PHE cc_start: 0.6643 (t80) cc_final: 0.6058 (t80) REVERT: D 74 LEU cc_start: 0.9037 (tp) cc_final: 0.8302 (mp) REVERT: D 245 LEU cc_start: 0.5920 (mm) cc_final: 0.5636 (pp) REVERT: D 350 PHE cc_start: 0.6674 (t80) cc_final: 0.6023 (t80) REVERT: D 427 ARG cc_start: 0.7473 (mmt180) cc_final: 0.6554 (mmm-85) outliers start: 3 outliers final: 0 residues processed: 455 average time/residue: 0.3135 time to fit residues: 196.0754 Evaluate side-chains 228 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 328 ASN A 379 ASN A 412 ASN B 79 GLN B 328 ASN B 379 ASN B 412 ASN C 79 GLN C 328 ASN C 379 ASN C 412 ASN D 79 GLN D 328 ASN D 379 ASN D 412 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15236 Z= 0.326 Angle : 0.667 7.263 20652 Z= 0.350 Chirality : 0.043 0.151 2420 Planarity : 0.005 0.033 2516 Dihedral : 5.711 36.239 2164 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.08 % Allowed : 10.40 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.18), residues: 1784 helix: -0.88 (0.15), residues: 1044 sheet: -0.96 (0.33), residues: 256 loop : -2.94 (0.23), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 444 HIS 0.004 0.001 HIS B 451 PHE 0.021 0.002 PHE A 474 TYR 0.024 0.002 TYR C 411 ARG 0.009 0.001 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 247 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7963 (m-30) cc_final: 0.7543 (p0) REVERT: A 45 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6631 (tp) REVERT: A 74 LEU cc_start: 0.8943 (tp) cc_final: 0.8668 (mp) REVERT: A 350 PHE cc_start: 0.6616 (t80) cc_final: 0.5902 (t80) REVERT: B 40 ASP cc_start: 0.8034 (m-30) cc_final: 0.7752 (p0) REVERT: B 45 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6510 (tp) REVERT: B 74 LEU cc_start: 0.8860 (tp) cc_final: 0.8320 (mp) REVERT: B 174 HIS cc_start: 0.7258 (t70) cc_final: 0.6671 (t-90) REVERT: B 245 LEU cc_start: 0.6076 (mm) cc_final: 0.5700 (pp) REVERT: B 350 PHE cc_start: 0.6581 (t80) cc_final: 0.5902 (t80) REVERT: B 503 SER cc_start: 0.9572 (t) cc_final: 0.9371 (p) REVERT: B 511 SER cc_start: 0.9303 (t) cc_final: 0.9088 (t) REVERT: C 45 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6639 (tp) REVERT: C 74 LEU cc_start: 0.8959 (tp) cc_final: 0.8574 (mp) REVERT: C 245 LEU cc_start: 0.6150 (mm) cc_final: 0.5839 (pp) REVERT: C 350 PHE cc_start: 0.6627 (t80) cc_final: 0.6005 (t80) REVERT: D 40 ASP cc_start: 0.8094 (m-30) cc_final: 0.7792 (p0) REVERT: D 45 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6553 (tp) REVERT: D 74 LEU cc_start: 0.8848 (tp) cc_final: 0.8312 (mp) REVERT: D 174 HIS cc_start: 0.7321 (t70) cc_final: 0.6743 (t-90) REVERT: D 245 LEU cc_start: 0.5954 (mm) cc_final: 0.5551 (pp) REVERT: D 350 PHE cc_start: 0.6597 (t80) cc_final: 0.5930 (t80) REVERT: D 511 SER cc_start: 0.9302 (t) cc_final: 0.9098 (t) outliers start: 67 outliers final: 36 residues processed: 298 average time/residue: 0.2005 time to fit residues: 95.7570 Evaluate side-chains 249 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 163 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15236 Z= 0.401 Angle : 0.662 6.788 20652 Z= 0.346 Chirality : 0.044 0.139 2420 Planarity : 0.004 0.032 2516 Dihedral : 5.823 43.101 2164 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.44 % Allowed : 12.59 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.19), residues: 1784 helix: 0.13 (0.16), residues: 1012 sheet: -0.82 (0.33), residues: 248 loop : -2.60 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 444 HIS 0.004 0.001 HIS D 409 PHE 0.021 0.002 PHE D 474 TYR 0.025 0.002 TYR C 411 ARG 0.006 0.001 ARG D 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 213 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8006 (m-30) cc_final: 0.7576 (p0) REVERT: A 45 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6497 (tp) REVERT: A 74 LEU cc_start: 0.9185 (tp) cc_final: 0.8649 (mp) REVERT: B 40 ASP cc_start: 0.8104 (m-30) cc_final: 0.7594 (p0) REVERT: B 45 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6438 (tp) REVERT: B 74 LEU cc_start: 0.9114 (tp) cc_final: 0.8565 (mp) REVERT: B 245 LEU cc_start: 0.6078 (mm) cc_final: 0.5681 (pp) REVERT: B 427 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6945 (mmp-170) REVERT: B 511 SER cc_start: 0.9328 (t) cc_final: 0.9098 (t) REVERT: C 45 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6590 (tp) REVERT: C 74 LEU cc_start: 0.9275 (tp) cc_final: 0.8732 (mp) REVERT: C 245 LEU cc_start: 0.6019 (mm) cc_final: 0.5699 (pp) REVERT: C 427 ARG cc_start: 0.7372 (mmt180) cc_final: 0.7137 (mmp-170) REVERT: D 40 ASP cc_start: 0.8094 (m-30) cc_final: 0.7582 (p0) REVERT: D 45 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6450 (tp) REVERT: D 74 LEU cc_start: 0.9098 (tp) cc_final: 0.8529 (mp) REVERT: D 245 LEU cc_start: 0.6048 (mm) cc_final: 0.5648 (pp) REVERT: D 511 SER cc_start: 0.9328 (t) cc_final: 0.9119 (t) outliers start: 73 outliers final: 49 residues processed: 277 average time/residue: 0.2178 time to fit residues: 95.5132 Evaluate side-chains 245 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 0.0060 chunk 46 optimal weight: 4.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 ASN C 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15236 Z= 0.181 Angle : 0.541 6.792 20652 Z= 0.284 Chirality : 0.040 0.147 2420 Planarity : 0.003 0.026 2516 Dihedral : 5.367 41.330 2164 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.53 % Allowed : 15.27 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1784 helix: 0.81 (0.17), residues: 1004 sheet: -0.43 (0.33), residues: 268 loop : -2.37 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 444 HIS 0.002 0.000 HIS A 409 PHE 0.017 0.001 PHE D 474 TYR 0.025 0.001 TYR A 411 ARG 0.007 0.000 ARG D 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7968 (m-30) cc_final: 0.7392 (p0) REVERT: A 74 LEU cc_start: 0.9169 (tp) cc_final: 0.8632 (mp) REVERT: A 274 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8261 (ptp90) REVERT: A 350 PHE cc_start: 0.6402 (t80) cc_final: 0.5682 (t80) REVERT: B 40 ASP cc_start: 0.8022 (m-30) cc_final: 0.7484 (p0) REVERT: B 74 LEU cc_start: 0.8914 (tp) cc_final: 0.8320 (mp) REVERT: B 245 LEU cc_start: 0.6174 (mm) cc_final: 0.5841 (pp) REVERT: B 350 PHE cc_start: 0.6398 (t80) cc_final: 0.5687 (t80) REVERT: C 45 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6446 (tp) REVERT: C 74 LEU cc_start: 0.9175 (tp) cc_final: 0.8549 (mp) REVERT: C 245 LEU cc_start: 0.6252 (mm) cc_final: 0.5969 (pp) REVERT: C 350 PHE cc_start: 0.6343 (t80) cc_final: 0.5647 (t80) REVERT: D 40 ASP cc_start: 0.8019 (m-30) cc_final: 0.7485 (p0) REVERT: D 74 LEU cc_start: 0.8897 (tp) cc_final: 0.8276 (mp) REVERT: D 245 LEU cc_start: 0.6133 (mm) cc_final: 0.5819 (pp) REVERT: D 274 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8274 (ptp90) REVERT: D 350 PHE cc_start: 0.6419 (t80) cc_final: 0.5693 (t80) REVERT: D 508 MET cc_start: 0.7899 (ttm) cc_final: 0.7678 (ttm) REVERT: D 512 LEU cc_start: 0.9185 (mt) cc_final: 0.8888 (mp) outliers start: 58 outliers final: 40 residues processed: 259 average time/residue: 0.2519 time to fit residues: 101.8957 Evaluate side-chains 244 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 516 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS C 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15236 Z= 0.305 Angle : 0.583 6.820 20652 Z= 0.305 Chirality : 0.042 0.140 2420 Planarity : 0.003 0.023 2516 Dihedral : 5.343 39.766 2164 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.26 % Allowed : 16.30 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1784 helix: 0.96 (0.17), residues: 1000 sheet: -0.38 (0.33), residues: 268 loop : -2.27 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 444 HIS 0.004 0.001 HIS C 451 PHE 0.015 0.001 PHE B 474 TYR 0.028 0.002 TYR A 411 ARG 0.014 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 188 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7926 (m-30) cc_final: 0.7296 (p0) REVERT: A 74 LEU cc_start: 0.9187 (tp) cc_final: 0.8639 (mp) REVERT: A 274 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8355 (ptp90) REVERT: B 56 PHE cc_start: 0.5445 (t80) cc_final: 0.4238 (m-10) REVERT: B 74 LEU cc_start: 0.9005 (tp) cc_final: 0.8487 (mp) REVERT: B 86 SER cc_start: 0.9248 (OUTLIER) cc_final: 0.8667 (p) REVERT: B 245 LEU cc_start: 0.6246 (mm) cc_final: 0.5771 (pp) REVERT: B 427 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6743 (mmp-170) REVERT: C 45 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6460 (tp) REVERT: C 56 PHE cc_start: 0.5362 (t80) cc_final: 0.4198 (m-10) REVERT: C 74 LEU cc_start: 0.9188 (tp) cc_final: 0.8692 (mp) REVERT: C 86 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 245 LEU cc_start: 0.6258 (mm) cc_final: 0.5843 (pp) REVERT: D 40 ASP cc_start: 0.8065 (m-30) cc_final: 0.7395 (p0) REVERT: D 56 PHE cc_start: 0.5505 (t80) cc_final: 0.4342 (m-10) REVERT: D 74 LEU cc_start: 0.8954 (tp) cc_final: 0.8411 (mp) REVERT: D 245 LEU cc_start: 0.6220 (mm) cc_final: 0.5749 (pp) REVERT: D 274 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8357 (ptp90) REVERT: D 508 MET cc_start: 0.7978 (ttm) cc_final: 0.7638 (ttm) outliers start: 70 outliers final: 46 residues processed: 245 average time/residue: 0.2077 time to fit residues: 80.5785 Evaluate side-chains 232 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 180 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7765 > 50: distance: 9 - 32: 17.864 distance: 14 - 39: 12.908 distance: 19 - 20: 23.917 distance: 19 - 25: 18.754 distance: 20 - 21: 37.573 distance: 20 - 23: 24.426 distance: 21 - 22: 32.910 distance: 21 - 26: 15.778 distance: 23 - 24: 38.847 distance: 24 - 25: 15.364 distance: 26 - 27: 3.598 distance: 27 - 28: 32.577 distance: 27 - 30: 15.391 distance: 28 - 29: 25.398 distance: 28 - 32: 40.744 distance: 29 - 58: 15.224 distance: 30 - 31: 39.575 distance: 32 - 33: 16.843 distance: 33 - 34: 9.511 distance: 33 - 36: 12.797 distance: 34 - 35: 18.441 distance: 35 - 69: 26.813 distance: 36 - 37: 4.814 distance: 36 - 38: 10.227 distance: 39 - 40: 10.502 distance: 40 - 41: 12.990 distance: 40 - 43: 11.161 distance: 41 - 42: 23.201 distance: 41 - 47: 16.729 distance: 43 - 44: 13.742 distance: 44 - 45: 13.243 distance: 45 - 46: 12.123 distance: 47 - 48: 16.216 distance: 48 - 49: 19.162 distance: 48 - 51: 10.401 distance: 49 - 50: 19.079 distance: 49 - 58: 8.643 distance: 51 - 52: 25.322 distance: 52 - 53: 17.722 distance: 53 - 54: 9.207 distance: 54 - 55: 10.987 distance: 55 - 56: 8.917 distance: 55 - 57: 8.618 distance: 58 - 59: 7.648 distance: 59 - 60: 20.518 distance: 59 - 62: 12.968 distance: 60 - 61: 16.194 distance: 60 - 69: 20.158 distance: 61 - 87: 28.914 distance: 62 - 63: 8.499 distance: 63 - 64: 16.598 distance: 63 - 65: 12.663 distance: 64 - 66: 11.818 distance: 65 - 67: 4.652 distance: 66 - 68: 7.991 distance: 67 - 68: 6.568 distance: 69 - 70: 4.407 distance: 70 - 71: 15.551 distance: 70 - 73: 3.915 distance: 71 - 72: 21.989 distance: 71 - 75: 16.627 distance: 72 - 94: 10.938 distance: 73 - 74: 16.065 distance: 75 - 76: 10.070 distance: 76 - 77: 24.031 distance: 76 - 79: 25.776 distance: 77 - 78: 24.405 distance: 77 - 81: 13.907 distance: 78 - 99: 12.163 distance: 79 - 80: 23.680 distance: 81 - 82: 18.793 distance: 82 - 83: 10.621 distance: 82 - 85: 23.642 distance: 83 - 84: 23.991 distance: 83 - 87: 15.191 distance: 85 - 86: 50.776 distance: 87 - 88: 10.900 distance: 88 - 89: 13.008 distance: 88 - 91: 14.842 distance: 89 - 90: 17.532 distance: 90 - 113: 21.028 distance: 91 - 92: 20.147 distance: 91 - 93: 23.376