Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 10:41:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/04_2023/5wpv_8883.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/04_2023/5wpv_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_8883/04_2023/5wpv_8883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/04_2023/5wpv_8883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/04_2023/5wpv_8883.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpv_8883/04_2023/5wpv_8883.pdb" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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: 8.78, per 1000 atoms: 0.59 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: 6.10 Conformation dependent library (CDL) restraints added in 2.2 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: 0.66 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: 4.49 Time building geometry restraints manager: 6.51 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: 8340 15.64 - 31.27: 392 31.27 - 46.91: 132 46.91 - 62.55: 12 62.55 - 78.18: 12 Dihedral angle restraints: 8888 sinusoidal: 3524 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 8885 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 2.520 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.372 2.440 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.373 2.440 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.373 2.440 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.373 2.440 ... (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 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: 0.570 Set stop_for_unknowns flag: 0.010 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: 3.200 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 39.550 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- 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 : 11.003 78.184 5416 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 % 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 *********************** 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 : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 455 average time/residue: 0.3383 time to fit residues: 211.6539 Evaluate side-chains 218 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4110 ------------------------------------------------------------------------------- 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: 7.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 C 451 HIS D 79 GLN D 328 ASN D 379 ASN D 412 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15236 Z= 0.222 Angle : 0.620 7.529 20652 Z= 0.322 Chirality : 0.041 0.152 2420 Planarity : 0.005 0.046 2516 Dihedral : 4.941 21.235 1996 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 3.59 % 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: -2.05 (0.18), residues: 1784 helix: -0.70 (0.15), residues: 1008 sheet: -0.86 (0.33), residues: 256 loop : -2.71 (0.22), residues: 520 *********************** 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 302 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 243 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 33 residues processed: 289 average time/residue: 0.2076 time to fit residues: 96.3017 Evaluate side-chains 220 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.693 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1468 time to fit residues: 11.0197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 163 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 0.0010 chunk 162 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 overall best weight: 4.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 15236 Z= 0.340 Angle : 0.640 7.075 20652 Z= 0.330 Chirality : 0.042 0.151 2420 Planarity : 0.004 0.047 2516 Dihedral : 4.721 19.530 1996 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 3.35 % 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: -1.07 (0.19), residues: 1784 helix: 0.21 (0.16), residues: 1024 sheet: -0.74 (0.33), residues: 248 loop : -2.46 (0.24), residues: 512 *********************** 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 258 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 203 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 38 residues processed: 244 average time/residue: 0.2332 time to fit residues: 88.0956 Evaluate side-chains 222 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1324 time to fit residues: 11.9158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15236 Z= 0.175 Angle : 0.526 6.756 20652 Z= 0.272 Chirality : 0.039 0.140 2420 Planarity : 0.003 0.027 2516 Dihedral : 4.416 19.009 1996 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1784 helix: 0.92 (0.17), residues: 1020 sheet: -0.49 (0.32), residues: 264 loop : -2.21 (0.26), residues: 500 *********************** 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 215 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 208 average time/residue: 0.2146 time to fit residues: 71.8431 Evaluate side-chains 193 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1335 time to fit residues: 3.5511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 0.0070 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 0.0000 chunk 0 optimal weight: 30.0000 chunk 88 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9806 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 15236 Z= 0.134 Angle : 0.502 8.038 20652 Z= 0.255 Chirality : 0.038 0.172 2420 Planarity : 0.003 0.050 2516 Dihedral : 4.102 18.590 1996 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 1.46 % 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: 0.41 (0.21), residues: 1784 helix: 1.51 (0.17), residues: 1008 sheet: -0.24 (0.33), residues: 268 loop : -1.98 (0.27), residues: 508 *********************** 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 243 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 238 average time/residue: 0.2166 time to fit residues: 82.3160 Evaluate side-chains 198 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1329 time to fit residues: 4.3238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15236 Z= 0.206 Angle : 0.526 6.899 20652 Z= 0.269 Chirality : 0.039 0.143 2420 Planarity : 0.003 0.045 2516 Dihedral : 4.106 17.727 1996 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.03 % 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 (0.21), residues: 1784 helix: 1.49 (0.17), residues: 1016 sheet: -0.23 (0.33), residues: 268 loop : -1.97 (0.28), residues: 500 *********************** REFINEMENT MACRO_CYCLE 6 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 212 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 209 average time/residue: 0.2132 time to fit residues: 71.9071 Evaluate side-chains 196 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1427 time to fit residues: 4.4654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 108 optimal weight: 0.0970 chunk 105 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 15236 Z= 0.128 Angle : 0.501 6.818 20652 Z= 0.253 Chirality : 0.038 0.136 2420 Planarity : 0.003 0.044 2516 Dihedral : 3.991 17.967 1996 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.73 % 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: 0.77 (0.21), residues: 1784 helix: 1.80 (0.17), residues: 1008 sheet: -0.13 (0.33), residues: 268 loop : -1.82 (0.28), residues: 508 *********************** REFINEMENT MACRO_CYCLE 7 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 219 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 216 average time/residue: 0.2126 time to fit residues: 75.1715 Evaluate side-chains 194 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1507 time to fit residues: 3.0333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 15236 Z= 0.429 Angle : 0.679 7.182 20652 Z= 0.347 Chirality : 0.044 0.135 2420 Planarity : 0.004 0.043 2516 Dihedral : 4.471 17.799 1996 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.97 % 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: 0.16 (0.20), residues: 1784 helix: 1.23 (0.16), residues: 1016 sheet: -0.39 (0.33), residues: 264 loop : -1.91 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 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 194 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 191 average time/residue: 0.2139 time to fit residues: 66.0158 Evaluate side-chains 178 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1322 time to fit residues: 5.4641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.8086 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 15236 Z= 0.282 Angle : 0.584 7.338 20652 Z= 0.298 Chirality : 0.040 0.132 2420 Planarity : 0.003 0.057 2516 Dihedral : 4.355 18.211 1996 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.36 % 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: 0.30 (0.20), residues: 1784 helix: 1.41 (0.16), residues: 1008 sheet: -0.34 (0.33), residues: 264 loop : -1.95 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 9 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 191 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 187 average time/residue: 0.2216 time to fit residues: 66.9963 Evaluate side-chains 175 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1247 time to fit residues: 2.8368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.8043 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15236 Z= 0.175 Angle : 0.533 7.365 20652 Z= 0.271 Chirality : 0.038 0.134 2420 Planarity : 0.003 0.056 2516 Dihedral : 4.135 18.942 1996 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.24 % 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: 0.52 (0.21), residues: 1784 helix: 1.63 (0.17), residues: 1008 sheet: -0.29 (0.33), residues: 264 loop : -1.94 (0.26), residues: 512 ********************** REFINEMENT MACRO_CYCLE 10 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 184 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 184 average time/residue: 0.2154 time to fit residues: 63.9844 Evaluate side-chains 175 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1473 time to fit residues: 2.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 0.0270 chunk 26 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102402 restraints weight = 26648.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105158 restraints weight = 15750.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106968 restraints weight = 11656.023| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15236 Z= 0.185 Angle : 0.538 7.130 20652 Z= 0.274 Chirality : 0.039 0.142 2420 Planarity : 0.003 0.055 2516 Dihedral : 4.116 18.653 1996 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1784 helix: 1.65 (0.17), residues: 1008 sheet: -0.16 (0.33), residues: 268 loop : -1.99 (0.26), residues: 508 =============================================================================== Job complete usr+sys time: 2543.07 seconds wall clock time: 47 minutes 28.41 seconds (2848.41 seconds total)