Starting phenix.real_space_refine on Fri Feb 16 13:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7p_9000/02_2024/6e7p_9000_updated.pdb" } resolution = 3.5 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= -0.040 sd= 0.383 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 100 5.16 5 C 10104 2.51 5 N 2560 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 318": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15508 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'HZ7': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'HZ7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'HZ7': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'HZ7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.13, per 1000 atoms: 0.52 Number of scatterers: 15508 At special positions: 0 Unit cell: (120.91, 120.91, 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 100 16.00 P 12 15.00 O 2732 8.00 N 2560 7.00 C 10104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.04 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.04 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 2.9 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 4 sheets defined 51.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 52 through 55 No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 64 through 105 removed outlier: 5.245A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 137 removed outlier: 3.764A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 302 through 331 removed outlier: 3.611A pdb=" N SER A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 372 removed outlier: 3.557A pdb=" N LEU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 407 removed outlier: 3.584A pdb=" N LEU A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 390 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 446 Proline residue: A 423 - end of helix removed outlier: 3.756A pdb=" N CYS A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.942A pdb=" N GLU A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.568A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.723A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 removed outlier: 3.964A pdb=" N ILE A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 52 through 55 No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 64 through 105 removed outlier: 5.245A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.763A pdb=" N TYR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 302 through 331 removed outlier: 3.611A pdb=" N SER B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.557A pdb=" N LEU B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 407 removed outlier: 3.582A pdb=" N LEU B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 390 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 446 Proline residue: B 423 - end of helix removed outlier: 3.756A pdb=" N CYS B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.940A pdb=" N GLU B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 468 No H-bonds generated for 'chain 'B' and resid 465 through 468' Processing helix chain 'B' and resid 474 through 482 removed outlier: 3.567A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.724A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 removed outlier: 3.964A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 523 " --> pdb=" O GLY B 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 64 through 105 removed outlier: 5.246A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.764A pdb=" N TYR C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 296 through 299 No H-bonds generated for 'chain 'C' and resid 296 through 299' Processing helix chain 'C' and resid 302 through 331 removed outlier: 3.610A pdb=" N SER C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN C 328 " --> pdb=" O PHE C 324 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 372 removed outlier: 3.557A pdb=" N LEU C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 407 removed outlier: 3.583A pdb=" N LEU C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 390 " --> pdb=" O CYS C 386 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 446 Proline residue: C 423 - end of helix removed outlier: 3.756A pdb=" N CYS C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 463 removed outlier: 3.940A pdb=" N GLU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 468 No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 474 through 482 removed outlier: 3.567A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 505 removed outlier: 3.723A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 525 removed outlier: 3.964A pdb=" N ILE C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR C 523 " --> pdb=" O GLY C 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 52 through 55 No H-bonds generated for 'chain 'D' and resid 52 through 55' Processing helix chain 'D' and resid 64 through 105 removed outlier: 5.245A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.764A pdb=" N TYR D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 296 through 299 No H-bonds generated for 'chain 'D' and resid 296 through 299' Processing helix chain 'D' and resid 302 through 331 removed outlier: 3.610A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 317 " --> pdb=" O PHE D 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 372 removed outlier: 3.558A pdb=" N LEU D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 407 removed outlier: 3.583A pdb=" N LEU D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 390 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 446 Proline residue: D 423 - end of helix removed outlier: 3.756A pdb=" N CYS D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.940A pdb=" N GLU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 474 through 482 removed outlier: 3.568A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA D 482 " --> pdb=" O ALA D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 505 removed outlier: 3.724A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 504 " --> pdb=" O SER D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 525 removed outlier: 3.965A pdb=" N ILE D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR D 523 " --> pdb=" O GLY D 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 189 through 195 removed outlier: 3.801A pdb=" N TYR A 169 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 191 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 230 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 261 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 189 through 195 removed outlier: 3.801A pdb=" N TYR B 169 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 191 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 230 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 261 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 189 through 195 removed outlier: 3.801A pdb=" N TYR C 169 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 191 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 230 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 261 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 189 through 195 removed outlier: 3.801A pdb=" N TYR D 169 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP D 191 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 230 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR D 261 " --> pdb=" O SER D 274 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1764 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: 4.26 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4764 1.34 - 1.47: 4245 1.47 - 1.60: 6723 1.60 - 1.72: 16 1.72 - 1.85: 140 Bond restraints: 15888 Sorted by residual: bond pdb=" C12 HZ7 C 801 " pdb=" O16 HZ7 C 801 " ideal model delta sigma weight residual 1.398 1.440 -0.042 2.00e-02 2.50e+03 4.48e+00 bond pdb=" O8 HZ7 C 801 " pdb=" P1 HZ7 C 801 " ideal model delta sigma weight residual 1.648 1.606 0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" O8 HZ7 B 801 " pdb=" P1 HZ7 B 801 " ideal model delta sigma weight residual 1.648 1.606 0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" O8 HZ7 A 801 " pdb=" P1 HZ7 A 801 " ideal model delta sigma weight residual 1.648 1.606 0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" O8 HZ7 D 801 " pdb=" P1 HZ7 D 801 " ideal model delta sigma weight residual 1.648 1.606 0.042 2.00e-02 2.50e+03 4.37e+00 ... (remaining 15883 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.23: 286 106.23 - 113.17: 8618 113.17 - 120.11: 6194 120.11 - 127.05: 6279 127.05 - 133.99: 187 Bond angle restraints: 21564 Sorted by residual: angle pdb=" CA SER B 488 " pdb=" C SER B 488 " pdb=" N LEU B 489 " ideal model delta sigma weight residual 116.84 124.22 -7.38 1.71e+00 3.42e-01 1.86e+01 angle pdb=" CA SER A 488 " pdb=" C SER A 488 " pdb=" N LEU A 489 " ideal model delta sigma weight residual 116.84 124.20 -7.36 1.71e+00 3.42e-01 1.85e+01 angle pdb=" CA SER D 488 " pdb=" C SER D 488 " pdb=" N LEU D 489 " ideal model delta sigma weight residual 116.84 124.20 -7.36 1.71e+00 3.42e-01 1.85e+01 angle pdb=" CA SER C 488 " pdb=" C SER C 488 " pdb=" N LEU C 489 " ideal model delta sigma weight residual 116.84 124.17 -7.33 1.71e+00 3.42e-01 1.84e+01 angle pdb=" C PRO C 177 " pdb=" N ALA C 178 " pdb=" CA ALA C 178 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 ... (remaining 21559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.82: 9052 26.82 - 53.65: 184 53.65 - 80.47: 48 80.47 - 107.30: 12 107.30 - 134.12: 4 Dihedral angle restraints: 9300 sinusoidal: 3736 harmonic: 5564 Sorted by residual: dihedral pdb=" CA TRP D 335 " pdb=" C TRP D 335 " pdb=" N ARG D 336 " pdb=" CA ARG D 336 " ideal model delta harmonic sigma weight residual -180.00 -130.54 -49.46 0 5.00e+00 4.00e-02 9.79e+01 dihedral pdb=" CA TRP A 335 " pdb=" C TRP A 335 " pdb=" N ARG A 336 " pdb=" CA ARG A 336 " ideal model delta harmonic sigma weight residual -180.00 -130.58 -49.42 0 5.00e+00 4.00e-02 9.77e+01 dihedral pdb=" CA TRP C 335 " pdb=" C TRP C 335 " pdb=" N ARG C 336 " pdb=" CA ARG C 336 " ideal model delta harmonic sigma weight residual 180.00 -130.58 -49.42 0 5.00e+00 4.00e-02 9.77e+01 ... (remaining 9297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.995: 2444 0.995 - 1.990: 0 1.990 - 2.985: 0 2.985 - 3.980: 0 3.980 - 4.975: 24 Chirality restraints: 2468 Sorted by residual: chirality pdb=" C4 HZ7 B 801 " pdb=" C3 HZ7 B 801 " pdb=" C5 HZ7 B 801 " pdb=" O6 HZ7 B 801 " both_signs ideal model delta sigma weight residual False -2.50 2.47 -4.98 2.00e-01 2.50e+01 6.19e+02 chirality pdb=" C4 HZ7 A 801 " pdb=" C3 HZ7 A 801 " pdb=" C5 HZ7 A 801 " pdb=" O6 HZ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.47 -4.97 2.00e-01 2.50e+01 6.18e+02 chirality pdb=" C4 HZ7 D 801 " pdb=" C3 HZ7 D 801 " pdb=" C5 HZ7 D 801 " pdb=" O6 HZ7 D 801 " both_signs ideal model delta sigma weight residual False -2.50 2.47 -4.97 2.00e-01 2.50e+01 6.18e+02 ... (remaining 2465 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 422 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO C 423 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 423 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 423 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 422 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO D 423 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 422 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 423 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.034 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4618 2.81 - 3.33: 13908 3.33 - 3.86: 23332 3.86 - 4.38: 27201 4.38 - 4.90: 45648 Nonbonded interactions: 114707 Sorted by model distance: nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.289 2.440 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.290 2.440 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.290 2.440 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.291 2.440 nonbonded pdb=" O THR B 158 " pdb=" OG SER B 161 " model vdw 2.323 2.440 ... (remaining 114702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.260 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 42.050 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.009 0.082 15888 Z= 0.590 Angle : 1.061 11.014 21564 Z= 0.555 Chirality : 0.482 4.975 2468 Planarity : 0.006 0.059 2648 Dihedral : 13.154 134.123 5692 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.01 % Favored : 91.77 % Rotamer: Outliers : 0.24 % Allowed : 2.84 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -5.15 (0.15), residues: 1884 helix: -3.95 (0.09), residues: 880 sheet: -2.39 (0.34), residues: 212 loop : -2.85 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 491 HIS 0.008 0.003 HIS A 234 PHE 0.024 0.003 PHE A 235 TYR 0.022 0.003 TYR C 404 ARG 0.007 0.001 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 1.788 Fit side-chains REVERT: A 57 ARG cc_start: 0.7281 (mtt180) cc_final: 0.5892 (mmt180) REVERT: A 295 ASN cc_start: 0.7073 (t0) cc_final: 0.6855 (m-40) REVERT: A 349 GLU cc_start: 0.8529 (pp20) cc_final: 0.8261 (pp20) REVERT: A 422 LEU cc_start: 0.9205 (tt) cc_final: 0.8990 (tp) REVERT: A 451 HIS cc_start: 0.7117 (m-70) cc_final: 0.6349 (m-70) REVERT: A 480 MET cc_start: 0.8259 (mmp) cc_final: 0.7891 (mmp) REVERT: B 57 ARG cc_start: 0.7286 (mtt180) cc_final: 0.5857 (mmt180) REVERT: B 295 ASN cc_start: 0.7217 (t0) cc_final: 0.6958 (m-40) REVERT: B 349 GLU cc_start: 0.8558 (pp20) cc_final: 0.8247 (pp20) REVERT: B 422 LEU cc_start: 0.9239 (tt) cc_final: 0.9036 (tp) REVERT: B 451 HIS cc_start: 0.7095 (m-70) cc_final: 0.6354 (m-70) REVERT: B 480 MET cc_start: 0.8266 (mmp) cc_final: 0.7884 (mmp) REVERT: C 57 ARG cc_start: 0.7284 (mtt180) cc_final: 0.5875 (mmt180) REVERT: C 295 ASN cc_start: 0.7237 (t0) cc_final: 0.6986 (m-40) REVERT: C 349 GLU cc_start: 0.8568 (pp20) cc_final: 0.8330 (pp20) REVERT: C 451 HIS cc_start: 0.7122 (m-70) cc_final: 0.6361 (m-70) REVERT: C 480 MET cc_start: 0.8259 (mmp) cc_final: 0.7881 (mmp) REVERT: D 57 ARG cc_start: 0.7171 (mtt180) cc_final: 0.5829 (mmt180) REVERT: D 295 ASN cc_start: 0.7222 (t0) cc_final: 0.6970 (m-40) REVERT: D 321 LEU cc_start: 0.8103 (mt) cc_final: 0.7890 (mt) REVERT: D 422 LEU cc_start: 0.9191 (tt) cc_final: 0.8968 (tp) REVERT: D 451 HIS cc_start: 0.7117 (m-70) cc_final: 0.6289 (m-70) REVERT: D 480 MET cc_start: 0.8284 (mmp) cc_final: 0.7890 (mmp) outliers start: 4 outliers final: 0 residues processed: 266 average time/residue: 0.2723 time to fit residues: 108.2952 Evaluate side-chains 148 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 97 ASN A 234 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS A 327 GLN B 79 GLN B 97 ASN B 234 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 327 GLN C 79 GLN C 97 ASN C 234 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS D 79 GLN D 97 ASN D 234 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS D 327 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15888 Z= 0.236 Angle : 0.760 12.914 21564 Z= 0.362 Chirality : 0.045 0.321 2468 Planarity : 0.004 0.044 2648 Dihedral : 11.037 111.554 2188 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.24 % Allowed : 9.99 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.17), residues: 1884 helix: -1.89 (0.14), residues: 960 sheet: -1.49 (0.36), residues: 212 loop : -3.30 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 491 HIS 0.003 0.001 HIS D 451 PHE 0.014 0.002 PHE D 493 TYR 0.011 0.001 TYR D 169 ARG 0.003 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.980 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6054 (tpt170) REVERT: A 295 ASN cc_start: 0.7185 (t0) cc_final: 0.6939 (m-40) REVERT: A 371 MET cc_start: 0.8672 (mtp) cc_final: 0.8421 (mtp) REVERT: A 451 HIS cc_start: 0.6839 (m-70) cc_final: 0.5984 (m-70) REVERT: A 459 MET cc_start: 0.8726 (mtp) cc_final: 0.8464 (mtm) REVERT: B 57 ARG cc_start: 0.7206 (mtt180) cc_final: 0.5990 (tpt170) REVERT: B 295 ASN cc_start: 0.7196 (t0) cc_final: 0.6921 (m-40) REVERT: B 451 HIS cc_start: 0.6911 (m-70) cc_final: 0.6094 (m-70) REVERT: B 459 MET cc_start: 0.8730 (mtp) cc_final: 0.8463 (mtm) REVERT: B 480 MET cc_start: 0.8061 (mmp) cc_final: 0.7834 (mmp) REVERT: C 57 ARG cc_start: 0.7214 (mtt180) cc_final: 0.5919 (mmt180) REVERT: C 295 ASN cc_start: 0.7299 (t0) cc_final: 0.6944 (m-40) REVERT: C 451 HIS cc_start: 0.6888 (m-70) cc_final: 0.6140 (m-70) REVERT: C 459 MET cc_start: 0.8728 (mtp) cc_final: 0.8469 (mtm) REVERT: C 480 MET cc_start: 0.8060 (mmp) cc_final: 0.7851 (mmp) REVERT: D 57 ARG cc_start: 0.7193 (mtt180) cc_final: 0.5909 (mmt180) REVERT: D 295 ASN cc_start: 0.7166 (t0) cc_final: 0.6909 (m-40) REVERT: D 334 MET cc_start: 0.2453 (mtm) cc_final: 0.1627 (ttm) REVERT: D 451 HIS cc_start: 0.6881 (m-70) cc_final: 0.5956 (m-70) REVERT: D 459 MET cc_start: 0.8734 (mtp) cc_final: 0.8451 (mtm) outliers start: 21 outliers final: 9 residues processed: 202 average time/residue: 0.2468 time to fit residues: 77.0661 Evaluate side-chains 141 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 0.0770 chunk 169 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 327 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 327 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS D 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15888 Z= 0.201 Angle : 0.675 8.889 21564 Z= 0.323 Chirality : 0.041 0.178 2468 Planarity : 0.004 0.042 2648 Dihedral : 10.193 88.063 2188 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.72 % Allowed : 9.75 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.54 (0.18), residues: 1884 helix: -0.87 (0.16), residues: 964 sheet: -1.13 (0.36), residues: 228 loop : -3.00 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 157 HIS 0.005 0.001 HIS D 451 PHE 0.013 0.001 PHE C 493 TYR 0.010 0.001 TYR B 169 ARG 0.003 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.7017 (t80) REVERT: A 50 MET cc_start: 0.6989 (mmm) cc_final: 0.6443 (mtt) REVERT: A 57 ARG cc_start: 0.7183 (mtt180) cc_final: 0.5980 (tpt170) REVERT: A 230 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7189 (p0) REVERT: A 295 ASN cc_start: 0.7190 (t0) cc_final: 0.6907 (m-40) REVERT: A 459 MET cc_start: 0.8691 (mtp) cc_final: 0.8329 (mtp) REVERT: B 47 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7043 (t80) REVERT: B 50 MET cc_start: 0.6990 (mmm) cc_final: 0.6453 (mtt) REVERT: B 57 ARG cc_start: 0.7217 (mtt180) cc_final: 0.6013 (tpt170) REVERT: B 230 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7063 (p0) REVERT: B 295 ASN cc_start: 0.7183 (t0) cc_final: 0.6875 (m-40) REVERT: B 451 HIS cc_start: 0.6892 (m-70) cc_final: 0.6098 (m-70) REVERT: C 47 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.7058 (t80) REVERT: C 50 MET cc_start: 0.6857 (mmm) cc_final: 0.6438 (mtt) REVERT: C 57 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6089 (tpt170) REVERT: C 230 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7192 (p0) REVERT: C 295 ASN cc_start: 0.7276 (t0) cc_final: 0.6909 (m-40) REVERT: C 451 HIS cc_start: 0.6920 (m-70) cc_final: 0.6135 (m-70) REVERT: D 57 ARG cc_start: 0.7121 (mtt180) cc_final: 0.5908 (mmt180) REVERT: D 230 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7231 (p0) REVERT: D 295 ASN cc_start: 0.7267 (t0) cc_final: 0.6886 (m-40) REVERT: D 334 MET cc_start: 0.2278 (mtm) cc_final: 0.0503 (ttt) outliers start: 46 outliers final: 24 residues processed: 192 average time/residue: 0.2695 time to fit residues: 79.9025 Evaluate side-chains 167 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15888 Z= 0.170 Angle : 0.607 7.488 21564 Z= 0.294 Chirality : 0.040 0.135 2468 Planarity : 0.003 0.040 2648 Dihedral : 9.628 72.499 2188 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.42 % Allowed : 10.11 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.80 (0.19), residues: 1884 helix: -0.19 (0.17), residues: 944 sheet: -1.14 (0.36), residues: 224 loop : -2.56 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 157 HIS 0.006 0.001 HIS A 451 PHE 0.012 0.001 PHE B 493 TYR 0.009 0.001 TYR D 169 ARG 0.003 0.000 ARG C 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6826 (t80) REVERT: A 57 ARG cc_start: 0.7247 (mtt180) cc_final: 0.5924 (tpt170) REVERT: A 67 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7169 (tmm) REVERT: A 230 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7078 (p0) REVERT: A 295 ASN cc_start: 0.7156 (t0) cc_final: 0.6845 (m-40) REVERT: A 350 PHE cc_start: 0.8504 (m-10) cc_final: 0.8167 (m-80) REVERT: B 47 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6895 (t80) REVERT: B 57 ARG cc_start: 0.7238 (mtt180) cc_final: 0.5875 (tpt170) REVERT: B 67 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7184 (tmm) REVERT: B 230 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7066 (p0) REVERT: B 295 ASN cc_start: 0.7176 (t0) cc_final: 0.6879 (m-40) REVERT: B 350 PHE cc_start: 0.8523 (m-10) cc_final: 0.8176 (m-80) REVERT: C 47 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6841 (t80) REVERT: C 57 ARG cc_start: 0.7246 (mtt180) cc_final: 0.5984 (tpt170) REVERT: C 67 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7104 (tmm) REVERT: C 230 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7085 (p0) REVERT: C 295 ASN cc_start: 0.7278 (t0) cc_final: 0.6894 (m-40) REVERT: C 350 PHE cc_start: 0.8493 (m-10) cc_final: 0.8170 (m-80) REVERT: D 57 ARG cc_start: 0.7157 (mtt180) cc_final: 0.5906 (mmt180) REVERT: D 230 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7226 (p0) REVERT: D 295 ASN cc_start: 0.7265 (t0) cc_final: 0.6889 (m-40) REVERT: D 334 MET cc_start: 0.2250 (mtm) cc_final: 0.0415 (ttt) REVERT: D 459 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8210 (mtp) outliers start: 41 outliers final: 18 residues processed: 188 average time/residue: 0.2425 time to fit residues: 70.9539 Evaluate side-chains 170 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 0.0070 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 327 GLN B 69 GLN B 327 GLN C 69 GLN D 69 GLN D 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15888 Z= 0.150 Angle : 0.565 7.747 21564 Z= 0.277 Chirality : 0.039 0.133 2468 Planarity : 0.003 0.039 2648 Dihedral : 9.092 67.836 2188 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.78 % Allowed : 10.40 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.49 (0.19), residues: 1884 helix: 0.15 (0.17), residues: 956 sheet: -1.05 (0.36), residues: 224 loop : -2.56 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 157 HIS 0.003 0.001 HIS D 451 PHE 0.011 0.001 PHE D 235 TYR 0.009 0.001 TYR B 169 ARG 0.002 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 165 time to evaluate : 1.916 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: A 47 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6816 (t80) REVERT: A 57 ARG cc_start: 0.7173 (mtt180) cc_final: 0.5865 (tpt170) REVERT: A 68 LEU cc_start: 0.8879 (tp) cc_final: 0.8556 (tt) REVERT: A 230 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.7081 (p0) REVERT: A 295 ASN cc_start: 0.7229 (t0) cc_final: 0.6901 (m-40) REVERT: A 350 PHE cc_start: 0.8472 (m-10) cc_final: 0.8142 (m-80) REVERT: A 459 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8131 (mtp) REVERT: B 47 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6892 (t80) REVERT: B 57 ARG cc_start: 0.7231 (mtt180) cc_final: 0.5837 (tpt170) REVERT: B 67 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7034 (tmm) REVERT: B 68 LEU cc_start: 0.8853 (tp) cc_final: 0.8489 (tt) REVERT: B 230 ASN cc_start: 0.7358 (OUTLIER) cc_final: 0.7070 (p0) REVERT: B 295 ASN cc_start: 0.7225 (t0) cc_final: 0.6928 (m-40) REVERT: B 350 PHE cc_start: 0.8458 (m-10) cc_final: 0.8137 (m-80) REVERT: B 459 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: C 47 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6831 (t80) REVERT: C 57 ARG cc_start: 0.7232 (mtt180) cc_final: 0.5932 (tpt170) REVERT: C 67 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7075 (tmm) REVERT: C 68 LEU cc_start: 0.8873 (tp) cc_final: 0.8557 (tt) REVERT: C 230 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.7088 (p0) REVERT: C 295 ASN cc_start: 0.7374 (t0) cc_final: 0.6966 (m-40) REVERT: C 334 MET cc_start: 0.1839 (mtt) cc_final: 0.0294 (ttt) REVERT: C 350 PHE cc_start: 0.8504 (m-10) cc_final: 0.8161 (m-80) REVERT: C 459 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: D 57 ARG cc_start: 0.7182 (mtt180) cc_final: 0.5980 (tpt170) REVERT: D 67 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7144 (tmm) REVERT: D 68 LEU cc_start: 0.8844 (tp) cc_final: 0.8549 (tt) REVERT: D 230 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7120 (p0) REVERT: D 295 ASN cc_start: 0.7223 (t0) cc_final: 0.6943 (m-40) REVERT: D 334 MET cc_start: 0.1911 (mtm) cc_final: 0.0189 (ttt) REVERT: D 459 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8121 (mtp) outliers start: 47 outliers final: 23 residues processed: 202 average time/residue: 0.2470 time to fit residues: 79.3982 Evaluate side-chains 182 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN C 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15888 Z= 0.284 Angle : 0.642 8.708 21564 Z= 0.320 Chirality : 0.041 0.127 2468 Planarity : 0.004 0.041 2648 Dihedral : 9.072 68.678 2188 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.84 % Allowed : 10.99 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.39 (0.19), residues: 1884 helix: 0.23 (0.17), residues: 952 sheet: -1.15 (0.36), residues: 212 loop : -2.43 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 157 HIS 0.005 0.001 HIS B 234 PHE 0.012 0.002 PHE B 301 TYR 0.013 0.001 TYR D 169 ARG 0.002 0.000 ARG D 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 142 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6876 (t80) REVERT: A 57 ARG cc_start: 0.7388 (mtt180) cc_final: 0.5861 (mmt180) REVERT: A 230 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.7044 (p0) REVERT: A 295 ASN cc_start: 0.7215 (t0) cc_final: 0.6893 (m-40) REVERT: A 350 PHE cc_start: 0.8463 (m-10) cc_final: 0.8165 (m-80) REVERT: B 47 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 57 ARG cc_start: 0.7361 (mtt180) cc_final: 0.5831 (mmt180) REVERT: B 67 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7176 (tmm) REVERT: B 230 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7095 (p0) REVERT: B 295 ASN cc_start: 0.7241 (t0) cc_final: 0.6928 (m-40) REVERT: B 350 PHE cc_start: 0.8472 (m-10) cc_final: 0.8161 (m-80) REVERT: C 47 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6889 (t80) REVERT: C 57 ARG cc_start: 0.7410 (mtt180) cc_final: 0.5922 (mmt180) REVERT: C 230 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7054 (p0) REVERT: C 295 ASN cc_start: 0.7268 (t0) cc_final: 0.6978 (m-40) REVERT: C 350 PHE cc_start: 0.8454 (m-10) cc_final: 0.8131 (m-80) REVERT: D 57 ARG cc_start: 0.7302 (mtt180) cc_final: 0.5937 (mmt180) REVERT: D 67 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7209 (tmm) REVERT: D 230 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.7024 (p0) REVERT: D 295 ASN cc_start: 0.7259 (t0) cc_final: 0.6974 (m-40) REVERT: D 334 MET cc_start: 0.1639 (mtm) cc_final: 0.0024 (ttt) outliers start: 65 outliers final: 40 residues processed: 192 average time/residue: 0.2246 time to fit residues: 68.2914 Evaluate side-chains 181 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 132 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN C 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15888 Z= 0.153 Angle : 0.564 8.146 21564 Z= 0.275 Chirality : 0.039 0.132 2468 Planarity : 0.003 0.040 2648 Dihedral : 8.610 64.215 2188 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.60 % Allowed : 12.12 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.14 (0.20), residues: 1884 helix: 0.44 (0.17), residues: 980 sheet: -1.03 (0.36), residues: 224 loop : -2.44 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 157 HIS 0.003 0.001 HIS A 234 PHE 0.012 0.001 PHE D 235 TYR 0.009 0.001 TYR D 169 ARG 0.002 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7119 (t80) REVERT: A 50 MET cc_start: 0.6975 (mmm) cc_final: 0.6424 (mtt) REVERT: A 68 LEU cc_start: 0.8893 (tp) cc_final: 0.8640 (tt) REVERT: A 230 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.7055 (p0) REVERT: A 295 ASN cc_start: 0.7196 (t0) cc_final: 0.6862 (m-40) REVERT: A 334 MET cc_start: 0.1741 (mtt) cc_final: 0.0326 (ttt) REVERT: A 350 PHE cc_start: 0.8419 (m-10) cc_final: 0.8100 (m-80) REVERT: B 47 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6934 (t80) REVERT: B 57 ARG cc_start: 0.7329 (mtt180) cc_final: 0.5810 (mmt180) REVERT: B 230 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.7064 (p0) REVERT: B 295 ASN cc_start: 0.7205 (t0) cc_final: 0.6850 (m-40) REVERT: B 334 MET cc_start: 0.1738 (mtt) cc_final: 0.0204 (ttt) REVERT: B 350 PHE cc_start: 0.8410 (m-10) cc_final: 0.8083 (m-80) REVERT: C 57 ARG cc_start: 0.7333 (mtt180) cc_final: 0.5951 (tpt170) REVERT: C 68 LEU cc_start: 0.8895 (tp) cc_final: 0.8638 (tt) REVERT: C 230 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.7065 (p0) REVERT: C 295 ASN cc_start: 0.7246 (t0) cc_final: 0.6941 (m-40) REVERT: C 334 MET cc_start: 0.1791 (mtt) cc_final: 0.0291 (ttt) REVERT: C 350 PHE cc_start: 0.8405 (m-10) cc_final: 0.8076 (m-80) REVERT: D 57 ARG cc_start: 0.7235 (mtt180) cc_final: 0.5867 (mmt180) REVERT: D 68 LEU cc_start: 0.8879 (tp) cc_final: 0.8608 (tt) REVERT: D 230 ASN cc_start: 0.7380 (OUTLIER) cc_final: 0.7102 (p0) REVERT: D 295 ASN cc_start: 0.7218 (t0) cc_final: 0.6899 (m-40) REVERT: D 334 MET cc_start: 0.1716 (mtm) cc_final: 0.0091 (ttt) outliers start: 44 outliers final: 26 residues processed: 192 average time/residue: 0.2313 time to fit residues: 70.5003 Evaluate side-chains 179 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 123 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN B 481 GLN C 327 GLN D 481 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15888 Z= 0.235 Angle : 0.597 7.869 21564 Z= 0.296 Chirality : 0.042 0.229 2468 Planarity : 0.003 0.040 2648 Dihedral : 8.456 64.476 2188 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.60 % Allowed : 12.94 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.97 (0.20), residues: 1884 helix: 0.59 (0.17), residues: 952 sheet: -1.06 (0.36), residues: 224 loop : -2.22 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 157 HIS 0.005 0.001 HIS D 234 PHE 0.012 0.001 PHE B 235 TYR 0.011 0.001 TYR D 169 ARG 0.002 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7067 (t80) REVERT: A 230 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.7013 (p0) REVERT: A 295 ASN cc_start: 0.7220 (t0) cc_final: 0.6881 (m-40) REVERT: A 334 MET cc_start: 0.1803 (mtt) cc_final: 0.0416 (ttt) REVERT: A 350 PHE cc_start: 0.8429 (m-10) cc_final: 0.8126 (m-80) REVERT: B 47 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6974 (t80) REVERT: B 57 ARG cc_start: 0.7359 (mtt180) cc_final: 0.5793 (mmt180) REVERT: B 230 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6997 (p0) REVERT: B 295 ASN cc_start: 0.7217 (t0) cc_final: 0.6866 (m-40) REVERT: B 350 PHE cc_start: 0.8437 (m-10) cc_final: 0.8122 (m-80) REVERT: C 57 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6066 (tpt170) REVERT: C 230 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.7027 (p0) REVERT: C 295 ASN cc_start: 0.7251 (t0) cc_final: 0.6931 (m-40) REVERT: C 334 MET cc_start: 0.1826 (mtt) cc_final: 0.0343 (ttt) REVERT: C 350 PHE cc_start: 0.8412 (m-10) cc_final: 0.8112 (m-80) REVERT: D 47 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.7370 (t80) REVERT: D 57 ARG cc_start: 0.7302 (mtt180) cc_final: 0.5891 (mmt180) REVERT: D 230 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7005 (p0) REVERT: D 295 ASN cc_start: 0.7232 (t0) cc_final: 0.6915 (m-40) REVERT: D 334 MET cc_start: 0.1635 (mtm) cc_final: 0.0013 (ttt) outliers start: 44 outliers final: 34 residues processed: 179 average time/residue: 0.2291 time to fit residues: 65.3199 Evaluate side-chains 180 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.0370 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 GLN D 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15888 Z= 0.139 Angle : 0.559 9.637 21564 Z= 0.274 Chirality : 0.040 0.146 2468 Planarity : 0.003 0.039 2648 Dihedral : 8.031 60.401 2188 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.36 % Allowed : 13.53 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.78 (0.20), residues: 1884 helix: 0.69 (0.17), residues: 984 sheet: -0.73 (0.37), residues: 224 loop : -2.27 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 444 HIS 0.003 0.001 HIS C 451 PHE 0.022 0.001 PHE C 48 TYR 0.009 0.001 TYR D 169 ARG 0.001 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7418 (t80) REVERT: A 50 MET cc_start: 0.7104 (mmm) cc_final: 0.6703 (mtt) REVERT: A 68 LEU cc_start: 0.8886 (tp) cc_final: 0.8578 (tt) REVERT: A 230 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.7019 (p0) REVERT: A 295 ASN cc_start: 0.7277 (t0) cc_final: 0.6904 (m-40) REVERT: A 334 MET cc_start: 0.1799 (mtt) cc_final: 0.0313 (ttt) REVERT: A 350 PHE cc_start: 0.8399 (m-10) cc_final: 0.8078 (m-80) REVERT: B 47 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6955 (t80) REVERT: B 230 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.7032 (p0) REVERT: B 295 ASN cc_start: 0.7194 (t0) cc_final: 0.6830 (m-40) REVERT: B 334 MET cc_start: 0.1735 (mtt) cc_final: 0.0273 (ttt) REVERT: B 350 PHE cc_start: 0.8401 (m-10) cc_final: 0.8090 (m-80) REVERT: C 57 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6015 (tpt170) REVERT: C 68 LEU cc_start: 0.8883 (tp) cc_final: 0.8520 (tt) REVERT: C 230 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.7030 (p0) REVERT: C 295 ASN cc_start: 0.7216 (t0) cc_final: 0.6864 (m-40) REVERT: C 334 MET cc_start: 0.1804 (mtt) cc_final: 0.0270 (ttt) REVERT: C 350 PHE cc_start: 0.8376 (m-10) cc_final: 0.8066 (m-80) REVERT: D 47 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7317 (t80) REVERT: D 57 ARG cc_start: 0.7310 (mtt180) cc_final: 0.5883 (mmt180) REVERT: D 68 LEU cc_start: 0.8887 (tp) cc_final: 0.8658 (tt) REVERT: D 230 ASN cc_start: 0.7322 (OUTLIER) cc_final: 0.7028 (p0) REVERT: D 295 ASN cc_start: 0.7209 (t0) cc_final: 0.6875 (m-40) REVERT: D 334 MET cc_start: 0.1746 (mtm) cc_final: 0.0034 (ttt) outliers start: 40 outliers final: 30 residues processed: 197 average time/residue: 0.2164 time to fit residues: 68.4706 Evaluate side-chains 188 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 118 optimal weight: 0.0570 chunk 158 optimal weight: 4.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN C 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15888 Z= 0.140 Angle : 0.547 9.930 21564 Z= 0.268 Chirality : 0.040 0.137 2468 Planarity : 0.003 0.038 2648 Dihedral : 7.534 59.632 2188 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.42 % Allowed : 13.95 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1884 helix: 0.82 (0.17), residues: 992 sheet: -0.47 (0.37), residues: 224 loop : -2.18 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 444 HIS 0.003 0.001 HIS D 234 PHE 0.011 0.001 PHE C 235 TYR 0.009 0.001 TYR B 169 ARG 0.001 0.000 ARG D 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7176 (mmm) cc_final: 0.6799 (mtt) REVERT: A 68 LEU cc_start: 0.8866 (tp) cc_final: 0.8546 (tt) REVERT: A 230 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.7023 (p0) REVERT: A 295 ASN cc_start: 0.7278 (t0) cc_final: 0.6902 (m-40) REVERT: A 334 MET cc_start: 0.1531 (mtt) cc_final: 0.0095 (ttt) REVERT: A 350 PHE cc_start: 0.8392 (m-10) cc_final: 0.8079 (m-80) REVERT: B 47 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7107 (t80) REVERT: B 68 LEU cc_start: 0.8873 (tp) cc_final: 0.8533 (tt) REVERT: B 230 ASN cc_start: 0.7325 (OUTLIER) cc_final: 0.7094 (p0) REVERT: B 295 ASN cc_start: 0.7293 (t0) cc_final: 0.6900 (m-40) REVERT: B 350 PHE cc_start: 0.8407 (m-10) cc_final: 0.8085 (m-80) REVERT: C 57 ARG cc_start: 0.7333 (mtt180) cc_final: 0.5919 (tpt170) REVERT: C 68 LEU cc_start: 0.8871 (tp) cc_final: 0.8550 (tt) REVERT: C 230 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.7020 (p0) REVERT: C 295 ASN cc_start: 0.7305 (t0) cc_final: 0.6913 (m-40) REVERT: C 334 MET cc_start: 0.1610 (mtt) cc_final: 0.0174 (ttt) REVERT: C 350 PHE cc_start: 0.8375 (m-10) cc_final: 0.8050 (m-80) REVERT: D 68 LEU cc_start: 0.8859 (tp) cc_final: 0.8533 (tt) REVERT: D 230 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7051 (p0) REVERT: D 295 ASN cc_start: 0.7221 (t0) cc_final: 0.6882 (m-40) REVERT: D 334 MET cc_start: 0.1805 (mtm) cc_final: 0.0232 (ttt) outliers start: 41 outliers final: 34 residues processed: 198 average time/residue: 0.2144 time to fit residues: 68.3800 Evaluate side-chains 192 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.119293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095455 restraints weight = 35165.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098075 restraints weight = 19344.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099858 restraints weight = 13092.792| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15888 Z= 0.213 Angle : 0.576 7.484 21564 Z= 0.286 Chirality : 0.041 0.157 2468 Planarity : 0.003 0.040 2648 Dihedral : 7.520 59.009 2188 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.54 % Allowed : 14.18 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.65 (0.20), residues: 1884 helix: 0.80 (0.17), residues: 984 sheet: -0.56 (0.37), residues: 224 loop : -2.27 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 444 HIS 0.004 0.001 HIS D 234 PHE 0.011 0.001 PHE B 235 TYR 0.011 0.001 TYR A 169 ARG 0.002 0.000 ARG C 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2774.07 seconds wall clock time: 51 minutes 51.17 seconds (3111.17 seconds total)