Starting phenix.real_space_refine on Fri Jan 19 19:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eti_3953/01_2024/6eti_3953_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eti_3953/01_2024/6eti_3953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eti_3953/01_2024/6eti_3953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eti_3953/01_2024/6eti_3953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eti_3953/01_2024/6eti_3953_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eti_3953/01_2024/6eti_3953_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8036 2.51 5 N 2042 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12442 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.31, per 1000 atoms: 0.59 Number of scatterers: 12442 At special positions: 0 Unit cell: (103.32, 99.96, 146.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2296 8.00 N 2042 7.00 C 8036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 5.01 Conformation dependent library (CDL) restraints added in 2.6 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 12 sheets defined 39.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.546A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.572A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.773A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.724A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.852A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.908A pdb=" N LEU A 274 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 278 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.860A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.743A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.507A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.518A pdb=" N LEU A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.525A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.521A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.791A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.584A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.507A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.776A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 624 through 649 removed outlier: 4.921A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.547A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 167 removed outlier: 3.573A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.774A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.724A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.852A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.908A pdb=" N LEU B 274 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 276 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 278 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.860A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.743A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.508A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.518A pdb=" N LEU B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 422 through 450 removed outlier: 3.526A pdb=" N GLN B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 478 through 497 removed outlier: 3.520A pdb=" N ARG B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 3.792A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 3.583A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.507A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.775A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 624 through 649 removed outlier: 4.921A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 68 through 71 Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.290A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 255 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLY A 80 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 68 through 71 Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.290A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 255 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 19 through 24 Processing sheet with id= F, first strand: chain 'C' and resid 85 through 90 removed outlier: 6.018A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= H, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.707A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 19 through 24 Processing sheet with id= J, first strand: chain 'E' and resid 85 through 90 removed outlier: 6.018A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= L, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.707A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1946 1.31 - 1.43: 3574 1.43 - 1.56: 7098 1.56 - 1.69: 0 1.69 - 1.82: 106 Bond restraints: 12724 Sorted by residual: bond pdb=" C36 BWQ B1101 " pdb=" O37 BWQ B1101 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C36 BWQ A1101 " pdb=" O37 BWQ A1101 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C23 BWQ A1101 " pdb=" O24 BWQ A1101 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C23 BWQ B1101 " pdb=" O24 BWQ B1101 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C23 BWQ A1101 " pdb=" N25 BWQ A1101 " ideal model delta sigma weight residual 1.333 1.466 -0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 12719 not shown) Histogram of bond angle deviations from ideal: 98.37 - 106.63: 351 106.63 - 114.88: 7480 114.88 - 123.14: 8721 123.14 - 131.39: 661 131.39 - 139.65: 41 Bond angle restraints: 17254 Sorted by residual: angle pdb=" C06 BWQ A1101 " pdb=" N07 BWQ A1101 " pdb=" C08 BWQ A1101 " ideal model delta sigma weight residual 109.00 123.58 -14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CA LEU B 64 " pdb=" CB LEU B 64 " pdb=" CG LEU B 64 " ideal model delta sigma weight residual 116.30 133.11 -16.81 3.50e+00 8.16e-02 2.31e+01 angle pdb=" C ILE A 63 " pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.29e+01 angle pdb=" CA LEU A 64 " pdb=" CB LEU A 64 " pdb=" CG LEU A 64 " ideal model delta sigma weight residual 116.30 133.05 -16.75 3.50e+00 8.16e-02 2.29e+01 angle pdb=" C ILE B 63 " pdb=" N LEU B 64 " pdb=" CA LEU B 64 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 ... (remaining 17249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.32: 7386 26.32 - 52.63: 165 52.63 - 78.94: 20 78.94 - 105.26: 2 105.26 - 131.57: 6 Dihedral angle restraints: 7579 sinusoidal: 3043 harmonic: 4536 Sorted by residual: dihedral pdb=" CA PHE A 414 " pdb=" C PHE A 414 " pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta harmonic sigma weight residual -180.00 -137.37 -42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE B 414 " pdb=" C PHE B 414 " pdb=" N GLY B 415 " pdb=" CA GLY B 415 " ideal model delta harmonic sigma weight residual 180.00 -137.44 -42.56 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 29.37 63.63 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 7576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1393 0.057 - 0.113: 460 0.113 - 0.170: 83 0.170 - 0.226: 32 0.226 - 0.283: 4 Chirality restraints: 1972 Sorted by residual: chirality pdb=" C22 BWQ A1101 " pdb=" C21 BWQ A1101 " pdb=" C23 BWQ A1101 " pdb=" N38 BWQ A1101 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C22 BWQ B1101 " pdb=" C21 BWQ B1101 " pdb=" C23 BWQ B1101 " pdb=" N38 BWQ B1101 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1969 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 BWQ B1101 " 0.030 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" C23 BWQ B1101 " 0.065 2.00e-02 2.50e+03 pdb=" C26 BWQ B1101 " -0.266 2.00e-02 2.50e+03 pdb=" N25 BWQ B1101 " 0.354 2.00e-02 2.50e+03 pdb=" O24 BWQ B1101 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 BWQ B1101 " -0.169 2.00e-02 2.50e+03 1.92e-01 5.54e+02 pdb=" C22 BWQ B1101 " 0.266 2.00e-02 2.50e+03 pdb=" C26 BWQ B1101 " -0.175 2.00e-02 2.50e+03 pdb=" C36 BWQ B1101 " -0.022 2.00e-02 2.50e+03 pdb=" N38 BWQ B1101 " -0.158 2.00e-02 2.50e+03 pdb=" O37 BWQ B1101 " 0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 BWQ A1101 " 0.010 2.00e-02 2.50e+03 8.66e-02 1.12e+02 pdb=" C22 BWQ A1101 " -0.120 2.00e-02 2.50e+03 pdb=" C26 BWQ A1101 " 0.036 2.00e-02 2.50e+03 pdb=" C36 BWQ A1101 " 0.029 2.00e-02 2.50e+03 pdb=" N38 BWQ A1101 " 0.140 2.00e-02 2.50e+03 pdb=" O37 BWQ A1101 " -0.094 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4038 2.83 - 3.35: 10590 3.35 - 3.87: 19732 3.87 - 4.38: 23810 4.38 - 4.90: 41388 Nonbonded interactions: 99558 Sorted by model distance: nonbonded pdb=" OG SER C 63 " pdb=" OG SER C 74 " model vdw 2.316 2.440 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 74 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.361 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.362 2.440 nonbonded pdb=" O GLY D 66 " pdb=" NH1 ARG D 84 " model vdw 2.366 2.520 ... (remaining 99553 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.020 Extract box with map and model: 12.280 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.770 Find NCS groups from input model: 0.740 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.010 0.173 12724 Z= 0.658 Angle : 1.090 16.810 17254 Z= 0.542 Chirality : 0.060 0.283 1972 Planarity : 0.010 0.217 2144 Dihedral : 11.802 131.573 4662 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.33 % Favored : 94.48 % Rotamer: Outliers : 0.30 % Allowed : 3.56 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.16), residues: 1558 helix: -4.25 (0.08), residues: 648 sheet: -1.42 (0.30), residues: 272 loop : -2.39 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP E 96 HIS 0.011 0.003 HIS B 457 PHE 0.048 0.004 PHE E 98 TYR 0.042 0.004 TYR A 570 ARG 0.009 0.002 ARG B 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 222 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8303 (t70) cc_final: 0.8096 (t-90) REVERT: A 475 LEU cc_start: 0.8865 (tp) cc_final: 0.8562 (mp) REVERT: B 243 HIS cc_start: 0.8289 (t70) cc_final: 0.7846 (t-90) REVERT: B 348 GLU cc_start: 0.8158 (tp30) cc_final: 0.7629 (mt-10) outliers start: 4 outliers final: 0 residues processed: 226 average time/residue: 0.3063 time to fit residues: 94.6026 Evaluate side-chains 145 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 68 ASN A 76 ASN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS A 375 HIS A 425 ASN A 437 GLN A 583 HIS B 41 ASN B 68 ASN B 76 ASN B 120 ASN B 243 HIS B 375 HIS B 425 ASN B 437 GLN B 583 HIS B 601 ASN F 3 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12724 Z= 0.205 Angle : 0.641 8.930 17254 Z= 0.328 Chirality : 0.042 0.171 1972 Planarity : 0.005 0.043 2144 Dihedral : 10.549 132.471 1874 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.41 % Allowed : 6.96 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.56 (0.19), residues: 1558 helix: -1.81 (0.17), residues: 636 sheet: -0.70 (0.31), residues: 272 loop : -1.86 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 109 HIS 0.005 0.001 HIS B 40 PHE 0.039 0.002 PHE A 293 TYR 0.017 0.002 TYR B 570 ARG 0.003 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7073 (p0) cc_final: 0.6711 (p0) REVERT: A 203 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7475 (t70) REVERT: A 220 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7272 (t) REVERT: A 226 LEU cc_start: 0.8677 (mt) cc_final: 0.8444 (mt) REVERT: A 271 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7340 (mp10) REVERT: B 127 ASP cc_start: 0.7367 (p0) cc_final: 0.6928 (p0) REVERT: B 226 LEU cc_start: 0.8715 (mt) cc_final: 0.8465 (mt) REVERT: B 243 HIS cc_start: 0.8289 (t-90) cc_final: 0.8042 (t70) REVERT: B 348 GLU cc_start: 0.8195 (tp30) cc_final: 0.7937 (tt0) REVERT: B 565 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (mt) outliers start: 19 outliers final: 9 residues processed: 174 average time/residue: 0.2727 time to fit residues: 67.6588 Evaluate side-chains 148 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 601 ASN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12724 Z= 0.230 Angle : 0.603 8.513 17254 Z= 0.305 Chirality : 0.042 0.155 1972 Planarity : 0.004 0.037 2144 Dihedral : 10.197 132.021 1874 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.00 % Allowed : 8.30 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1558 helix: -0.24 (0.20), residues: 638 sheet: -0.34 (0.31), residues: 274 loop : -1.53 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 109 HIS 0.008 0.001 HIS A 243 PHE 0.033 0.002 PHE B 293 TYR 0.017 0.002 TYR A 570 ARG 0.003 0.000 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.561 Fit side-chains REVERT: A 127 ASP cc_start: 0.7006 (p0) cc_final: 0.6679 (p0) REVERT: A 203 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7478 (t70) REVERT: A 220 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7079 (t) REVERT: A 271 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7295 (mp10) REVERT: B 127 ASP cc_start: 0.7379 (p0) cc_final: 0.6953 (p0) REVERT: B 226 LEU cc_start: 0.8700 (mt) cc_final: 0.8449 (mt) REVERT: B 243 HIS cc_start: 0.8343 (t-90) cc_final: 0.8050 (t70) outliers start: 27 outliers final: 20 residues processed: 158 average time/residue: 0.2541 time to fit residues: 58.0530 Evaluate side-chains 143 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12724 Z= 0.374 Angle : 0.667 8.093 17254 Z= 0.334 Chirality : 0.046 0.187 1972 Planarity : 0.004 0.038 2144 Dihedral : 10.200 129.316 1874 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.52 % Allowed : 8.74 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.92 (0.21), residues: 1558 helix: 0.22 (0.21), residues: 630 sheet: -0.22 (0.32), residues: 276 loop : -1.56 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 109 HIS 0.006 0.002 HIS A 40 PHE 0.032 0.002 PHE B 293 TYR 0.021 0.002 TYR B 570 ARG 0.004 0.001 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 1.418 Fit side-chains REVERT: A 127 ASP cc_start: 0.7062 (p0) cc_final: 0.6744 (p0) REVERT: A 203 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7449 (t70) REVERT: A 220 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.7143 (t) REVERT: A 271 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7316 (mp10) REVERT: B 127 ASP cc_start: 0.7276 (p0) cc_final: 0.6858 (p0) REVERT: B 226 LEU cc_start: 0.8679 (mt) cc_final: 0.8416 (mt) REVERT: D 47 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8138 (tt0) outliers start: 34 outliers final: 24 residues processed: 163 average time/residue: 0.2596 time to fit residues: 61.0813 Evaluate side-chains 152 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 133 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN B 243 HIS B 582 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12724 Z= 0.146 Angle : 0.542 7.703 17254 Z= 0.275 Chirality : 0.040 0.135 1972 Planarity : 0.003 0.034 2144 Dihedral : 9.880 131.665 1874 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 10.15 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1558 helix: 0.82 (0.21), residues: 632 sheet: -0.08 (0.32), residues: 276 loop : -1.33 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.007 0.001 HIS B 243 PHE 0.033 0.001 PHE A 293 TYR 0.018 0.001 TYR B 342 ARG 0.004 0.000 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.482 Fit side-chains REVERT: A 127 ASP cc_start: 0.7015 (p0) cc_final: 0.6446 (p0) REVERT: A 203 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7447 (t70) REVERT: A 220 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6972 (t) REVERT: A 271 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7897 (mp10) REVERT: A 349 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6585 (mp) REVERT: A 616 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8620 (mttm) REVERT: B 127 ASP cc_start: 0.7262 (p0) cc_final: 0.6657 (p0) REVERT: B 226 LEU cc_start: 0.8638 (mt) cc_final: 0.8388 (mt) REVERT: B 243 HIS cc_start: 0.8234 (t-90) cc_final: 0.7923 (t-90) REVERT: B 446 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7491 (mm-30) REVERT: E 79 GLN cc_start: 0.8533 (mp10) cc_final: 0.8131 (mp10) REVERT: E 103 LYS cc_start: 0.8876 (tttp) cc_final: 0.8594 (tttp) outliers start: 28 outliers final: 15 residues processed: 161 average time/residue: 0.2571 time to fit residues: 59.5971 Evaluate side-chains 147 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN B 582 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12724 Z= 0.418 Angle : 0.690 8.569 17254 Z= 0.344 Chirality : 0.047 0.236 1972 Planarity : 0.004 0.035 2144 Dihedral : 10.115 129.887 1874 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.96 % Allowed : 9.41 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.46 (0.21), residues: 1558 helix: 0.73 (0.21), residues: 636 sheet: -0.15 (0.32), residues: 276 loop : -1.39 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 35 HIS 0.008 0.002 HIS A 243 PHE 0.031 0.002 PHE A 293 TYR 0.017 0.002 TYR B 570 ARG 0.004 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.608 Fit side-chains REVERT: A 127 ASP cc_start: 0.7158 (p0) cc_final: 0.6820 (p0) REVERT: A 203 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7443 (t70) REVERT: A 243 HIS cc_start: 0.8268 (t70) cc_final: 0.7750 (t-90) REVERT: A 349 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6760 (mp) REVERT: B 127 ASP cc_start: 0.7448 (p0) cc_final: 0.6994 (p0) REVERT: B 616 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8467 (mttm) REVERT: D 47 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: F 47 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8186 (tt0) outliers start: 40 outliers final: 22 residues processed: 169 average time/residue: 0.2599 time to fit residues: 62.8140 Evaluate side-chains 149 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.0060 chunk 108 optimal weight: 0.4980 chunk 125 optimal weight: 0.4980 chunk 83 optimal weight: 0.0170 chunk 148 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 222 ASN A 582 GLN B 582 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12724 Z= 0.139 Angle : 0.547 7.478 17254 Z= 0.277 Chirality : 0.040 0.176 1972 Planarity : 0.003 0.034 2144 Dihedral : 9.802 132.101 1874 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.78 % Allowed : 10.74 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.22), residues: 1558 helix: 1.23 (0.21), residues: 632 sheet: -0.03 (0.32), residues: 276 loop : -1.20 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.008 0.001 HIS A 243 PHE 0.033 0.001 PHE A 293 TYR 0.018 0.001 TYR A 342 ARG 0.004 0.000 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.347 Fit side-chains REVERT: A 127 ASP cc_start: 0.7066 (p0) cc_final: 0.6759 (p0) REVERT: A 243 HIS cc_start: 0.8272 (t70) cc_final: 0.8059 (t-90) REVERT: A 349 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6374 (mp) REVERT: A 446 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7627 (mm-30) REVERT: B 127 ASP cc_start: 0.7293 (p0) cc_final: 0.6894 (p0) REVERT: B 243 HIS cc_start: 0.8301 (t-90) cc_final: 0.8029 (t-90) REVERT: B 616 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8407 (mttm) outliers start: 24 outliers final: 19 residues processed: 156 average time/residue: 0.2397 time to fit residues: 54.5890 Evaluate side-chains 144 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.0170 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 116 optimal weight: 0.0060 chunk 135 optimal weight: 2.9990 overall best weight: 1.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3053 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: