Starting phenix.real_space_refine on Sun Mar 17 20:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw9_20920/03_2024/6uw9_20920.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw9_20920/03_2024/6uw9_20920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw9_20920/03_2024/6uw9_20920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw9_20920/03_2024/6uw9_20920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw9_20920/03_2024/6uw9_20920.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw9_20920/03_2024/6uw9_20920.pdb" } resolution = 4.33 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= 0.004 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 112 5.16 5 C 12340 2.51 5 N 3136 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 117": "NH1" <-> "NH2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D GLU 355": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 682": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 702": "OE1" <-> "OE2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4731 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 571} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4731 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 571} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4731 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 571} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4731 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 571} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 9.86, per 1000 atoms: 0.52 Number of scatterers: 18924 At special positions: 0 Unit cell: (159.5, 159.5, 117.7, 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 112 16.00 O 3336 8.00 N 3136 7.00 C 12340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.0 seconds 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 67.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 removed outlier: 4.008A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.621A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 567' Processing helix chain 'A' and resid 569 through 586 removed outlier: 4.360A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.883A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 706 removed outlier: 3.605A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 4.438A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.537A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 335 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 removed outlier: 4.008A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.904A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.883A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.166A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.622A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 567' Processing helix chain 'B' and resid 569 through 586 removed outlier: 4.361A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 706 removed outlier: 3.606A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.611A pdb=" N LEU C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.591A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C 335 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 4.007A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 501 removed outlier: 4.236A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.622A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 563 through 567' Processing helix chain 'C' and resid 569 through 586 removed outlier: 4.361A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 679 removed outlier: 3.704A pdb=" N PHE C 654 " --> pdb=" O TYR C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 706 removed outlier: 3.606A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.935A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 335 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 removed outlier: 4.007A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 431 " --> pdb=" O THR D 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 removed outlier: 3.621A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 563 through 567' Processing helix chain 'D' and resid 569 through 586 removed outlier: 4.360A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 706 removed outlier: 3.605A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2940 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: 5.19 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5464 1.34 - 1.46: 3429 1.46 - 1.57: 10235 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 19320 Sorted by residual: bond pdb=" C PRO B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.71e+01 bond pdb=" C PRO D 424 " pdb=" N LEU D 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.70e+01 bond pdb=" C PRO C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.70e+01 bond pdb=" C PRO A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.332 1.220 0.112 1.29e-02 6.01e+03 7.59e+01 bond pdb=" C GLU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.331 1.386 -0.054 7.90e-03 1.60e+04 4.75e+01 ... (remaining 19315 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.67: 203 104.67 - 112.38: 9078 112.38 - 120.08: 8933 120.08 - 127.79: 7711 127.79 - 135.50: 195 Bond angle restraints: 26120 Sorted by residual: angle pdb=" CA PRO A 424 " pdb=" C PRO A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 118.81 103.11 15.70 1.61e+00 3.86e-01 9.51e+01 angle pdb=" CA PRO C 424 " pdb=" C PRO C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 118.81 103.15 15.66 1.61e+00 3.86e-01 9.46e+01 angle pdb=" CA PRO B 424 " pdb=" C PRO B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 118.81 103.17 15.64 1.61e+00 3.86e-01 9.44e+01 angle pdb=" CA PRO D 424 " pdb=" C PRO D 424 " pdb=" N LEU D 425 " ideal model delta sigma weight residual 118.81 103.17 15.64 1.61e+00 3.86e-01 9.44e+01 angle pdb=" C PRO A 424 " pdb=" N LEU A 425 " pdb=" CA LEU A 425 " ideal model delta sigma weight residual 122.60 106.13 16.47 1.88e+00 2.83e-01 7.67e+01 ... (remaining 26115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 9869 16.86 - 33.72: 1254 33.72 - 50.59: 277 50.59 - 67.45: 28 67.45 - 84.31: 16 Dihedral angle restraints: 11444 sinusoidal: 4600 harmonic: 6844 Sorted by residual: dihedral pdb=" CA ILE A 199 " pdb=" C ILE A 199 " pdb=" N LEU A 200 " pdb=" CA LEU A 200 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE B 199 " pdb=" C ILE B 199 " pdb=" N LEU B 200 " pdb=" CA LEU B 200 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE C 199 " pdb=" C ILE C 199 " pdb=" N LEU C 200 " pdb=" CA LEU C 200 " ideal model delta harmonic sigma weight residual 180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2332 0.064 - 0.127: 528 0.127 - 0.191: 106 0.191 - 0.254: 26 0.254 - 0.318: 8 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA ASP B 586 " pdb=" N ASP B 586 " pdb=" C ASP B 586 " pdb=" CB ASP B 586 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA ASP A 586 " pdb=" N ASP A 586 " pdb=" C ASP A 586 " pdb=" CB ASP A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ASP C 586 " pdb=" N ASP C 586 " pdb=" C ASP C 586 " pdb=" CB ASP C 586 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2997 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 343 " 0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 344 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 344 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 344 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 344 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO D 344 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " 0.044 5.00e-02 4.00e+02 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 152 2.53 - 3.12: 12859 3.12 - 3.71: 29738 3.71 - 4.31: 37668 4.31 - 4.90: 62242 Nonbonded interactions: 142659 Sorted by model distance: nonbonded pdb=" SD MET A 431 " pdb=" NH1 ARG A 716 " model vdw 1.932 2.880 nonbonded pdb=" SD MET D 431 " pdb=" NH1 ARG D 716 " model vdw 1.933 2.880 nonbonded pdb=" SD MET C 431 " pdb=" NH1 ARG C 716 " model vdw 1.933 2.880 nonbonded pdb=" SD MET B 431 " pdb=" NH1 ARG B 716 " model vdw 1.933 2.880 nonbonded pdb=" SD MET D 431 " pdb=" CZ ARG D 716 " model vdw 1.973 3.630 ... (remaining 142654 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 4.790 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 45.710 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 19320 Z= 0.356 Angle : 1.144 16.467 26120 Z= 0.630 Chirality : 0.060 0.318 3000 Planarity : 0.007 0.081 3236 Dihedral : 15.426 84.310 6996 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.20 % Allowed : 11.22 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.13), residues: 2288 helix: -3.02 (0.09), residues: 1424 sheet: -1.63 (0.86), residues: 40 loop : -3.58 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 380 HIS 0.005 0.001 HIS A 301 PHE 0.034 0.002 PHE D 656 TYR 0.015 0.002 TYR B 451 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 532 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8780 (m-40) cc_final: 0.8363 (p0) REVERT: A 268 LEU cc_start: 0.9407 (tp) cc_final: 0.9163 (tp) REVERT: A 366 LYS cc_start: 0.8790 (mppt) cc_final: 0.8352 (mmmt) REVERT: A 562 MET cc_start: 0.8934 (tpp) cc_final: 0.8652 (tpp) REVERT: A 574 MET cc_start: 0.8821 (mtm) cc_final: 0.8555 (mtm) REVERT: A 592 PHE cc_start: 0.8665 (t80) cc_final: 0.8404 (t80) REVERT: A 595 ILE cc_start: 0.9398 (mm) cc_final: 0.9094 (tp) REVERT: A 672 MET cc_start: 0.9048 (tmm) cc_final: 0.8756 (tmm) REVERT: B 188 ARG cc_start: 0.8723 (mmp-170) cc_final: 0.8388 (tpp-160) REVERT: B 205 ASN cc_start: 0.8811 (m-40) cc_final: 0.8362 (p0) REVERT: B 268 LEU cc_start: 0.9425 (tp) cc_final: 0.9184 (tp) REVERT: B 366 LYS cc_start: 0.8792 (mppt) cc_final: 0.8375 (mmmt) REVERT: B 409 TYR cc_start: 0.8276 (m-10) cc_final: 0.6999 (m-10) REVERT: B 562 MET cc_start: 0.9009 (tpp) cc_final: 0.8756 (tpp) REVERT: B 574 MET cc_start: 0.8849 (mtm) cc_final: 0.8465 (mtm) REVERT: B 592 PHE cc_start: 0.8664 (t80) cc_final: 0.8353 (t80) REVERT: B 595 ILE cc_start: 0.9393 (mm) cc_final: 0.9042 (tp) REVERT: B 672 MET cc_start: 0.9067 (tmm) cc_final: 0.8737 (tmm) REVERT: C 188 ARG cc_start: 0.8726 (mmp-170) cc_final: 0.8517 (mmp80) REVERT: C 205 ASN cc_start: 0.8768 (m-40) cc_final: 0.8246 (p0) REVERT: C 268 LEU cc_start: 0.9419 (tp) cc_final: 0.9180 (tp) REVERT: C 366 LYS cc_start: 0.8864 (mppt) cc_final: 0.8470 (mmmt) REVERT: C 497 ILE cc_start: 0.9093 (tp) cc_final: 0.8869 (tt) REVERT: C 562 MET cc_start: 0.8998 (tpp) cc_final: 0.8733 (tpp) REVERT: C 572 MET cc_start: 0.8447 (tpp) cc_final: 0.7823 (mmm) REVERT: C 574 MET cc_start: 0.8834 (mtm) cc_final: 0.8450 (mtm) REVERT: C 592 PHE cc_start: 0.8701 (t80) cc_final: 0.8442 (t80) REVERT: C 595 ILE cc_start: 0.9390 (mm) cc_final: 0.9023 (tp) REVERT: C 672 MET cc_start: 0.9061 (tmm) cc_final: 0.8741 (tmm) REVERT: D 188 ARG cc_start: 0.8720 (mmp-170) cc_final: 0.8499 (mmp80) REVERT: D 205 ASN cc_start: 0.8816 (m-40) cc_final: 0.8358 (p0) REVERT: D 268 LEU cc_start: 0.9422 (tp) cc_final: 0.9175 (tp) REVERT: D 366 LYS cc_start: 0.8846 (mppt) cc_final: 0.8412 (mmmt) REVERT: D 497 ILE cc_start: 0.9089 (tp) cc_final: 0.8880 (tt) REVERT: D 562 MET cc_start: 0.8993 (tpp) cc_final: 0.8698 (tpp) REVERT: D 574 MET cc_start: 0.8863 (mtm) cc_final: 0.8459 (mtm) REVERT: D 592 PHE cc_start: 0.8690 (t80) cc_final: 0.8428 (t80) REVERT: D 595 ILE cc_start: 0.9397 (mm) cc_final: 0.9070 (tp) REVERT: D 672 MET cc_start: 0.9079 (tmm) cc_final: 0.8743 (tmm) REVERT: D 677 MET cc_start: 0.8556 (ttm) cc_final: 0.7932 (ttm) outliers start: 4 outliers final: 4 residues processed: 536 average time/residue: 0.2942 time to fit residues: 238.5950 Evaluate side-chains 371 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 367 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 297 ASN A 561 ASN A 570 GLN A 580 GLN A 671 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 297 ASN B 561 ASN B 570 GLN B 580 GLN B 671 ASN B 683 ASN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS C 297 ASN C 561 ASN C 570 GLN C 580 GLN C 671 ASN C 683 ASN ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 297 ASN D 561 ASN D 570 GLN D 580 GLN D 671 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19320 Z= 0.188 Angle : 0.642 8.768 26120 Z= 0.328 Chirality : 0.041 0.190 3000 Planarity : 0.005 0.068 3236 Dihedral : 5.046 21.067 2524 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.39 % Allowed : 5.71 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.16), residues: 2288 helix: -0.87 (0.13), residues: 1472 sheet: -3.09 (0.58), residues: 64 loop : -3.35 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 380 HIS 0.003 0.001 HIS A 430 PHE 0.019 0.001 PHE B 656 TYR 0.015 0.001 TYR A 661 ARG 0.006 0.000 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 476 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6381 (mpp) cc_final: 0.6000 (mpp) REVERT: A 205 ASN cc_start: 0.8628 (m-40) cc_final: 0.8400 (p0) REVERT: A 246 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7629 (ttpp) REVERT: A 366 LYS cc_start: 0.8838 (mppt) cc_final: 0.8341 (mmmt) REVERT: A 431 MET cc_start: 0.8704 (ttm) cc_final: 0.8297 (ttm) REVERT: A 561 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8748 (t0) REVERT: A 562 MET cc_start: 0.8985 (tpp) cc_final: 0.8698 (tpp) REVERT: A 595 ILE cc_start: 0.9368 (mm) cc_final: 0.9022 (tp) REVERT: A 677 MET cc_start: 0.8179 (ttt) cc_final: 0.7840 (tpp) REVERT: A 740 THR cc_start: 0.7495 (m) cc_final: 0.7224 (p) REVERT: B 159 MET cc_start: 0.6434 (mpp) cc_final: 0.5977 (mpp) REVERT: B 246 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7463 (ttpp) REVERT: B 366 LYS cc_start: 0.8834 (mppt) cc_final: 0.8361 (mmmt) REVERT: B 431 MET cc_start: 0.8663 (ttm) cc_final: 0.8290 (ttm) REVERT: B 527 PHE cc_start: 0.8311 (t80) cc_final: 0.8032 (t80) REVERT: B 561 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8774 (t0) REVERT: B 562 MET cc_start: 0.9036 (tpp) cc_final: 0.8713 (tpp) REVERT: B 592 PHE cc_start: 0.8633 (t80) cc_final: 0.8400 (t80) REVERT: B 595 ILE cc_start: 0.9392 (mm) cc_final: 0.9021 (tp) REVERT: B 662 VAL cc_start: 0.9492 (t) cc_final: 0.9289 (p) REVERT: B 740 THR cc_start: 0.7416 (m) cc_final: 0.7167 (p) REVERT: C 159 MET cc_start: 0.6353 (mpp) cc_final: 0.5951 (mpp) REVERT: C 205 ASN cc_start: 0.8593 (m-40) cc_final: 0.8327 (p0) REVERT: C 246 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7533 (ttpp) REVERT: C 366 LYS cc_start: 0.8881 (mppt) cc_final: 0.8457 (mmmt) REVERT: C 431 MET cc_start: 0.8755 (ttm) cc_final: 0.8378 (ttm) REVERT: C 497 ILE cc_start: 0.9085 (tp) cc_final: 0.8786 (tt) REVERT: C 561 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8793 (t0) REVERT: C 562 MET cc_start: 0.9054 (tpp) cc_final: 0.8716 (tpp) REVERT: C 572 MET cc_start: 0.8326 (tpp) cc_final: 0.7663 (mmm) REVERT: C 575 TYR cc_start: 0.8309 (t80) cc_final: 0.8071 (t80) REVERT: C 595 ILE cc_start: 0.9373 (mm) cc_final: 0.9011 (tp) REVERT: C 662 VAL cc_start: 0.9485 (t) cc_final: 0.9281 (p) REVERT: D 159 MET cc_start: 0.6453 (mpp) cc_final: 0.5981 (mpp) REVERT: D 246 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7515 (ttpp) REVERT: D 366 LYS cc_start: 0.8853 (mppt) cc_final: 0.8373 (mmmt) REVERT: D 431 MET cc_start: 0.8714 (ttm) cc_final: 0.8330 (ttm) REVERT: D 497 ILE cc_start: 0.9083 (tp) cc_final: 0.8791 (tt) REVERT: D 561 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8748 (t0) REVERT: D 562 MET cc_start: 0.9038 (tpp) cc_final: 0.8707 (tpp) REVERT: D 595 ILE cc_start: 0.9387 (mm) cc_final: 0.9010 (tp) REVERT: D 662 VAL cc_start: 0.9485 (t) cc_final: 0.9261 (p) REVERT: D 740 THR cc_start: 0.7449 (m) cc_final: 0.7215 (p) outliers start: 8 outliers final: 4 residues processed: 484 average time/residue: 0.2724 time to fit residues: 210.9318 Evaluate side-chains 366 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 358 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 175 optimal weight: 0.0040 chunk 143 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 211 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN B 671 ASN D 671 ASN D 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19320 Z= 0.155 Angle : 0.617 10.087 26120 Z= 0.305 Chirality : 0.040 0.169 3000 Planarity : 0.005 0.066 3236 Dihedral : 4.504 21.276 2524 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % 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: -1.61 (0.17), residues: 2288 helix: -0.05 (0.14), residues: 1468 sheet: -2.50 (0.58), residues: 64 loop : -2.95 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 380 HIS 0.003 0.001 HIS C 430 PHE 0.016 0.001 PHE A 656 TYR 0.012 0.001 TYR A 575 ARG 0.002 0.000 ARG C 696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6490 (mpp) cc_final: 0.6204 (mpp) REVERT: A 174 LYS cc_start: 0.8937 (tptt) cc_final: 0.8544 (mmmt) REVERT: A 246 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7666 (ttpp) REVERT: A 366 LYS cc_start: 0.8888 (mppt) cc_final: 0.8361 (mmmt) REVERT: A 431 MET cc_start: 0.8622 (ttm) cc_final: 0.8202 (ttm) REVERT: A 555 MET cc_start: 0.8104 (tpp) cc_final: 0.7723 (tpp) REVERT: A 592 PHE cc_start: 0.8728 (t80) cc_final: 0.8502 (t80) REVERT: A 595 ILE cc_start: 0.9333 (mm) cc_final: 0.9079 (tp) REVERT: A 740 THR cc_start: 0.7460 (m) cc_final: 0.7248 (p) REVERT: B 174 LYS cc_start: 0.8948 (tptt) cc_final: 0.8539 (tptt) REVERT: B 246 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7592 (ttpp) REVERT: B 366 LYS cc_start: 0.8875 (mppt) cc_final: 0.8374 (mmmt) REVERT: B 431 MET cc_start: 0.8649 (ttm) cc_final: 0.8244 (ttm) REVERT: B 527 PHE cc_start: 0.8184 (t80) cc_final: 0.7835 (t80) REVERT: B 595 ILE cc_start: 0.9341 (mm) cc_final: 0.9064 (tp) REVERT: B 740 THR cc_start: 0.7393 (m) cc_final: 0.7131 (t) REVERT: C 159 MET cc_start: 0.6288 (mpp) cc_final: 0.5990 (mpp) REVERT: C 174 LYS cc_start: 0.8955 (tptt) cc_final: 0.8569 (tptt) REVERT: C 205 ASN cc_start: 0.8715 (m-40) cc_final: 0.8316 (p0) REVERT: C 233 LEU cc_start: 0.9213 (pp) cc_final: 0.8794 (tt) REVERT: C 246 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7575 (ttpp) REVERT: C 366 LYS cc_start: 0.8885 (mppt) cc_final: 0.8462 (mmmt) REVERT: C 431 MET cc_start: 0.8681 (ttm) cc_final: 0.8343 (ttm) REVERT: C 592 PHE cc_start: 0.8736 (t80) cc_final: 0.8494 (t80) REVERT: C 595 ILE cc_start: 0.9328 (mm) cc_final: 0.9049 (tp) REVERT: D 174 LYS cc_start: 0.8937 (tptt) cc_final: 0.8524 (tptt) REVERT: D 246 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7590 (ttpp) REVERT: D 366 LYS cc_start: 0.8879 (mppt) cc_final: 0.8410 (mmmt) REVERT: D 431 MET cc_start: 0.8679 (ttm) cc_final: 0.8262 (ttm) REVERT: D 575 TYR cc_start: 0.8156 (t80) cc_final: 0.7916 (t80) REVERT: D 592 PHE cc_start: 0.8720 (t80) cc_final: 0.8468 (t80) REVERT: D 595 ILE cc_start: 0.9330 (mm) cc_final: 0.9061 (tp) REVERT: D 740 THR cc_start: 0.7414 (m) cc_final: 0.7161 (t) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2595 time to fit residues: 186.0919 Evaluate side-chains 362 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 23 optimal weight: 0.0980 chunk 100 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 200 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 671 ASN C 273 ASN C 671 ASN D 273 ASN D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19320 Z= 0.154 Angle : 0.624 9.461 26120 Z= 0.304 Chirality : 0.040 0.179 3000 Planarity : 0.004 0.064 3236 Dihedral : 4.294 20.809 2524 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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: -1.19 (0.18), residues: 2288 helix: 0.27 (0.14), residues: 1476 sheet: -2.38 (0.55), residues: 64 loop : -2.81 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 380 HIS 0.003 0.000 HIS A 426 PHE 0.021 0.001 PHE C 527 TYR 0.012 0.001 TYR C 575 ARG 0.002 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8896 (tptt) cc_final: 0.8500 (mmmt) REVERT: A 233 LEU cc_start: 0.9230 (pp) cc_final: 0.8812 (tt) REVERT: A 246 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7642 (ttpp) REVERT: A 366 LYS cc_start: 0.8861 (mppt) cc_final: 0.8325 (mmmt) REVERT: A 391 ASP cc_start: 0.8178 (t0) cc_final: 0.7978 (t0) REVERT: A 431 MET cc_start: 0.8595 (ttm) cc_final: 0.8338 (ttm) REVERT: A 527 PHE cc_start: 0.8211 (t80) cc_final: 0.7987 (t80) REVERT: A 555 MET cc_start: 0.8094 (tpp) cc_final: 0.7732 (tpp) REVERT: A 595 ILE cc_start: 0.9380 (mm) cc_final: 0.9094 (tp) REVERT: A 689 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 740 THR cc_start: 0.7438 (m) cc_final: 0.7211 (p) REVERT: B 174 LYS cc_start: 0.8932 (tptt) cc_final: 0.8451 (tptt) REVERT: B 178 ASN cc_start: 0.8663 (m110) cc_final: 0.8426 (m110) REVERT: B 188 ARG cc_start: 0.8954 (mmp-170) cc_final: 0.8559 (tpp-160) REVERT: B 246 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7542 (ttpp) REVERT: B 366 LYS cc_start: 0.8873 (mppt) cc_final: 0.8349 (mmmt) REVERT: B 431 MET cc_start: 0.8581 (ttm) cc_final: 0.8336 (ttm) REVERT: B 592 PHE cc_start: 0.8743 (t80) cc_final: 0.8536 (t80) REVERT: B 677 MET cc_start: 0.8338 (tpp) cc_final: 0.8125 (tpt) REVERT: B 740 THR cc_start: 0.7318 (m) cc_final: 0.7029 (t) REVERT: C 174 LYS cc_start: 0.8921 (tptt) cc_final: 0.8513 (tptt) REVERT: C 205 ASN cc_start: 0.8696 (m-40) cc_final: 0.8354 (p0) REVERT: C 233 LEU cc_start: 0.9224 (pp) cc_final: 0.8825 (tt) REVERT: C 246 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7536 (ttpp) REVERT: C 366 LYS cc_start: 0.8895 (mppt) cc_final: 0.8424 (mmmt) REVERT: C 431 MET cc_start: 0.8673 (ttm) cc_final: 0.8461 (ttm) REVERT: C 553 LEU cc_start: 0.9135 (tp) cc_final: 0.8823 (mm) REVERT: C 592 PHE cc_start: 0.8772 (t80) cc_final: 0.8541 (t80) REVERT: C 743 LYS cc_start: 0.7816 (mttt) cc_final: 0.7549 (mmtp) REVERT: D 174 LYS cc_start: 0.8924 (tptt) cc_final: 0.8430 (tptt) REVERT: D 178 ASN cc_start: 0.8654 (m110) cc_final: 0.8437 (m110) REVERT: D 233 LEU cc_start: 0.9207 (pp) cc_final: 0.8810 (tt) REVERT: D 246 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7594 (ttpp) REVERT: D 366 LYS cc_start: 0.8879 (mppt) cc_final: 0.8355 (mmmt) REVERT: D 431 MET cc_start: 0.8598 (ttm) cc_final: 0.8390 (ttm) REVERT: D 592 PHE cc_start: 0.8755 (t80) cc_final: 0.8526 (t80) REVERT: D 740 THR cc_start: 0.7352 (m) cc_final: 0.7040 (t) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.2595 time to fit residues: 190.6747 Evaluate side-chains 361 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 155 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 529 GLN A 561 ASN A 671 ASN B 242 ASN B 297 ASN B 529 GLN B 561 ASN B 671 ASN C 242 ASN C 529 GLN C 561 ASN C 671 ASN D 242 ASN D 529 GLN D 561 ASN D 671 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19320 Z= 0.178 Angle : 0.650 9.545 26120 Z= 0.319 Chirality : 0.040 0.174 3000 Planarity : 0.004 0.062 3236 Dihedral : 4.198 21.412 2524 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.39 % Allowed : 4.82 % Favored : 94.78 % 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: -1.06 (0.18), residues: 2288 helix: 0.34 (0.14), residues: 1496 sheet: -2.20 (0.56), residues: 64 loop : -2.76 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.003 0.001 HIS D 417 PHE 0.020 0.001 PHE C 442 TYR 0.014 0.001 TYR B 575 ARG 0.002 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 450 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8915 (tptt) cc_final: 0.8431 (tptt) REVERT: A 178 ASN cc_start: 0.8767 (m110) cc_final: 0.8554 (m110) REVERT: A 233 LEU cc_start: 0.9236 (pp) cc_final: 0.8837 (tt) REVERT: A 246 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7672 (ttpp) REVERT: A 366 LYS cc_start: 0.8876 (mppt) cc_final: 0.8403 (mmmt) REVERT: A 431 MET cc_start: 0.8651 (ttm) cc_final: 0.8426 (ttm) REVERT: A 501 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8021 (mm-30) REVERT: A 527 PHE cc_start: 0.8293 (t80) cc_final: 0.7991 (t80) REVERT: A 555 MET cc_start: 0.8121 (tpp) cc_final: 0.7791 (tpp) REVERT: A 574 MET cc_start: 0.8842 (mmt) cc_final: 0.8353 (tpp) REVERT: A 575 TYR cc_start: 0.8240 (t80) cc_final: 0.8012 (t80) REVERT: A 595 ILE cc_start: 0.9369 (mm) cc_final: 0.9095 (tp) REVERT: B 159 MET cc_start: 0.6352 (mpp) cc_final: 0.6134 (mpp) REVERT: B 174 LYS cc_start: 0.8944 (tptt) cc_final: 0.8434 (tptt) REVERT: B 178 ASN cc_start: 0.8655 (m110) cc_final: 0.8390 (m110) REVERT: B 246 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7634 (ttpp) REVERT: B 366 LYS cc_start: 0.8853 (mppt) cc_final: 0.8428 (mmmt) REVERT: B 431 MET cc_start: 0.8682 (ttm) cc_final: 0.8451 (ttm) REVERT: B 501 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 574 MET cc_start: 0.8823 (mmt) cc_final: 0.8257 (tpp) REVERT: B 575 TYR cc_start: 0.8294 (t80) cc_final: 0.8081 (t80) REVERT: B 595 ILE cc_start: 0.9342 (mm) cc_final: 0.9051 (tp) REVERT: C 159 MET cc_start: 0.6421 (mpp) cc_final: 0.5897 (mpp) REVERT: C 174 LYS cc_start: 0.8935 (tptt) cc_final: 0.8407 (tptt) REVERT: C 178 ASN cc_start: 0.8703 (m110) cc_final: 0.8488 (m110) REVERT: C 205 ASN cc_start: 0.8655 (m-40) cc_final: 0.8438 (p0) REVERT: C 233 LEU cc_start: 0.9195 (pp) cc_final: 0.8812 (tt) REVERT: C 246 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7583 (ttpp) REVERT: C 366 LYS cc_start: 0.8877 (mppt) cc_final: 0.8371 (mmmt) REVERT: C 431 MET cc_start: 0.8688 (ttm) cc_final: 0.8442 (ttm) REVERT: C 501 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 553 LEU cc_start: 0.9117 (tp) cc_final: 0.8690 (mp) REVERT: C 575 TYR cc_start: 0.8252 (t80) cc_final: 0.8027 (t80) REVERT: C 592 PHE cc_start: 0.8783 (t80) cc_final: 0.8574 (t80) REVERT: C 595 ILE cc_start: 0.9339 (mm) cc_final: 0.9049 (tp) REVERT: C 677 MET cc_start: 0.8677 (ttm) cc_final: 0.7698 (ttm) REVERT: D 159 MET cc_start: 0.6432 (mpp) cc_final: 0.5988 (mpp) REVERT: D 174 LYS cc_start: 0.8919 (tptt) cc_final: 0.8401 (tptt) REVERT: D 178 ASN cc_start: 0.8634 (m110) cc_final: 0.8370 (m110) REVERT: D 233 LEU cc_start: 0.9213 (pp) cc_final: 0.8820 (tt) REVERT: D 246 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7658 (ttpp) REVERT: D 366 LYS cc_start: 0.8860 (mppt) cc_final: 0.8338 (mmmt) REVERT: D 431 MET cc_start: 0.8678 (ttm) cc_final: 0.8433 (ttm) REVERT: D 501 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7954 (tp30) REVERT: D 574 MET cc_start: 0.8845 (mmt) cc_final: 0.8327 (tpp) REVERT: D 592 PHE cc_start: 0.8793 (t80) cc_final: 0.8554 (t80) REVERT: D 595 ILE cc_start: 0.9346 (mm) cc_final: 0.9051 (tp) outliers start: 8 outliers final: 4 residues processed: 458 average time/residue: 0.2786 time to fit residues: 199.1922 Evaluate side-chains 378 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 374 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 117 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19320 Z= 0.156 Angle : 0.645 9.695 26120 Z= 0.313 Chirality : 0.040 0.176 3000 Planarity : 0.004 0.058 3236 Dihedral : 4.174 21.123 2524 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -0.83 (0.18), residues: 2288 helix: 0.56 (0.14), residues: 1488 sheet: -1.96 (0.58), residues: 64 loop : -2.75 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 380 HIS 0.002 0.000 HIS A 150 PHE 0.021 0.001 PHE B 442 TYR 0.011 0.001 TYR B 575 ARG 0.004 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8915 (tptt) cc_final: 0.8360 (tptt) REVERT: A 178 ASN cc_start: 0.8647 (m110) cc_final: 0.8379 (m110) REVERT: A 233 LEU cc_start: 0.9231 (pp) cc_final: 0.8833 (tt) REVERT: A 246 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7661 (ttpp) REVERT: A 366 LYS cc_start: 0.8850 (mppt) cc_final: 0.8373 (mmmt) REVERT: A 431 MET cc_start: 0.8607 (ttm) cc_final: 0.8362 (ttm) REVERT: A 501 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7781 (tm-30) REVERT: A 527 PHE cc_start: 0.8185 (t80) cc_final: 0.7810 (t80) REVERT: A 555 MET cc_start: 0.8118 (tpp) cc_final: 0.7855 (tpp) REVERT: A 677 MET cc_start: 0.8694 (ttt) cc_final: 0.8379 (ttm) REVERT: A 695 GLN cc_start: 0.8480 (mp10) cc_final: 0.8036 (mp10) REVERT: A 740 THR cc_start: 0.7474 (m) cc_final: 0.7205 (t) REVERT: B 159 MET cc_start: 0.6535 (mpp) cc_final: 0.6302 (mpp) REVERT: B 174 LYS cc_start: 0.8903 (tptt) cc_final: 0.8393 (tptt) REVERT: B 178 ASN cc_start: 0.8667 (m110) cc_final: 0.8385 (m110) REVERT: B 233 LEU cc_start: 0.9230 (pp) cc_final: 0.8807 (tt) REVERT: B 246 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7523 (ttpp) REVERT: B 366 LYS cc_start: 0.8866 (mppt) cc_final: 0.8395 (mmmt) REVERT: B 501 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8070 (mm-30) REVERT: B 574 MET cc_start: 0.8669 (mmt) cc_final: 0.8425 (mmt) REVERT: B 740 THR cc_start: 0.7366 (m) cc_final: 0.7089 (t) REVERT: C 159 MET cc_start: 0.6536 (mpp) cc_final: 0.6258 (mpp) REVERT: C 174 LYS cc_start: 0.8910 (tptt) cc_final: 0.8403 (tptt) REVERT: C 178 ASN cc_start: 0.8720 (m110) cc_final: 0.8482 (m110) REVERT: C 205 ASN cc_start: 0.8713 (m-40) cc_final: 0.8487 (p0) REVERT: C 233 LEU cc_start: 0.9208 (pp) cc_final: 0.8825 (tt) REVERT: C 246 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7557 (ttpp) REVERT: C 366 LYS cc_start: 0.8871 (mppt) cc_final: 0.8355 (mmmt) REVERT: C 501 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 553 LEU cc_start: 0.9033 (tp) cc_final: 0.8585 (mt) REVERT: C 743 LYS cc_start: 0.7897 (mttt) cc_final: 0.7658 (mmtp) REVERT: D 159 MET cc_start: 0.6551 (mpp) cc_final: 0.6325 (mpp) REVERT: D 174 LYS cc_start: 0.8887 (tptt) cc_final: 0.8370 (tptt) REVERT: D 178 ASN cc_start: 0.8660 (m110) cc_final: 0.8377 (m110) REVERT: D 233 LEU cc_start: 0.9204 (pp) cc_final: 0.8823 (tt) REVERT: D 366 LYS cc_start: 0.8850 (mppt) cc_final: 0.8435 (mmmt) REVERT: D 501 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8044 (mm-30) REVERT: D 555 MET cc_start: 0.8094 (tpp) cc_final: 0.7840 (tpp) REVERT: D 574 MET cc_start: 0.8716 (mmt) cc_final: 0.8457 (mmt) REVERT: D 677 MET cc_start: 0.8646 (tpp) cc_final: 0.8333 (tpp) REVERT: D 695 GLN cc_start: 0.8464 (mp10) cc_final: 0.8008 (mp10) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2744 time to fit residues: 193.4433 Evaluate side-chains 371 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 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 297 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN C 273 ASN C 297 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 297 ASN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19320 Z= 0.234 Angle : 0.695 9.667 26120 Z= 0.343 Chirality : 0.042 0.176 3000 Planarity : 0.004 0.055 3236 Dihedral : 4.253 21.755 2524 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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: -0.81 (0.18), residues: 2288 helix: 0.53 (0.14), residues: 1496 sheet: -2.07 (0.58), residues: 64 loop : -2.68 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 742 HIS 0.003 0.001 HIS D 417 PHE 0.021 0.002 PHE C 442 TYR 0.010 0.001 TYR A 575 ARG 0.005 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.235 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 174 LYS cc_start: 0.8931 (tptt) cc_final: 0.8403 (tptt) REVERT: A 178 ASN cc_start: 0.8651 (m110) cc_final: 0.8395 (m110) REVERT: A 366 LYS cc_start: 0.8831 (mppt) cc_final: 0.8343 (mmmt) REVERT: A 391 ASP cc_start: 0.8225 (t0) cc_final: 0.8000 (t0) REVERT: A 431 MET cc_start: 0.8857 (ttm) cc_final: 0.8610 (ttm) REVERT: A 527 PHE cc_start: 0.8360 (t80) cc_final: 0.8097 (t80) REVERT: A 555 MET cc_start: 0.8222 (tpp) cc_final: 0.7927 (tpp) REVERT: A 595 ILE cc_start: 0.9379 (mm) cc_final: 0.9088 (tp) REVERT: A 695 GLN cc_start: 0.8660 (mp10) cc_final: 0.8280 (mp10) REVERT: B 159 MET cc_start: 0.6620 (mpp) cc_final: 0.6353 (mpp) REVERT: B 174 LYS cc_start: 0.8949 (tptt) cc_final: 0.8473 (tptt) REVERT: B 178 ASN cc_start: 0.8696 (m110) cc_final: 0.8420 (m-40) REVERT: B 246 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7556 (ttpp) REVERT: B 366 LYS cc_start: 0.8838 (mppt) cc_final: 0.8350 (mmmt) REVERT: B 527 PHE cc_start: 0.8294 (t80) cc_final: 0.8058 (t80) REVERT: B 574 MET cc_start: 0.8780 (mmt) cc_final: 0.8401 (mmt) REVERT: B 592 PHE cc_start: 0.8776 (t80) cc_final: 0.8565 (t80) REVERT: B 595 ILE cc_start: 0.9362 (mm) cc_final: 0.9051 (tp) REVERT: B 716 ARG cc_start: 0.8513 (mmp80) cc_final: 0.8155 (mmp80) REVERT: C 159 MET cc_start: 0.6570 (mpp) cc_final: 0.6212 (mpp) REVERT: C 174 LYS cc_start: 0.8958 (tptt) cc_final: 0.8453 (tptt) REVERT: C 178 ASN cc_start: 0.8703 (m110) cc_final: 0.8462 (m110) REVERT: C 205 ASN cc_start: 0.8821 (m-40) cc_final: 0.8473 (p0) REVERT: C 246 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7436 (ttpt) REVERT: C 366 LYS cc_start: 0.8864 (mppt) cc_final: 0.8441 (mmmt) REVERT: C 595 ILE cc_start: 0.9362 (mm) cc_final: 0.9066 (tp) REVERT: D 159 MET cc_start: 0.6436 (mpp) cc_final: 0.6140 (mpp) REVERT: D 174 LYS cc_start: 0.8930 (tptt) cc_final: 0.8441 (tptt) REVERT: D 178 ASN cc_start: 0.8744 (m110) cc_final: 0.8477 (m-40) REVERT: D 366 LYS cc_start: 0.8822 (mppt) cc_final: 0.8389 (mmmt) REVERT: D 527 PHE cc_start: 0.8279 (t80) cc_final: 0.8078 (t80) REVERT: D 555 MET cc_start: 0.8268 (tpp) cc_final: 0.7983 (tpp) REVERT: D 574 MET cc_start: 0.8802 (mmt) cc_final: 0.8443 (mmt) REVERT: D 595 ILE cc_start: 0.9372 (mm) cc_final: 0.9069 (tp) REVERT: D 695 GLN cc_start: 0.8637 (mp10) cc_final: 0.8265 (mp10) REVERT: D 716 ARG cc_start: 0.8453 (mmp80) cc_final: 0.8124 (mmp80) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.2763 time to fit residues: 188.2291 Evaluate side-chains 345 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 67 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 142 optimal weight: 0.0270 chunk 152 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 297 ASN A 671 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 671 ASN C 297 ASN C 671 ASN D 242 ASN D 273 ASN D 297 ASN D 671 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19320 Z= 0.169 Angle : 0.684 9.872 26120 Z= 0.326 Chirality : 0.040 0.167 3000 Planarity : 0.004 0.053 3236 Dihedral : 4.153 20.733 2524 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2288 helix: 0.74 (0.14), residues: 1472 sheet: -2.02 (0.58), residues: 64 loop : -2.51 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 493 HIS 0.003 0.000 HIS A 426 PHE 0.021 0.001 PHE C 527 TYR 0.011 0.001 TYR A 575 ARG 0.004 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8901 (tptt) cc_final: 0.8331 (tptt) REVERT: A 178 ASN cc_start: 0.8674 (m110) cc_final: 0.8414 (m110) REVERT: A 233 LEU cc_start: 0.9233 (pp) cc_final: 0.8816 (tt) REVERT: A 366 LYS cc_start: 0.8806 (mppt) cc_final: 0.8321 (mmmt) REVERT: A 527 PHE cc_start: 0.8157 (t80) cc_final: 0.7947 (t80) REVERT: A 677 MET cc_start: 0.8888 (ttp) cc_final: 0.8487 (ttm) REVERT: B 159 MET cc_start: 0.6672 (mpp) cc_final: 0.6300 (mpp) REVERT: B 174 LYS cc_start: 0.8936 (tptt) cc_final: 0.8513 (tptt) REVERT: B 178 ASN cc_start: 0.8731 (m110) cc_final: 0.8493 (m-40) REVERT: B 285 GLU cc_start: 0.8324 (pt0) cc_final: 0.7843 (pp20) REVERT: B 366 LYS cc_start: 0.8818 (mppt) cc_final: 0.8333 (mmmt) REVERT: B 527 PHE cc_start: 0.8205 (t80) cc_final: 0.7909 (t80) REVERT: B 574 MET cc_start: 0.8645 (mmt) cc_final: 0.8260 (mmt) REVERT: C 159 MET cc_start: 0.6606 (mpp) cc_final: 0.6283 (mpp) REVERT: C 174 LYS cc_start: 0.8936 (tptt) cc_final: 0.8413 (tptt) REVERT: C 178 ASN cc_start: 0.8711 (m110) cc_final: 0.8478 (m110) REVERT: C 233 LEU cc_start: 0.9233 (pp) cc_final: 0.8853 (tt) REVERT: C 246 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7421 (ttpt) REVERT: C 285 GLU cc_start: 0.8309 (pt0) cc_final: 0.7810 (pp20) REVERT: C 366 LYS cc_start: 0.8871 (mppt) cc_final: 0.8398 (mmmt) REVERT: D 159 MET cc_start: 0.6610 (mpp) cc_final: 0.6308 (mpp) REVERT: D 174 LYS cc_start: 0.8908 (tptt) cc_final: 0.8507 (tptt) REVERT: D 366 LYS cc_start: 0.8851 (mppt) cc_final: 0.8377 (mmmt) REVERT: D 574 MET cc_start: 0.8649 (mmt) cc_final: 0.8297 (mmt) REVERT: D 674 ILE cc_start: 0.9170 (pt) cc_final: 0.8968 (mm) REVERT: D 695 GLN cc_start: 0.8483 (mp10) cc_final: 0.8176 (mp10) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2670 time to fit residues: 184.2932 Evaluate side-chains 356 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 242 ASN B 286 GLN B 671 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19320 Z= 0.170 Angle : 0.672 9.661 26120 Z= 0.326 Chirality : 0.040 0.168 3000 Planarity : 0.004 0.053 3236 Dihedral : 4.090 19.654 2524 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: -0.48 (0.18), residues: 2288 helix: 0.81 (0.14), residues: 1472 sheet: -1.97 (0.57), residues: 64 loop : -2.48 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 742 HIS 0.003 0.000 HIS C 745 PHE 0.022 0.001 PHE D 538 TYR 0.021 0.001 TYR D 451 ARG 0.003 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8891 (tptt) cc_final: 0.8295 (tptt) REVERT: A 178 ASN cc_start: 0.8626 (m110) cc_final: 0.8327 (m110) REVERT: A 366 LYS cc_start: 0.8794 (mppt) cc_final: 0.8297 (mmmt) REVERT: A 391 ASP cc_start: 0.8218 (t0) cc_final: 0.7938 (t0) REVERT: A 527 PHE cc_start: 0.8169 (t80) cc_final: 0.7957 (t80) REVERT: A 555 MET cc_start: 0.7786 (tpp) cc_final: 0.7571 (tpp) REVERT: A 668 LEU cc_start: 0.9332 (tp) cc_final: 0.8794 (tp) REVERT: B 159 MET cc_start: 0.6675 (mpp) cc_final: 0.6354 (mpp) REVERT: B 174 LYS cc_start: 0.8930 (tptt) cc_final: 0.8719 (tptp) REVERT: B 366 LYS cc_start: 0.8803 (mppt) cc_final: 0.8317 (mmmt) REVERT: B 527 PHE cc_start: 0.8189 (t80) cc_final: 0.7832 (t80) REVERT: B 574 MET cc_start: 0.8660 (mmt) cc_final: 0.8323 (mmt) REVERT: B 668 LEU cc_start: 0.9331 (tp) cc_final: 0.8777 (tp) REVERT: B 674 ILE cc_start: 0.9203 (pt) cc_final: 0.8980 (mm) REVERT: C 159 MET cc_start: 0.6606 (mpp) cc_final: 0.6284 (mpp) REVERT: C 174 LYS cc_start: 0.8918 (tptt) cc_final: 0.8398 (tptt) REVERT: C 178 ASN cc_start: 0.8728 (m110) cc_final: 0.8472 (m110) REVERT: C 285 GLU cc_start: 0.8262 (pt0) cc_final: 0.7755 (pp20) REVERT: C 366 LYS cc_start: 0.8860 (mppt) cc_final: 0.8382 (mmmt) REVERT: C 419 MET cc_start: 0.9023 (mmt) cc_final: 0.8439 (mmt) REVERT: D 159 MET cc_start: 0.6608 (mpp) cc_final: 0.6286 (mpp) REVERT: D 174 LYS cc_start: 0.8931 (tptt) cc_final: 0.8491 (tptt) REVERT: D 178 ASN cc_start: 0.8727 (m110) cc_final: 0.8482 (m-40) REVERT: D 366 LYS cc_start: 0.8830 (mppt) cc_final: 0.8349 (mmmt) REVERT: D 574 MET cc_start: 0.8579 (mmt) cc_final: 0.8174 (mmt) REVERT: D 668 LEU cc_start: 0.9362 (tp) cc_final: 0.8822 (tp) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2682 time to fit residues: 182.8231 Evaluate side-chains 349 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 104 optimal weight: 0.1980 chunk 153 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 279 GLN A 286 GLN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 242 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 279 GLN D 671 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19320 Z= 0.171 Angle : 0.671 9.805 26120 Z= 0.322 Chirality : 0.040 0.163 3000 Planarity : 0.004 0.053 3236 Dihedral : 4.060 19.262 2524 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.44 (0.18), residues: 2288 helix: 0.84 (0.14), residues: 1468 sheet: -1.83 (0.58), residues: 64 loop : -2.47 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 742 HIS 0.002 0.000 HIS A 426 PHE 0.021 0.001 PHE B 442 TYR 0.020 0.001 TYR A 451 ARG 0.007 0.000 ARG D 716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8950 (tptt) cc_final: 0.8659 (tptp) REVERT: A 366 LYS cc_start: 0.8773 (mppt) cc_final: 0.8272 (mmmt) REVERT: A 391 ASP cc_start: 0.8216 (t0) cc_final: 0.7959 (t0) REVERT: A 575 TYR cc_start: 0.7990 (t80) cc_final: 0.7717 (t80) REVERT: A 668 LEU cc_start: 0.9385 (tp) cc_final: 0.9012 (tp) REVERT: B 159 MET cc_start: 0.6653 (mpp) cc_final: 0.6304 (mpp) REVERT: B 174 LYS cc_start: 0.8958 (tptt) cc_final: 0.8718 (tptp) REVERT: B 366 LYS cc_start: 0.8792 (mppt) cc_final: 0.8299 (mmmt) REVERT: B 527 PHE cc_start: 0.8210 (t80) cc_final: 0.7849 (t80) REVERT: B 574 MET cc_start: 0.8704 (mmt) cc_final: 0.8300 (mmt) REVERT: B 575 TYR cc_start: 0.7922 (t80) cc_final: 0.7667 (t80) REVERT: B 668 LEU cc_start: 0.9331 (tp) cc_final: 0.8923 (tp) REVERT: C 159 MET cc_start: 0.6637 (mpp) cc_final: 0.6292 (mpp) REVERT: C 174 LYS cc_start: 0.8920 (tptt) cc_final: 0.8414 (tptt) REVERT: C 178 ASN cc_start: 0.8728 (m110) cc_final: 0.8458 (m-40) REVERT: C 366 LYS cc_start: 0.8816 (mppt) cc_final: 0.8353 (mmmt) REVERT: C 527 PHE cc_start: 0.8080 (t80) cc_final: 0.7845 (t80) REVERT: C 575 TYR cc_start: 0.7960 (t80) cc_final: 0.7691 (t80) REVERT: D 159 MET cc_start: 0.6655 (mpp) cc_final: 0.6317 (mpp) REVERT: D 174 LYS cc_start: 0.8937 (tptt) cc_final: 0.8678 (tptp) REVERT: D 366 LYS cc_start: 0.8795 (mppt) cc_final: 0.8316 (mmmt) REVERT: D 574 MET cc_start: 0.8563 (mmt) cc_final: 0.8201 (mmt) REVERT: D 668 LEU cc_start: 0.9347 (tp) cc_final: 0.8940 (tp) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2572 time to fit residues: 177.5070 Evaluate side-chains 347 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 184 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097251 restraints weight = 40196.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099520 restraints weight = 26030.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100980 restraints weight = 18839.890| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19320 Z= 0.179 Angle : 0.673 9.634 26120 Z= 0.325 Chirality : 0.040 0.165 3000 Planarity : 0.004 0.053 3236 Dihedral : 4.038 19.526 2524 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.39 (0.18), residues: 2288 helix: 0.86 (0.14), residues: 1468 sheet: -1.87 (0.58), residues: 64 loop : -2.40 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.002 0.000 HIS A 417 PHE 0.025 0.001 PHE C 442 TYR 0.029 0.001 TYR C 451 ARG 0.006 0.000 ARG D 716 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.73 seconds wall clock time: 73 minutes 34.92 seconds (4414.92 seconds total)