Starting phenix.real_space_refine on Thu Aug 8 03:34:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/08_2024/8v6n_42997.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/08_2024/8v6n_42997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/08_2024/8v6n_42997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/08_2024/8v6n_42997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/08_2024/8v6n_42997.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/08_2024/8v6n_42997.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.074 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: 7 Type Number sf(0) Gaussians P 20 5.49 5 S 132 5.16 5 Na 1 4.78 5 B 8 2.79 5 C 14500 2.51 5 N 3460 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 22185 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "B" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "C" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "D" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 369 Unusual residues: {' NA': 1, 'ACD': 1, 'FZ4': 2, 'POV': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 11.85, per 1000 atoms: 0.53 Number of scatterers: 22185 At special positions: 0 Unit cell: (152.8, 152.8, 125.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 132 16.00 P 20 15.00 Na 1 11.00 O 4064 8.00 N 3460 7.00 C 14500 6.00 B 8 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.91 Conformation dependent library (CDL) restraints added in 3.4 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4872 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 7 sheets defined 62.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.802A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.566A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.517A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.726A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.514A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.624A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.503A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 424 through 434 removed outlier: 3.733A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 460 removed outlier: 3.560A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.829A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.593A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.822A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.547A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.801A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.567A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.517A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.726A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.515A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.625A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.503A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 424 through 434 removed outlier: 3.733A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 460 removed outlier: 3.558A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.829A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.594A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.822A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.547A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS B 745 " --> pdb=" O GLU B 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.801A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.567A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.516A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.725A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.514A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.625A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.503A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 424 through 434 removed outlier: 3.733A pdb=" N TRP C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 460 removed outlier: 3.559A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.828A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.594A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.823A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 687 removed outlier: 3.547A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS C 745 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.801A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS D 161 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.567A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 236 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.517A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.726A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.515A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.626A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.504A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 424 through 434 removed outlier: 3.732A pdb=" N TRP D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 460 removed outlier: 3.559A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.828A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.593A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 574 through 586 Processing helix chain 'D' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.822A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 687 removed outlier: 3.546A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing helix chain 'D' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS D 745 " --> pdb=" O GLU D 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 747 " --> pdb=" O LYS D 743 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 4.315A pdb=" N ARG A 73 " --> pdb=" O LYS D 722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.845A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.845A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 721 through 722 removed outlier: 4.286A pdb=" N ARG C 73 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.846A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 721 through 722 removed outlier: 4.333A pdb=" N ARG D 73 " --> pdb=" O LYS C 722 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.845A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 919 hydrogen bonds defined for protein. 2709 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: 5.95 Time building geometry restraints manager: 8.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3392 1.31 - 1.44: 5996 1.44 - 1.56: 12764 1.56 - 1.69: 60 1.69 - 1.81: 216 Bond restraints: 22428 Sorted by residual: bond pdb=" C21 POV A 901 " pdb=" O21 POV A 901 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C21 POV A 908 " pdb=" O21 POV A 908 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C31 POV A 903 " pdb=" O31 POV A 903 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 22423 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.25: 433 106.25 - 113.22: 12130 113.22 - 120.19: 8427 120.19 - 127.16: 8885 127.16 - 134.12: 193 Bond angle restraints: 30068 Sorted by residual: angle pdb=" N LEU A 513 " pdb=" CA LEU A 513 " pdb=" C LEU A 513 " ideal model delta sigma weight residual 114.56 106.69 7.87 1.27e+00 6.20e-01 3.84e+01 angle pdb=" N LEU C 513 " pdb=" CA LEU C 513 " pdb=" C LEU C 513 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" N LEU B 513 " pdb=" CA LEU B 513 " pdb=" C LEU B 513 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" N LEU D 513 " pdb=" CA LEU D 513 " pdb=" C LEU D 513 " ideal model delta sigma weight residual 114.56 106.71 7.85 1.27e+00 6.20e-01 3.82e+01 angle pdb=" N ILE C 644 " pdb=" CA ILE C 644 " pdb=" C ILE C 644 " ideal model delta sigma weight residual 113.10 108.24 4.86 9.70e-01 1.06e+00 2.51e+01 ... (remaining 30063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 13147 35.82 - 71.63: 411 71.63 - 107.45: 66 107.45 - 143.26: 13 143.26 - 179.08: 3 Dihedral angle restraints: 13640 sinusoidal: 6144 harmonic: 7496 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -165.67 79.67 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual -86.00 -165.66 79.66 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -165.63 79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 13637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2714 0.058 - 0.116: 503 0.116 - 0.173: 43 0.173 - 0.231: 0 0.231 - 0.289: 12 Chirality restraints: 3272 Sorted by residual: chirality pdb=" CA GLU A 423 " pdb=" N GLU A 423 " pdb=" C GLU A 423 " pdb=" CB GLU A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLU B 423 " pdb=" N GLU B 423 " pdb=" C GLU B 423 " pdb=" CB GLU B 423 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA GLU D 423 " pdb=" N GLU D 423 " pdb=" C GLU D 423 " pdb=" CB GLU D 423 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3269 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 509 " 0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO D 510 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 510 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 509 " 0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO C 510 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 510 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.034 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5819 2.80 - 3.32: 18051 3.32 - 3.85: 35570 3.85 - 4.37: 43892 4.37 - 4.90: 73625 Nonbonded interactions: 176957 Sorted by model distance: nonbonded pdb=" O GLU C 308 " pdb=" O HOH C1001 " model vdw 2.274 3.040 nonbonded pdb=" O GLU B 308 " pdb=" O HOH B1001 " model vdw 2.274 3.040 nonbonded pdb=" O GLU D 308 " pdb=" O HOH D1001 " model vdw 2.276 3.040 nonbonded pdb=" O GLU A 308 " pdb=" O HOH A1001 " model vdw 2.311 3.040 nonbonded pdb=" O HIS D 417 " pdb=" OG1 THR D 421 " model vdw 2.314 3.040 ... (remaining 176952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'B' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'C' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'D' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.030 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 53.280 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.080 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.008 0.096 22428 Z= 0.484 Angle : 1.216 12.999 30068 Z= 0.593 Chirality : 0.046 0.289 3272 Planarity : 0.005 0.062 3668 Dihedral : 16.896 179.078 8744 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -6.02 (0.11), residues: 2520 helix: -4.67 (0.04), residues: 1544 sheet: -0.30 (0.62), residues: 88 loop : -2.61 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 559 HIS 0.006 0.001 HIS D 160 PHE 0.018 0.002 PHE B 447 TYR 0.010 0.001 TYR C 451 ARG 0.003 0.001 ARG D 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.6801 (tt0) cc_final: 0.6466 (tp30) REVERT: A 332 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 488 MET cc_start: 0.6624 (mtp) cc_final: 0.6061 (mmm) REVERT: A 501 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 207 GLU cc_start: 0.7614 (pt0) cc_final: 0.7373 (pt0) REVERT: B 214 GLU cc_start: 0.6787 (tt0) cc_final: 0.6364 (tp30) REVERT: B 351 MET cc_start: 0.8730 (mtp) cc_final: 0.8510 (mtp) REVERT: B 488 MET cc_start: 0.6618 (mtp) cc_final: 0.5996 (mmm) REVERT: C 129 GLU cc_start: 0.6840 (mp0) cc_final: 0.6595 (mp0) REVERT: C 207 GLU cc_start: 0.7738 (pt0) cc_final: 0.7523 (pt0) REVERT: C 332 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 488 MET cc_start: 0.6628 (mtp) cc_final: 0.5994 (mmm) REVERT: D 129 GLU cc_start: 0.6827 (mp0) cc_final: 0.6605 (mp0) REVERT: D 207 GLU cc_start: 0.7572 (pt0) cc_final: 0.7367 (pt0) REVERT: D 488 MET cc_start: 0.6630 (mtp) cc_final: 0.6107 (mmp) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 1.2373 time to fit residues: 792.7133 Evaluate side-chains 339 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 205 ASN A 242 ASN A 251 ASN A 274 GLN A 410 ASN A 412 ASN A 643 ASN A 646 GLN A 671 ASN B 71 ASN B 182 ASN B 205 ASN B 227 GLN B 242 ASN B 251 ASN B 412 ASN B 643 ASN B 646 GLN B 671 ASN C 71 ASN C 205 ASN C 220 ASN C 242 ASN C 251 ASN C 274 GLN C 412 ASN C 643 ASN C 646 GLN C 671 ASN D 71 ASN D 205 ASN D 242 ASN D 251 ASN D 274 GLN D 412 ASN D 643 ASN D 646 GLN D 671 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22428 Z= 0.354 Angle : 0.733 10.958 30068 Z= 0.361 Chirality : 0.045 0.221 3272 Planarity : 0.006 0.052 3668 Dihedral : 19.174 137.846 3724 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.33 % Allowed : 9.72 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.73 (0.14), residues: 2520 helix: -1.57 (0.11), residues: 1524 sheet: 0.42 (0.64), residues: 84 loop : -2.24 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 559 HIS 0.005 0.002 HIS B 244 PHE 0.028 0.002 PHE B 259 TYR 0.016 0.002 TYR A 451 ARG 0.007 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 362 time to evaluate : 2.237 Fit side-chains REVERT: A 121 LYS cc_start: 0.7707 (mptt) cc_final: 0.7426 (tttm) REVERT: A 289 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7639 (mm) REVERT: A 488 MET cc_start: 0.6634 (mtp) cc_final: 0.5891 (mpm) REVERT: A 574 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6856 (ptm) REVERT: A 717 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7414 (mmm) REVERT: A 719 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: B 145 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6612 (mt) REVERT: B 229 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7177 (p0) REVERT: B 289 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7605 (mm) REVERT: B 320 MET cc_start: 0.8536 (mmt) cc_final: 0.8261 (mmt) REVERT: B 412 ASN cc_start: 0.7749 (m-40) cc_final: 0.7538 (m-40) REVERT: B 488 MET cc_start: 0.6671 (mtp) cc_final: 0.5943 (mpm) REVERT: B 717 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7361 (mmm) REVERT: C 145 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6738 (mt) REVERT: C 229 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7240 (p0) REVERT: C 289 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7626 (mm) REVERT: C 320 MET cc_start: 0.8542 (mmt) cc_final: 0.8278 (mmt) REVERT: C 488 MET cc_start: 0.6593 (mtp) cc_final: 0.5875 (mpm) REVERT: C 641 ASP cc_start: 0.7487 (t0) cc_final: 0.7199 (t70) REVERT: C 717 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7388 (mmm) REVERT: D 145 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6688 (mt) REVERT: D 289 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7626 (mm) REVERT: D 320 MET cc_start: 0.8527 (mmt) cc_final: 0.8234 (mmt) REVERT: D 355 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6724 (pm20) REVERT: D 412 ASN cc_start: 0.7694 (m-40) cc_final: 0.7490 (m-40) REVERT: D 488 MET cc_start: 0.6615 (mtp) cc_final: 0.5862 (mpm) REVERT: D 641 ASP cc_start: 0.7498 (t0) cc_final: 0.7220 (t70) REVERT: D 717 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7380 (mmm) outliers start: 98 outliers final: 27 residues processed: 424 average time/residue: 1.2389 time to fit residues: 601.1757 Evaluate side-chains 354 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 717 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 410 ASN B 160 HIS C 160 HIS D 160 HIS D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22428 Z= 0.179 Angle : 0.530 7.873 30068 Z= 0.268 Chirality : 0.039 0.234 3272 Planarity : 0.004 0.046 3668 Dihedral : 17.459 117.037 3724 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.75 % Allowed : 12.15 % Favored : 84.10 % 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: -0.98 (0.16), residues: 2520 helix: 0.15 (0.13), residues: 1516 sheet: 0.41 (0.62), residues: 88 loop : -2.08 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 559 HIS 0.003 0.001 HIS C 256 PHE 0.013 0.001 PHE B 259 TYR 0.013 0.001 TYR B 451 ARG 0.003 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 339 time to evaluate : 2.297 Fit side-chains REVERT: A 121 LYS cc_start: 0.7601 (mptt) cc_final: 0.7318 (tttm) REVERT: A 412 ASN cc_start: 0.7641 (m-40) cc_final: 0.7438 (m-40) REVERT: A 488 MET cc_start: 0.6669 (mtp) cc_final: 0.5908 (mpm) REVERT: A 655 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 717 MET cc_start: 0.7732 (mpp) cc_final: 0.7403 (mmm) REVERT: A 719 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: B 129 GLU cc_start: 0.6300 (mp0) cc_final: 0.6035 (mp0) REVERT: B 145 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6752 (mt) REVERT: B 289 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7728 (mm) REVERT: B 320 MET cc_start: 0.8554 (mmt) cc_final: 0.8285 (mmt) REVERT: B 327 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7347 (mtp180) REVERT: B 488 MET cc_start: 0.6660 (mtp) cc_final: 0.5902 (mpm) REVERT: B 641 ASP cc_start: 0.7405 (t0) cc_final: 0.7106 (t70) REVERT: B 655 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8065 (tt) REVERT: B 717 MET cc_start: 0.7749 (mpp) cc_final: 0.7386 (mmm) REVERT: C 145 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6744 (mt) REVERT: C 289 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7735 (mm) REVERT: C 320 MET cc_start: 0.8571 (mmt) cc_final: 0.8342 (mmt) REVERT: C 327 ARG cc_start: 0.7523 (mtp180) cc_final: 0.7312 (mtp180) REVERT: C 488 MET cc_start: 0.6655 (mtp) cc_final: 0.5921 (mpm) REVERT: C 641 ASP cc_start: 0.7381 (t0) cc_final: 0.7082 (t70) REVERT: C 717 MET cc_start: 0.7734 (mpp) cc_final: 0.7392 (mmm) REVERT: D 289 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7718 (mm) REVERT: D 320 MET cc_start: 0.8578 (mmt) cc_final: 0.8339 (mmt) REVERT: D 355 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6669 (pm20) REVERT: D 488 MET cc_start: 0.6635 (mtp) cc_final: 0.5899 (mpm) REVERT: D 641 ASP cc_start: 0.7385 (t0) cc_final: 0.7077 (t70) REVERT: D 655 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8057 (tt) REVERT: D 717 MET cc_start: 0.7765 (mpp) cc_final: 0.7390 (mmm) outliers start: 85 outliers final: 36 residues processed: 393 average time/residue: 1.2042 time to fit residues: 543.7760 Evaluate side-chains 354 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 309 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 65 optimal weight: 0.0870 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 HIS A 645 GLN A 750 ASN B 523 HIS B 750 ASN C 284 HIS C 645 GLN C 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22428 Z= 0.140 Angle : 0.503 10.602 30068 Z= 0.250 Chirality : 0.038 0.217 3272 Planarity : 0.003 0.041 3668 Dihedral : 16.268 106.641 3724 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.69 % Allowed : 15.15 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2520 helix: 0.90 (0.13), residues: 1548 sheet: 0.64 (0.62), residues: 88 loop : -2.02 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 559 HIS 0.003 0.001 HIS C 439 PHE 0.012 0.001 PHE D 748 TYR 0.012 0.001 TYR C 451 ARG 0.004 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 323 time to evaluate : 2.528 Fit side-chains REVERT: A 121 LYS cc_start: 0.7610 (mptt) cc_final: 0.7234 (tttm) REVERT: A 129 GLU cc_start: 0.6834 (mp0) cc_final: 0.6482 (pt0) REVERT: A 488 MET cc_start: 0.6638 (mtp) cc_final: 0.5940 (mpm) REVERT: A 717 MET cc_start: 0.7674 (mpp) cc_final: 0.7374 (mmm) REVERT: A 719 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: B 129 GLU cc_start: 0.6293 (mp0) cc_final: 0.6083 (mp0) REVERT: B 320 MET cc_start: 0.8593 (mmt) cc_final: 0.8326 (mmt) REVERT: B 488 MET cc_start: 0.6696 (mtp) cc_final: 0.5998 (mpm) REVERT: B 717 MET cc_start: 0.7683 (mpp) cc_final: 0.7363 (mmm) REVERT: C 289 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7758 (mm) REVERT: C 320 MET cc_start: 0.8621 (mmt) cc_final: 0.8348 (mmt) REVERT: C 488 MET cc_start: 0.6694 (mtp) cc_final: 0.6016 (mpm) REVERT: C 677 MET cc_start: 0.8426 (mtp) cc_final: 0.8196 (mtm) REVERT: C 717 MET cc_start: 0.7693 (mpp) cc_final: 0.7368 (mmm) REVERT: D 320 MET cc_start: 0.8615 (mmt) cc_final: 0.8330 (mmt) REVERT: D 355 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6582 (pm20) REVERT: D 488 MET cc_start: 0.6699 (mtp) cc_final: 0.5988 (mpm) REVERT: D 717 MET cc_start: 0.7672 (mpp) cc_final: 0.7356 (mmm) outliers start: 61 outliers final: 36 residues processed: 358 average time/residue: 1.3051 time to fit residues: 532.4260 Evaluate side-chains 346 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN A 735 ASN B 410 ASN B 735 ASN C 645 GLN C 735 ASN D 735 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 22428 Z= 0.490 Angle : 0.757 9.922 30068 Z= 0.371 Chirality : 0.051 0.260 3272 Planarity : 0.005 0.043 3668 Dihedral : 17.859 119.687 3724 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.64 % Allowed : 13.96 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.47 (0.16), residues: 2520 helix: 0.53 (0.12), residues: 1584 sheet: 0.84 (0.62), residues: 84 loop : -2.02 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 521 HIS 0.008 0.002 HIS B 301 PHE 0.025 0.003 PHE B 259 TYR 0.016 0.003 TYR B 565 ARG 0.009 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 317 time to evaluate : 2.360 Fit side-chains REVERT: A 129 GLU cc_start: 0.6951 (mp0) cc_final: 0.6698 (pt0) REVERT: A 289 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 431 MET cc_start: 0.7225 (mmm) cc_final: 0.6976 (mtp) REVERT: A 488 MET cc_start: 0.6691 (mtp) cc_final: 0.6245 (mmp) REVERT: A 641 ASP cc_start: 0.7435 (t0) cc_final: 0.7203 (t70) REVERT: A 719 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: B 129 GLU cc_start: 0.6464 (mp0) cc_final: 0.6205 (mp0) REVERT: B 289 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7758 (mm) REVERT: B 320 MET cc_start: 0.8597 (mmt) cc_final: 0.8181 (mmt) REVERT: B 431 MET cc_start: 0.7171 (mmm) cc_final: 0.6905 (mtp) REVERT: B 488 MET cc_start: 0.6707 (mtp) cc_final: 0.6270 (mmp) REVERT: B 641 ASP cc_start: 0.7505 (t0) cc_final: 0.7257 (t70) REVERT: B 719 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: C 289 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7776 (mm) REVERT: C 320 MET cc_start: 0.8615 (mmt) cc_final: 0.8208 (mmt) REVERT: C 369 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7089 (tmt170) REVERT: C 431 MET cc_start: 0.7189 (mmm) cc_final: 0.6921 (mtp) REVERT: C 488 MET cc_start: 0.6722 (mtp) cc_final: 0.6277 (mmp) REVERT: C 641 ASP cc_start: 0.7506 (t0) cc_final: 0.7257 (t70) REVERT: C 738 LYS cc_start: 0.8468 (mttt) cc_final: 0.7904 (mtmm) REVERT: D 289 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7744 (mm) REVERT: D 355 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6829 (pm20) REVERT: D 369 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.7072 (tmt170) REVERT: D 431 MET cc_start: 0.7178 (mmm) cc_final: 0.6913 (mtp) REVERT: D 488 MET cc_start: 0.6719 (mtp) cc_final: 0.6263 (mmp) REVERT: D 546 GLU cc_start: 0.7086 (mp0) cc_final: 0.6811 (mp0) REVERT: D 641 ASP cc_start: 0.7500 (t0) cc_final: 0.7256 (t70) outliers start: 105 outliers final: 47 residues processed: 392 average time/residue: 1.2710 time to fit residues: 570.3309 Evaluate side-chains 364 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 309 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN A 750 ASN B 279 GLN B 645 GLN B 750 ASN C 227 GLN C 645 GLN C 750 ASN D 645 GLN D 750 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22428 Z= 0.143 Angle : 0.523 8.776 30068 Z= 0.261 Chirality : 0.038 0.210 3272 Planarity : 0.003 0.041 3668 Dihedral : 16.350 107.042 3724 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.31 % Allowed : 16.08 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2520 helix: 1.18 (0.13), residues: 1580 sheet: 0.96 (0.63), residues: 84 loop : -1.89 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 692 HIS 0.004 0.001 HIS C 439 PHE 0.009 0.001 PHE A 316 TYR 0.013 0.001 TYR A 451 ARG 0.002 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 346 time to evaluate : 2.361 Fit side-chains REVERT: A 121 LYS cc_start: 0.7733 (mptt) cc_final: 0.7170 (tttm) REVERT: A 289 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 431 MET cc_start: 0.7150 (mmm) cc_final: 0.6899 (mtp) REVERT: A 488 MET cc_start: 0.6619 (mtp) cc_final: 0.5948 (mpm) REVERT: A 555 MET cc_start: 0.7829 (tmm) cc_final: 0.7478 (ttm) REVERT: A 641 ASP cc_start: 0.7348 (t0) cc_final: 0.7057 (t70) REVERT: B 129 GLU cc_start: 0.6333 (mp0) cc_final: 0.6008 (mp0) REVERT: B 289 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7766 (mm) REVERT: B 320 MET cc_start: 0.8623 (mmt) cc_final: 0.8275 (mmt) REVERT: B 488 MET cc_start: 0.6613 (mtp) cc_final: 0.5927 (mpm) REVERT: B 555 MET cc_start: 0.7829 (tmm) cc_final: 0.7469 (ttm) REVERT: B 581 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7895 (mttm) REVERT: B 641 ASP cc_start: 0.7395 (t0) cc_final: 0.7103 (t70) REVERT: B 717 MET cc_start: 0.7628 (mpp) cc_final: 0.7334 (mmm) REVERT: C 320 MET cc_start: 0.8628 (mmt) cc_final: 0.8304 (mmt) REVERT: C 488 MET cc_start: 0.6678 (mtp) cc_final: 0.5999 (mpm) REVERT: C 641 ASP cc_start: 0.7380 (t0) cc_final: 0.7084 (t70) REVERT: C 717 MET cc_start: 0.7670 (mpp) cc_final: 0.7386 (mmm) REVERT: C 738 LYS cc_start: 0.8422 (mttt) cc_final: 0.7965 (mtmp) REVERT: D 289 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7770 (mm) REVERT: D 320 MET cc_start: 0.8623 (mmt) cc_final: 0.8295 (mmt) REVERT: D 355 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6579 (pm20) REVERT: D 488 MET cc_start: 0.6665 (mtp) cc_final: 0.5960 (mpm) REVERT: D 555 MET cc_start: 0.7830 (tmm) cc_final: 0.7462 (ttm) REVERT: D 641 ASP cc_start: 0.7350 (t0) cc_final: 0.7054 (t70) REVERT: D 717 MET cc_start: 0.7630 (mpp) cc_final: 0.7354 (mmm) outliers start: 75 outliers final: 39 residues processed: 389 average time/residue: 1.3542 time to fit residues: 598.2083 Evaluate side-chains 362 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 319 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 242 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 279 GLN B 750 ASN C 750 ASN D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22428 Z= 0.149 Angle : 0.511 9.117 30068 Z= 0.255 Chirality : 0.038 0.200 3272 Planarity : 0.003 0.040 3668 Dihedral : 15.542 97.868 3724 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.52 % Allowed : 17.01 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2520 helix: 1.47 (0.13), residues: 1580 sheet: 0.76 (0.64), residues: 88 loop : -1.83 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 692 HIS 0.004 0.001 HIS D 439 PHE 0.009 0.001 PHE D 569 TYR 0.014 0.001 TYR B 451 ARG 0.003 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 333 time to evaluate : 2.327 Fit side-chains REVERT: A 121 LYS cc_start: 0.7728 (mptt) cc_final: 0.7137 (tttm) REVERT: A 431 MET cc_start: 0.7160 (mmm) cc_final: 0.6911 (mtp) REVERT: A 488 MET cc_start: 0.6599 (mtp) cc_final: 0.5951 (mpm) REVERT: A 641 ASP cc_start: 0.7329 (t0) cc_final: 0.7023 (t70) REVERT: B 129 GLU cc_start: 0.6294 (mp0) cc_final: 0.6015 (mp0) REVERT: B 286 GLN cc_start: 0.7777 (mm110) cc_final: 0.7448 (mm110) REVERT: B 289 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7827 (mm) REVERT: B 320 MET cc_start: 0.8652 (mmt) cc_final: 0.8306 (mmt) REVERT: B 431 MET cc_start: 0.7165 (mmm) cc_final: 0.6906 (mtp) REVERT: B 488 MET cc_start: 0.6653 (mtp) cc_final: 0.5952 (mpm) REVERT: B 641 ASP cc_start: 0.7364 (t0) cc_final: 0.7050 (t70) REVERT: C 320 MET cc_start: 0.8636 (mmt) cc_final: 0.8274 (mmt) REVERT: C 431 MET cc_start: 0.7169 (mmm) cc_final: 0.6911 (mtp) REVERT: C 488 MET cc_start: 0.6619 (mtp) cc_final: 0.5926 (mpm) REVERT: C 555 MET cc_start: 0.7711 (tmm) cc_final: 0.7281 (ttm) REVERT: C 738 LYS cc_start: 0.8449 (mttt) cc_final: 0.7991 (mtmp) REVERT: D 286 GLN cc_start: 0.7786 (mm110) cc_final: 0.7454 (mm110) REVERT: D 289 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7794 (mm) REVERT: D 320 MET cc_start: 0.8633 (mmt) cc_final: 0.8262 (mmt) REVERT: D 355 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6586 (pm20) REVERT: D 431 MET cc_start: 0.7156 (mmm) cc_final: 0.6897 (mtp) REVERT: D 488 MET cc_start: 0.6644 (mtp) cc_final: 0.5901 (mpm) REVERT: D 641 ASP cc_start: 0.7348 (t0) cc_final: 0.7032 (t70) outliers start: 57 outliers final: 41 residues processed: 363 average time/residue: 1.3751 time to fit residues: 565.1596 Evaluate side-chains 362 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 319 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 chunk 220 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN D 645 GLN D 750 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22428 Z= 0.287 Angle : 0.613 10.929 30068 Z= 0.304 Chirality : 0.043 0.218 3272 Planarity : 0.004 0.039 3668 Dihedral : 16.154 98.990 3724 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.56 % Allowed : 16.87 % Favored : 80.57 % 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: 0.37 (0.17), residues: 2520 helix: 1.28 (0.13), residues: 1584 sheet: 1.01 (0.63), residues: 84 loop : -1.89 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 521 HIS 0.006 0.001 HIS B 301 PHE 0.016 0.002 PHE C 569 TYR 0.017 0.002 TYR C 451 ARG 0.005 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 319 time to evaluate : 2.517 Fit side-chains REVERT: A 431 MET cc_start: 0.7126 (mmm) cc_final: 0.6887 (mtp) REVERT: A 488 MET cc_start: 0.6668 (mtp) cc_final: 0.5994 (mpm) REVERT: A 641 ASP cc_start: 0.7328 (t0) cc_final: 0.7049 (t70) REVERT: B 129 GLU cc_start: 0.6338 (mp0) cc_final: 0.6015 (mp0) REVERT: B 320 MET cc_start: 0.8607 (mmt) cc_final: 0.8228 (mmt) REVERT: B 431 MET cc_start: 0.7167 (mmm) cc_final: 0.6899 (mtp) REVERT: B 488 MET cc_start: 0.6655 (mtp) cc_final: 0.5930 (mpm) REVERT: B 555 MET cc_start: 0.7829 (tmm) cc_final: 0.7382 (ttm) REVERT: B 641 ASP cc_start: 0.7366 (t0) cc_final: 0.7077 (t70) REVERT: C 129 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6847 (mm-30) REVERT: C 320 MET cc_start: 0.8629 (mmt) cc_final: 0.8227 (mmt) REVERT: C 431 MET cc_start: 0.7149 (mmm) cc_final: 0.6892 (mtp) REVERT: C 488 MET cc_start: 0.6674 (mtp) cc_final: 0.5992 (mpm) REVERT: C 641 ASP cc_start: 0.7408 (t0) cc_final: 0.7128 (t70) REVERT: D 134 GLU cc_start: 0.7030 (mp0) cc_final: 0.6770 (tt0) REVERT: D 289 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7794 (mm) REVERT: D 320 MET cc_start: 0.8623 (mmt) cc_final: 0.8212 (mmt) REVERT: D 355 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6742 (pm20) REVERT: D 488 MET cc_start: 0.6670 (mtp) cc_final: 0.5946 (mpm) REVERT: D 641 ASP cc_start: 0.7330 (t0) cc_final: 0.7042 (t70) REVERT: D 717 MET cc_start: 0.7831 (mpp) cc_final: 0.7416 (mmm) outliers start: 58 outliers final: 44 residues processed: 355 average time/residue: 1.3462 time to fit residues: 542.7139 Evaluate side-chains 354 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 309 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 279 GLN B 750 ASN C 750 ASN D 645 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22428 Z= 0.184 Angle : 0.549 10.297 30068 Z= 0.272 Chirality : 0.040 0.205 3272 Planarity : 0.003 0.040 3668 Dihedral : 15.544 89.897 3724 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.39 % Allowed : 17.23 % Favored : 80.39 % 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: 0.59 (0.17), residues: 2520 helix: 1.47 (0.13), residues: 1580 sheet: 0.74 (0.63), residues: 88 loop : -1.78 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.005 0.001 HIS B 439 PHE 0.011 0.001 PHE C 569 TYR 0.014 0.001 TYR C 451 ARG 0.004 0.000 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 315 time to evaluate : 2.405 Fit side-chains REVERT: A 184 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6819 (tptm) REVERT: A 431 MET cc_start: 0.7130 (mmm) cc_final: 0.6902 (mtp) REVERT: A 488 MET cc_start: 0.6615 (mtp) cc_final: 0.5972 (mpm) REVERT: A 555 MET cc_start: 0.7859 (tmm) cc_final: 0.7339 (ttm) REVERT: A 641 ASP cc_start: 0.7330 (t0) cc_final: 0.7030 (t70) REVERT: B 129 GLU cc_start: 0.6383 (mp0) cc_final: 0.6088 (mp0) REVERT: B 320 MET cc_start: 0.8645 (mmt) cc_final: 0.8268 (mmt) REVERT: B 488 MET cc_start: 0.6616 (mtp) cc_final: 0.5932 (mpm) REVERT: B 555 MET cc_start: 0.7780 (tmm) cc_final: 0.7380 (ttm) REVERT: B 641 ASP cc_start: 0.7385 (t0) cc_final: 0.7075 (t70) REVERT: B 717 MET cc_start: 0.7719 (mpp) cc_final: 0.7344 (mmm) REVERT: C 320 MET cc_start: 0.8651 (mmt) cc_final: 0.8302 (mmt) REVERT: C 488 MET cc_start: 0.6613 (mtp) cc_final: 0.5938 (mpm) REVERT: C 555 MET cc_start: 0.7857 (tmm) cc_final: 0.7346 (ttm) REVERT: C 641 ASP cc_start: 0.7396 (t0) cc_final: 0.7098 (t70) REVERT: C 717 MET cc_start: 0.7714 (mpp) cc_final: 0.7347 (mmm) REVERT: C 738 LYS cc_start: 0.8453 (mttt) cc_final: 0.8003 (mtmp) REVERT: D 134 GLU cc_start: 0.7077 (mp0) cc_final: 0.6838 (tt0) REVERT: D 289 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7828 (mm) REVERT: D 320 MET cc_start: 0.8638 (mmt) cc_final: 0.8235 (mmt) REVERT: D 355 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6636 (pm20) REVERT: D 488 MET cc_start: 0.6651 (mtp) cc_final: 0.5925 (mpm) REVERT: D 555 MET cc_start: 0.7850 (tmm) cc_final: 0.7346 (ttm) REVERT: D 641 ASP cc_start: 0.7342 (t0) cc_final: 0.7031 (t70) REVERT: D 717 MET cc_start: 0.7718 (mpp) cc_final: 0.7343 (mmm) outliers start: 54 outliers final: 41 residues processed: 345 average time/residue: 1.3787 time to fit residues: 538.8843 Evaluate side-chains 350 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 308 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.0270 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 0.0870 chunk 166 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 overall best weight: 3.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22428 Z= 0.277 Angle : 0.619 11.072 30068 Z= 0.306 Chirality : 0.043 0.218 3272 Planarity : 0.004 0.039 3668 Dihedral : 15.886 89.576 3724 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.21 % Allowed : 17.31 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2520 helix: 1.31 (0.13), residues: 1584 sheet: 0.97 (0.63), residues: 84 loop : -1.86 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.006 0.001 HIS D 301 PHE 0.016 0.002 PHE C 569 TYR 0.017 0.002 TYR C 451 ARG 0.005 0.001 ARG B 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 316 time to evaluate : 2.506 Fit side-chains REVERT: A 184 LYS cc_start: 0.7160 (ttpt) cc_final: 0.6842 (tptm) REVERT: A 289 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7866 (mm) REVERT: A 431 MET cc_start: 0.7135 (mmm) cc_final: 0.6901 (mtp) REVERT: A 488 MET cc_start: 0.6633 (mtp) cc_final: 0.5999 (mpm) REVERT: A 555 MET cc_start: 0.7928 (tmm) cc_final: 0.7403 (ttm) REVERT: A 641 ASP cc_start: 0.7322 (t0) cc_final: 0.7034 (t70) REVERT: B 129 GLU cc_start: 0.6419 (mp0) cc_final: 0.6125 (mp0) REVERT: B 320 MET cc_start: 0.8606 (mmt) cc_final: 0.8178 (mmt) REVERT: B 488 MET cc_start: 0.6636 (mtp) cc_final: 0.5929 (mpm) REVERT: B 581 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7979 (mttm) REVERT: B 641 ASP cc_start: 0.7364 (t0) cc_final: 0.7072 (t70) REVERT: B 717 MET cc_start: 0.7716 (mpp) cc_final: 0.7359 (mmm) REVERT: C 320 MET cc_start: 0.8634 (mmt) cc_final: 0.8240 (mmt) REVERT: C 431 MET cc_start: 0.7143 (mmm) cc_final: 0.6886 (mtp) REVERT: C 488 MET cc_start: 0.6658 (mtp) cc_final: 0.5973 (mpm) REVERT: C 555 MET cc_start: 0.7921 (tmm) cc_final: 0.7378 (ttm) REVERT: C 641 ASP cc_start: 0.7372 (t0) cc_final: 0.7086 (t70) REVERT: D 134 GLU cc_start: 0.7028 (mp0) cc_final: 0.6802 (tt0) REVERT: D 289 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (mm) REVERT: D 320 MET cc_start: 0.8623 (mmt) cc_final: 0.8222 (mmt) REVERT: D 355 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6718 (pm20) REVERT: D 488 MET cc_start: 0.6687 (mtp) cc_final: 0.5962 (mpm) REVERT: D 555 MET cc_start: 0.7926 (tmm) cc_final: 0.7391 (ttm) REVERT: D 641 ASP cc_start: 0.7316 (t0) cc_final: 0.7028 (t70) REVERT: D 717 MET cc_start: 0.7791 (mpp) cc_final: 0.7381 (mmm) outliers start: 50 outliers final: 41 residues processed: 344 average time/residue: 1.3122 time to fit residues: 514.4874 Evaluate side-chains 351 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 307 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 279 GLN B 750 ASN C 750 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.182340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131270 restraints weight = 22046.624| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.12 r_work: 0.3237 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22428 Z= 0.172 Angle : 0.549 10.727 30068 Z= 0.271 Chirality : 0.039 0.203 3272 Planarity : 0.003 0.040 3668 Dihedral : 15.333 87.726 3724 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.90 % Allowed : 17.84 % Favored : 80.26 % 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: 0.66 (0.17), residues: 2520 helix: 1.52 (0.13), residues: 1584 sheet: 0.71 (0.63), residues: 88 loop : -1.74 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.005 0.001 HIS C 439 PHE 0.010 0.001 PHE D 569 TYR 0.015 0.001 TYR C 451 ARG 0.004 0.000 ARG C 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9644.12 seconds wall clock time: 168 minutes 45.42 seconds (10125.42 seconds total)