Starting phenix.real_space_refine (version: dev) on Thu Feb 23 17:25:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2023/7s89_24891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2023/7s89_24891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2023/7s89_24891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2023/7s89_24891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2023/7s89_24891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2023/7s89_24891.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Process input model Symmetric amino acids flipped Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20425 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "C" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 339 Unusual residues: {' CA': 1, 'PCW': 1, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 3, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 318 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 318 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 298 Unusual residues: {'PCW': 1, 'POV': 6, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 1, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 12.02, per 1000 atoms: 0.59 Number of scatterers: 20425 At special positions: 0 Unit cell: (125.179, 125.179, 119.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 156 16.00 P 8 15.00 O 3592 8.00 N 3232 7.00 C 13436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.75 Conformation dependent library (CDL) restraints added in 3.0 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 8 sheets defined 65.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.509A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.535A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.556A pdb=" N PHE A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.575A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.063A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.533A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 4.859A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.854A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.618A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.508A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.535A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.556A pdb=" N PHE B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.575A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.062A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.533A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 4.858A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.853A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.618A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.509A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.535A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.556A pdb=" N PHE C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.576A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 308 Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.063A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.533A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.859A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.854A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.619A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.509A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.536A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.555A pdb=" N PHE D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.575A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 308 Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.062A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.532A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.858A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.853A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.619A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.635A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.635A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.634A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.634A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1096 hydrogen bonds defined for protein. 3144 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: 6.32 Time building geometry restraints manager: 9.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3126 1.31 - 1.44: 5344 1.44 - 1.57: 12018 1.57 - 1.69: 16 1.69 - 1.82: 264 Bond restraints: 20768 Sorted by residual: bond pdb=" C29 POV D 710 " pdb="C210 POV D 710 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C29 POV C 708 " pdb="C210 POV C 708 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C29 POV A 807 " pdb="C210 POV A 807 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C29 POV B 708 " pdb="C210 POV B 708 " ideal model delta sigma weight residual 1.333 1.549 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C21 POV D 704 " pdb=" O21 POV D 704 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 20763 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.26: 399 104.26 - 111.74: 9117 111.74 - 119.21: 8000 119.21 - 126.68: 10167 126.68 - 134.15: 317 Bond angle restraints: 28000 Sorted by residual: angle pdb=" C28 POV B 708 " pdb=" C29 POV B 708 " pdb="C210 POV B 708 " ideal model delta sigma weight residual 127.79 110.49 17.30 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C28 POV D 710 " pdb=" C29 POV D 710 " pdb="C210 POV D 710 " ideal model delta sigma weight residual 127.79 110.50 17.29 3.00e+00 1.11e-01 3.32e+01 angle pdb=" C28 POV A 807 " pdb=" C29 POV A 807 " pdb="C210 POV A 807 " ideal model delta sigma weight residual 127.79 110.56 17.23 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C28 POV C 708 " pdb=" C29 POV C 708 " pdb="C210 POV C 708 " ideal model delta sigma weight residual 127.79 110.58 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C12 POV D 708 " pdb=" N POV D 708 " pdb=" C14 POV D 708 " ideal model delta sigma weight residual 107.13 120.91 -13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 27995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.55: 11880 31.55 - 63.09: 512 63.09 - 94.64: 36 94.64 - 126.18: 4 126.18 - 157.73: 16 Dihedral angle restraints: 12448 sinusoidal: 5484 harmonic: 6964 Sorted by residual: dihedral pdb=" C29 POV B 707 " pdb="C210 POV B 707 " pdb="C211 POV B 707 " pdb="C212 POV B 707 " ideal model delta sinusoidal sigma weight residual 112.25 -90.02 -157.73 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C29 POV C 707 " pdb="C210 POV C 707 " pdb="C211 POV C 707 " pdb="C212 POV C 707 " ideal model delta sinusoidal sigma weight residual 112.25 -90.04 -157.71 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C29 POV D 709 " pdb="C210 POV D 709 " pdb="C211 POV D 709 " pdb="C212 POV D 709 " ideal model delta sinusoidal sigma weight residual 112.25 -90.06 -157.69 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2841 0.097 - 0.194: 231 0.194 - 0.291: 28 0.291 - 0.388: 12 0.388 - 0.485: 4 Chirality restraints: 3116 Sorted by residual: chirality pdb=" CG LEU C 458 " pdb=" CB LEU C 458 " pdb=" CD1 LEU C 458 " pdb=" CD2 LEU C 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 3113 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 230 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO D 231 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 231 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 231 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 230 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO B 231 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 230 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO C 231 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 231 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 231 " -0.043 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3422 2.76 - 3.29: 18865 3.29 - 3.83: 34590 3.83 - 4.36: 44769 4.36 - 4.90: 72306 Nonbonded interactions: 173952 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.223 2.440 nonbonded pdb=" OE2 GLU D 535 " pdb=" O HOH D 801 " model vdw 2.293 2.440 ... (remaining 173947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or (resid 810 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'B' and (resid 28 through 637 or (resid 710 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 28 through 637 or (resid 710 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 28 through 637 or (resid 710 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 8 5.49 5 S 156 5.16 5 C 13436 2.51 5 N 3232 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.420 Check model and map are aligned: 0.300 Process input model: 54.090 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.012 0.217 20768 Z= 0.761 Angle : 1.281 17.305 28000 Z= 0.617 Chirality : 0.065 0.485 3116 Planarity : 0.009 0.078 3416 Dihedral : 16.921 157.730 7944 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.18 % 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: -3.47 (0.14), residues: 2360 helix: -2.75 (0.09), residues: 1464 sheet: -1.10 (0.53), residues: 84 loop : -1.06 (0.21), residues: 812 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 522 time to evaluate : 2.626 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 5 residues processed: 550 average time/residue: 1.5222 time to fit residues: 930.7441 Evaluate side-chains 423 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 418 time to evaluate : 2.401 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 3.2168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 37 ASN A 62 ASN A 174 ASN A 217 ASN A 365 ASN A 369 GLN A 374 GLN A 426 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 62 ASN B 174 ASN B 217 ASN B 365 ASN B 369 GLN B 374 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 62 ASN C 174 ASN C 217 ASN C 365 ASN C 369 GLN C 374 GLN C 426 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 174 ASN D 217 ASN D 365 ASN D 369 GLN D 374 GLN ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 20768 Z= 0.207 Angle : 0.656 10.330 28000 Z= 0.327 Chirality : 0.040 0.216 3116 Planarity : 0.006 0.059 3416 Dihedral : 18.512 164.554 3356 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 3.00 % 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: -0.31 (0.17), residues: 2360 helix: -0.06 (0.12), residues: 1460 sheet: -0.76 (0.54), residues: 84 loop : -0.11 (0.24), residues: 816 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 443 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 26 residues processed: 472 average time/residue: 1.4913 time to fit residues: 785.6003 Evaluate side-chains 406 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 380 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 9 average time/residue: 0.4440 time to fit residues: 8.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.0040 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 118 GLN A 208 ASN A 238 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 37 ASN B 118 GLN B 208 ASN B 238 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN C 37 ASN C 118 GLN C 208 ASN C 238 HIS ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN D 118 GLN D 208 ASN D 238 HIS D 374 GLN ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 20768 Z= 0.290 Angle : 0.686 12.750 28000 Z= 0.339 Chirality : 0.043 0.225 3116 Planarity : 0.006 0.065 3416 Dihedral : 17.416 167.946 3356 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 3.39 % 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: 0.52 (0.18), residues: 2360 helix: 0.68 (0.13), residues: 1468 sheet: -0.78 (0.56), residues: 84 loop : 0.09 (0.25), residues: 808 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 398 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 36 residues processed: 441 average time/residue: 1.4765 time to fit residues: 728.9468 Evaluate side-chains 399 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 363 time to evaluate : 2.373 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 19 residues processed: 17 average time/residue: 0.5136 time to fit residues: 14.6246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 0.3980 chunk 228 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20768 Z= 0.169 Angle : 0.584 12.629 28000 Z= 0.287 Chirality : 0.039 0.197 3116 Planarity : 0.005 0.067 3416 Dihedral : 16.491 167.504 3356 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2360 helix: 1.26 (0.14), residues: 1468 sheet: -0.39 (0.57), residues: 84 loop : 0.08 (0.25), residues: 808 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 377 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 16 residues processed: 422 average time/residue: 1.4974 time to fit residues: 706.2949 Evaluate side-chains 378 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 362 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 3.2612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 0.0270 chunk 204 optimal weight: 8.9990 chunk 57 optimal weight: 0.0980 overall best weight: 1.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 374 GLN B 208 ASN B 257 GLN B 374 GLN C 257 GLN C 374 GLN D 208 ASN D 257 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 20768 Z= 0.231 Angle : 0.627 12.244 28000 Z= 0.308 Chirality : 0.041 0.208 3116 Planarity : 0.005 0.070 3416 Dihedral : 16.271 168.218 3356 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 2360 helix: 1.29 (0.13), residues: 1472 sheet: -0.60 (0.55), residues: 88 loop : 0.17 (0.26), residues: 800 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 375 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 29 residues processed: 422 average time/residue: 1.5233 time to fit residues: 715.7111 Evaluate side-chains 393 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 364 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.2188 time to fit residues: 5.4713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN B 257 GLN B 374 GLN C 257 GLN C 374 GLN D 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20768 Z= 0.207 Angle : 0.604 8.171 28000 Z= 0.299 Chirality : 0.040 0.220 3116 Planarity : 0.005 0.067 3416 Dihedral : 15.852 168.523 3356 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2360 helix: 1.44 (0.14), residues: 1468 sheet: -0.49 (0.55), residues: 88 loop : 0.12 (0.26), residues: 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 373 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 33 residues processed: 416 average time/residue: 1.5578 time to fit residues: 723.7209 Evaluate side-chains 386 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 353 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 26 residues processed: 7 average time/residue: 0.6663 time to fit residues: 9.0130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 374 GLN B 257 GLN B 374 GLN C 257 GLN C 374 GLN D 257 GLN D 374 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 20768 Z= 0.283 Angle : 0.662 8.331 28000 Z= 0.327 Chirality : 0.043 0.210 3116 Planarity : 0.005 0.060 3416 Dihedral : 15.832 169.180 3356 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2360 helix: 1.34 (0.13), residues: 1448 sheet: -0.50 (0.56), residues: 88 loop : 0.35 (0.26), residues: 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 377 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 412 average time/residue: 1.5385 time to fit residues: 705.9273 Evaluate side-chains 401 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 370 time to evaluate : 2.351 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 8 average time/residue: 0.2326 time to fit residues: 6.3913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 374 GLN B 257 GLN B 374 GLN C 257 GLN C 374 GLN D 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20768 Z= 0.177 Angle : 0.601 8.764 28000 Z= 0.293 Chirality : 0.039 0.199 3116 Planarity : 0.005 0.060 3416 Dihedral : 15.093 168.479 3356 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2360 helix: 1.66 (0.14), residues: 1448 sheet: -0.30 (0.57), residues: 88 loop : 0.28 (0.26), residues: 824 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 362 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 393 average time/residue: 1.5866 time to fit residues: 693.1915 Evaluate side-chains 380 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 354 time to evaluate : 2.491 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.5414 time to fit residues: 6.5796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.0970 chunk 198 optimal weight: 0.6980 chunk 211 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 0.0270 chunk 166 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 257 GLN A 374 GLN B 206 GLN B 257 GLN B 374 GLN C 206 GLN C 257 GLN C 374 GLN D 62 ASN D 206 GLN D 257 GLN D 374 GLN D 572 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 20768 Z= 0.160 Angle : 0.583 9.063 28000 Z= 0.285 Chirality : 0.038 0.202 3116 Planarity : 0.005 0.061 3416 Dihedral : 14.460 167.513 3356 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.18), residues: 2360 helix: 1.82 (0.14), residues: 1448 sheet: -0.26 (0.57), residues: 88 loop : 0.19 (0.25), residues: 824 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 357 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 25 residues processed: 383 average time/residue: 1.5741 time to fit residues: 674.8496 Evaluate side-chains 367 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 342 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 1.2917 time to fit residues: 10.4822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20768 Z= 0.200 Angle : 0.626 10.717 28000 Z= 0.303 Chirality : 0.040 0.213 3116 Planarity : 0.005 0.062 3416 Dihedral : 14.422 167.793 3356 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.18), residues: 2360 helix: 1.77 (0.14), residues: 1448 sheet: -0.32 (0.56), residues: 88 loop : 0.25 (0.26), residues: 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 352 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 379 average time/residue: 1.5893 time to fit residues: 669.9482 Evaluate side-chains 362 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 340 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 1.1811 time to fit residues: 4.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 257 GLN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132154 restraints weight = 20361.114| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.34 r_work: 0.3068 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20768 Z= 0.187 Angle : 0.625 12.484 28000 Z= 0.300 Chirality : 0.040 0.208 3116 Planarity : 0.005 0.063 3416 Dihedral : 14.241 167.516 3356 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2360 helix: 1.79 (0.14), residues: 1448 sheet: -0.34 (0.56), residues: 88 loop : 0.21 (0.25), residues: 824 =============================================================================== Job complete usr+sys time: 9843.39 seconds wall clock time: 173 minutes 53.78 seconds (10433.78 seconds total)