Starting phenix.real_space_refine on Sun Feb 18 01:53:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2024/7s89_24891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2024/7s89_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_2024/7s89_24891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2024/7s89_24891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2024/7s89_24891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s89_24891/02_2024/7s89_24891.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 215 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: 185 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: 185 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: 155 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: 10.84, per 1000 atoms: 0.53 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: 8.23 Conformation dependent library (CDL) restraints added in 3.5 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: 2.19 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: 7.05 Time building geometry restraints manager: 8.87 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: 12539 31.55 - 63.09: 605 63.09 - 94.64: 36 94.64 - 126.18: 4 126.18 - 157.73: 16 Dihedral angle restraints: 13200 sinusoidal: 6236 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 13197 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 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.820 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 55.910 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.130 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 16.969 157.730 8696 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 % Allowed : 2.86 % Favored : 95.40 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 593 HIS 0.021 0.004 HIS A 238 PHE 0.032 0.005 PHE A 169 TYR 0.019 0.004 TYR C 349 ARG 0.011 0.002 ARG B 470 *********************** 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 : 2.216 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6745 (tm) REVERT: A 98 LEU cc_start: 0.5990 (mt) cc_final: 0.5504 (tt) REVERT: A 233 ASP cc_start: 0.7091 (p0) cc_final: 0.6868 (p0) REVERT: A 260 MET cc_start: 0.7738 (tpt) cc_final: 0.7259 (tpt) REVERT: A 358 ASN cc_start: 0.7182 (m110) cc_final: 0.6928 (m110) REVERT: A 383 ASP cc_start: 0.7557 (m-30) cc_final: 0.7202 (m-30) REVERT: A 458 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 260 MET cc_start: 0.7725 (tpt) cc_final: 0.7213 (tpt) REVERT: B 263 ARG cc_start: 0.7750 (mtt-85) cc_final: 0.7446 (mtp85) REVERT: B 358 ASN cc_start: 0.7133 (m110) cc_final: 0.6857 (m110) REVERT: B 383 ASP cc_start: 0.7533 (m-30) cc_final: 0.7176 (m-30) REVERT: B 434 PHE cc_start: 0.7601 (t80) cc_final: 0.7285 (t80) REVERT: B 458 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8620 (mt) REVERT: C 260 MET cc_start: 0.7719 (tpt) cc_final: 0.7203 (tpt) REVERT: C 358 ASN cc_start: 0.7168 (m110) cc_final: 0.6925 (m110) REVERT: C 383 ASP cc_start: 0.7585 (m-30) cc_final: 0.7245 (m-30) REVERT: C 434 PHE cc_start: 0.7625 (t80) cc_final: 0.7308 (t80) REVERT: C 458 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8640 (mt) REVERT: D 83 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6605 (tm) REVERT: D 85 ILE cc_start: 0.7656 (mm) cc_final: 0.7311 (mp) REVERT: D 93 GLU cc_start: 0.7432 (mp0) cc_final: 0.7217 (mp0) REVERT: D 257 GLN cc_start: 0.7447 (mt0) cc_final: 0.7228 (mt0) REVERT: D 260 MET cc_start: 0.7644 (tpt) cc_final: 0.7109 (tpt) REVERT: D 263 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7419 (mtp85) REVERT: D 358 ASN cc_start: 0.7151 (m110) cc_final: 0.6826 (m110) REVERT: D 383 ASP cc_start: 0.7621 (m-30) cc_final: 0.7156 (m-30) REVERT: D 434 PHE cc_start: 0.7585 (t80) cc_final: 0.7207 (t80) REVERT: D 458 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8568 (mt) outliers start: 36 outliers final: 5 residues processed: 550 average time/residue: 1.5041 time to fit residues: 921.3964 Evaluate side-chains 424 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 413 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 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: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 62 ASN A 174 ASN A 217 ASN A 365 ASN A 369 GLN A 374 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 238 HIS C 365 ASN C 369 GLN C 374 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20768 Z= 0.212 Angle : 0.655 10.191 28000 Z= 0.325 Chirality : 0.040 0.211 3116 Planarity : 0.006 0.058 3416 Dihedral : 17.930 165.194 4125 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.34 % Allowed : 10.80 % Favored : 85.85 % 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: -0.32 (0.17), residues: 2360 helix: -0.08 (0.12), residues: 1468 sheet: -0.74 (0.55), residues: 84 loop : -0.08 (0.25), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 593 HIS 0.004 0.001 HIS D 522 PHE 0.013 0.002 PHE A 456 TYR 0.016 0.002 TYR A 524 ARG 0.007 0.001 ARG C 606 *********************** 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 524 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 455 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASN cc_start: 0.7241 (m110) cc_final: 0.6954 (m110) REVERT: A 381 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7368 (mtpp) REVERT: A 383 ASP cc_start: 0.7453 (m-30) cc_final: 0.7217 (m-30) REVERT: A 458 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 177 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6239 (mm-30) REVERT: B 233 ASP cc_start: 0.6995 (p0) cc_final: 0.6674 (p0) REVERT: B 260 MET cc_start: 0.7667 (tpt) cc_final: 0.7347 (tpt) REVERT: B 358 ASN cc_start: 0.7103 (m110) cc_final: 0.6869 (m110) REVERT: B 381 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7392 (mtpp) REVERT: B 383 ASP cc_start: 0.7424 (m-30) cc_final: 0.7181 (m-30) REVERT: C 177 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6285 (mm-30) REVERT: C 233 ASP cc_start: 0.7034 (p0) cc_final: 0.6692 (p0) REVERT: C 358 ASN cc_start: 0.7148 (m110) cc_final: 0.6898 (m110) REVERT: C 381 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7402 (mtpp) REVERT: C 383 ASP cc_start: 0.7420 (m-30) cc_final: 0.7179 (m-30) REVERT: D 218 LEU cc_start: 0.8011 (tt) cc_final: 0.7787 (tp) REVERT: D 233 ASP cc_start: 0.6774 (p0) cc_final: 0.6242 (p0) REVERT: D 257 GLN cc_start: 0.7265 (mt0) cc_final: 0.7030 (mt0) REVERT: D 260 MET cc_start: 0.7622 (tpt) cc_final: 0.7266 (tpt) REVERT: D 309 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7278 (p0) REVERT: D 358 ASN cc_start: 0.7138 (m110) cc_final: 0.6864 (m110) REVERT: D 381 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7332 (mtpp) REVERT: D 383 ASP cc_start: 0.7457 (m-30) cc_final: 0.7109 (m-30) REVERT: D 458 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8726 (mt) REVERT: D 610 ARG cc_start: 0.6435 (mmp-170) cc_final: 0.6203 (tpt170) outliers start: 69 outliers final: 27 residues processed: 488 average time/residue: 1.4180 time to fit residues: 776.0211 Evaluate side-chains 406 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 376 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 238 HIS ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20768 Z= 0.308 Angle : 0.690 12.304 28000 Z= 0.341 Chirality : 0.044 0.202 3116 Planarity : 0.006 0.057 3416 Dihedral : 17.001 168.370 4119 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.49 % Allowed : 12.35 % Favored : 84.16 % 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: 0.48 (0.18), residues: 2360 helix: 0.61 (0.13), residues: 1468 sheet: -0.77 (0.56), residues: 84 loop : 0.15 (0.26), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 593 HIS 0.005 0.002 HIS A 238 PHE 0.022 0.002 PHE A 537 TYR 0.018 0.003 TYR D 89 ARG 0.005 0.001 ARG A 615 *********************** 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 465 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 393 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6817 (ttmm) REVERT: A 88 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7402 (mt) REVERT: A 358 ASN cc_start: 0.7277 (m110) cc_final: 0.7042 (m110) REVERT: A 383 ASP cc_start: 0.7473 (m-30) cc_final: 0.7262 (m-30) REVERT: A 458 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8750 (mt) REVERT: B 88 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7537 (mt) REVERT: B 358 ASN cc_start: 0.7175 (m110) cc_final: 0.6906 (m110) REVERT: B 383 ASP cc_start: 0.7493 (m-30) cc_final: 0.7288 (m-30) REVERT: C 88 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7383 (mt) REVERT: C 358 ASN cc_start: 0.7222 (m110) cc_final: 0.6951 (m110) REVERT: C 383 ASP cc_start: 0.7494 (m-30) cc_final: 0.7282 (m-30) REVERT: C 610 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5620 (tpt170) REVERT: D 42 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6814 (ttmm) REVERT: D 88 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6758 (mt) REVERT: D 328 TYR cc_start: 0.7891 (m-10) cc_final: 0.7623 (m-80) REVERT: D 358 ASN cc_start: 0.7184 (m110) cc_final: 0.6918 (m110) REVERT: D 383 ASP cc_start: 0.7534 (m-30) cc_final: 0.7245 (m-30) REVERT: D 458 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8700 (mt) outliers start: 72 outliers final: 35 residues processed: 438 average time/residue: 1.4339 time to fit residues: 703.2287 Evaluate side-chains 395 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 351 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 610 ARG Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 631 LEU 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: 0.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 144 optimal weight: 0.0060 chunk 215 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN B 257 GLN B 374 GLN C 257 GLN C 464 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20768 Z= 0.161 Angle : 0.579 11.952 28000 Z= 0.283 Chirality : 0.039 0.196 3116 Planarity : 0.005 0.055 3416 Dihedral : 16.055 167.807 4119 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.15 % Allowed : 14.24 % Favored : 82.61 % 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: 1.10 (0.18), residues: 2360 helix: 1.23 (0.14), residues: 1468 sheet: -0.41 (0.57), residues: 84 loop : 0.09 (0.25), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 593 HIS 0.003 0.001 HIS B 258 PHE 0.013 0.001 PHE A 456 TYR 0.015 0.002 TYR D 115 ARG 0.005 0.000 ARG B 606 *********************** 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 435 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 370 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6750 (ttmm) REVERT: A 358 ASN cc_start: 0.7272 (m110) cc_final: 0.7033 (m110) REVERT: A 381 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7415 (mtpp) REVERT: A 458 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8801 (mt) REVERT: A 588 GLU cc_start: 0.7590 (pt0) cc_final: 0.7352 (pt0) REVERT: A 612 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6879 (mm) REVERT: B 42 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6903 (ttmm) REVERT: B 358 ASN cc_start: 0.7132 (m110) cc_final: 0.6887 (m110) REVERT: B 381 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7627 (mttp) REVERT: B 588 GLU cc_start: 0.7586 (pt0) cc_final: 0.7343 (pt0) REVERT: C 42 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6905 (ttmm) REVERT: C 90 ASP cc_start: 0.6206 (t70) cc_final: 0.5991 (t70) REVERT: C 358 ASN cc_start: 0.7157 (m110) cc_final: 0.6896 (m110) REVERT: C 381 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7604 (mttp) REVERT: C 588 GLU cc_start: 0.7580 (pt0) cc_final: 0.7337 (pt0) REVERT: D 42 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6761 (ttmm) REVERT: D 90 ASP cc_start: 0.6324 (t70) cc_final: 0.5931 (t70) REVERT: D 257 GLN cc_start: 0.7328 (mt0) cc_final: 0.7117 (tt0) REVERT: D 358 ASN cc_start: 0.7143 (m110) cc_final: 0.6869 (m110) REVERT: D 381 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7506 (mttp) REVERT: D 383 ASP cc_start: 0.7574 (m-30) cc_final: 0.7312 (m-30) REVERT: D 458 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8704 (mt) REVERT: D 612 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6848 (mm) outliers start: 65 outliers final: 19 residues processed: 425 average time/residue: 1.4507 time to fit residues: 690.1693 Evaluate side-chains 376 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 349 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 612 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 0.0060 chunk 57 optimal weight: 7.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- 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 ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20768 Z= 0.260 Angle : 0.649 12.189 28000 Z= 0.316 Chirality : 0.043 0.201 3116 Planarity : 0.005 0.056 3416 Dihedral : 15.999 168.202 4119 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.34 % Allowed : 14.68 % Favored : 81.98 % 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: 1.14 (0.18), residues: 2360 helix: 1.24 (0.13), residues: 1472 sheet: -0.67 (0.56), residues: 88 loop : 0.21 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 593 HIS 0.004 0.001 HIS C 201 PHE 0.016 0.002 PHE B 537 TYR 0.016 0.002 TYR A 524 ARG 0.008 0.001 ARG B 606 *********************** 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 438 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 369 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6774 (ttmm) REVERT: A 358 ASN cc_start: 0.7294 (m110) cc_final: 0.7066 (m110) REVERT: A 381 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7690 (mttp) REVERT: A 458 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8749 (mt) REVERT: B 42 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6916 (ttmm) REVERT: B 322 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7988 (mtmt) REVERT: B 358 ASN cc_start: 0.7192 (m110) cc_final: 0.6969 (m110) REVERT: B 381 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7747 (mttp) REVERT: C 42 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6966 (ttmm) REVERT: C 90 ASP cc_start: 0.6289 (t70) cc_final: 0.6059 (t70) REVERT: C 322 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: C 358 ASN cc_start: 0.7199 (m110) cc_final: 0.6969 (m110) REVERT: C 381 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7738 (mttp) REVERT: D 42 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6849 (ttmm) REVERT: D 108 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6257 (mm-30) REVERT: D 257 GLN cc_start: 0.7353 (mt0) cc_final: 0.7113 (tt0) REVERT: D 322 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7980 (mtmt) REVERT: D 358 ASN cc_start: 0.7184 (m110) cc_final: 0.6938 (m110) REVERT: D 381 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7623 (mttp) REVERT: D 383 ASP cc_start: 0.7587 (m-30) cc_final: 0.7310 (m-30) REVERT: D 458 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8716 (mt) REVERT: D 622 GLU cc_start: 0.6601 (pt0) cc_final: 0.6347 (pp20) outliers start: 69 outliers final: 31 residues processed: 424 average time/residue: 1.4577 time to fit residues: 691.4075 Evaluate side-chains 396 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 356 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3131 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= 0.181 Angle : 0.589 8.116 28000 Z= 0.288 Chirality : 0.040 0.191 3116 Planarity : 0.005 0.057 3416 Dihedral : 15.449 168.154 4119 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.44 % Allowed : 14.78 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.18), residues: 2360 helix: 1.47 (0.14), residues: 1472 sheet: -0.46 (0.56), residues: 88 loop : 0.16 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 593 HIS 0.003 0.001 HIS D 258 PHE 0.011 0.001 PHE A 537 TYR 0.015 0.002 TYR B 324 ARG 0.007 0.000 ARG C 606 *********************** 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 428 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 357 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6751 (ttmm) REVERT: A 358 ASN cc_start: 0.7286 (m110) cc_final: 0.7061 (m110) REVERT: A 381 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7686 (mttp) REVERT: A 458 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8781 (mt) REVERT: B 42 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6888 (ttmm) REVERT: B 108 GLU cc_start: 0.6384 (mm-30) cc_final: 0.6148 (mm-30) REVERT: B 358 ASN cc_start: 0.7169 (m110) cc_final: 0.6954 (m110) REVERT: B 381 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7719 (mttp) REVERT: B 612 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6998 (mm) REVERT: C 42 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6918 (ttmm) REVERT: C 78 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6166 (mpp) REVERT: C 358 ASN cc_start: 0.7209 (m110) cc_final: 0.6983 (m110) REVERT: C 381 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7720 (mttp) REVERT: C 606 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.7039 (ttm-80) REVERT: D 42 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6799 (ttmm) REVERT: D 90 ASP cc_start: 0.6226 (t70) cc_final: 0.5829 (t70) REVERT: D 358 ASN cc_start: 0.7186 (m110) cc_final: 0.6936 (m110) REVERT: D 381 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7573 (mttp) REVERT: D 383 ASP cc_start: 0.7562 (m-30) cc_final: 0.7303 (m-30) REVERT: D 458 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8703 (mt) REVERT: D 606 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.7138 (ttm-80) REVERT: D 622 GLU cc_start: 0.6560 (pt0) cc_final: 0.6295 (pp20) outliers start: 71 outliers final: 26 residues processed: 408 average time/residue: 1.4706 time to fit residues: 670.9640 Evaluate side-chains 384 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 350 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 257 GLN D 374 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: 0.8010 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20768 Z= 0.225 Angle : 0.628 8.574 28000 Z= 0.305 Chirality : 0.041 0.194 3116 Planarity : 0.005 0.059 3416 Dihedral : 15.244 168.738 4119 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.81 % Allowed : 15.60 % Favored : 81.59 % 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: 1.33 (0.18), residues: 2360 helix: 1.42 (0.13), residues: 1472 sheet: -0.42 (0.57), residues: 88 loop : 0.18 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 613 HIS 0.003 0.001 HIS A 122 PHE 0.013 0.001 PHE C 537 TYR 0.018 0.002 TYR B 324 ARG 0.009 0.000 ARG B 606 *********************** 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 415 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 357 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6778 (ttmm) REVERT: A 160 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8893 (pp) REVERT: A 381 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7701 (mttp) REVERT: A 458 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8749 (mt) REVERT: B 42 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6929 (ttmm) REVERT: B 108 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6143 (mm-30) REVERT: B 160 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8863 (pp) REVERT: B 358 ASN cc_start: 0.7197 (m110) cc_final: 0.6980 (m110) REVERT: B 381 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7698 (mttp) REVERT: B 606 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.7039 (ttm-80) REVERT: C 42 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6942 (ttmm) REVERT: C 78 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6182 (mpp) REVERT: C 90 ASP cc_start: 0.6357 (t70) cc_final: 0.6113 (t70) REVERT: C 108 GLU cc_start: 0.6378 (mm-30) cc_final: 0.6162 (mm-30) REVERT: C 160 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8874 (pp) REVERT: C 358 ASN cc_start: 0.7211 (m110) cc_final: 0.6978 (m110) REVERT: C 381 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7689 (mttp) REVERT: D 42 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6841 (ttmm) REVERT: D 99 MET cc_start: 0.5173 (mmm) cc_final: 0.4674 (mmp) REVERT: D 108 GLU cc_start: 0.6519 (mm-30) cc_final: 0.6201 (mm-30) REVERT: D 160 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8778 (pp) REVERT: D 357 ASN cc_start: 0.7605 (p0) cc_final: 0.7392 (p0) REVERT: D 358 ASN cc_start: 0.7187 (m110) cc_final: 0.6895 (m110) REVERT: D 381 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7580 (mttp) REVERT: D 383 ASP cc_start: 0.7562 (m-30) cc_final: 0.7286 (m-30) REVERT: D 458 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8688 (mt) REVERT: D 622 GLU cc_start: 0.6512 (pt0) cc_final: 0.6276 (pp20) outliers start: 58 outliers final: 31 residues processed: 401 average time/residue: 1.4500 time to fit residues: 650.1993 Evaluate side-chains 391 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 349 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 206 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 62 ASN C 257 GLN C 374 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 374 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: 0.7988 moved from start: 0.3237 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= 0.190 Angle : 0.606 8.714 28000 Z= 0.293 Chirality : 0.040 0.196 3116 Planarity : 0.005 0.060 3416 Dihedral : 14.826 168.507 4119 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.42 % Allowed : 15.89 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2360 helix: 1.56 (0.14), residues: 1472 sheet: -0.26 (0.60), residues: 88 loop : 0.14 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 613 HIS 0.002 0.001 HIS A 122 PHE 0.011 0.001 PHE A 537 TYR 0.019 0.002 TYR D 324 ARG 0.008 0.000 ARG B 606 *********************** 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 403 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 353 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6731 (ttmm) REVERT: A 381 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7679 (mttp) REVERT: A 458 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8773 (mt) REVERT: B 42 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6907 (ttmm) REVERT: B 108 GLU cc_start: 0.6302 (mm-30) cc_final: 0.6091 (mm-30) REVERT: B 358 ASN cc_start: 0.7177 (m110) cc_final: 0.6959 (m110) REVERT: B 381 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7698 (mttp) REVERT: B 606 ARG cc_start: 0.7216 (ttm-80) cc_final: 0.6978 (ttm-80) REVERT: C 42 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6917 (ttmm) REVERT: C 108 GLU cc_start: 0.6366 (mm-30) cc_final: 0.6151 (mm-30) REVERT: C 358 ASN cc_start: 0.7194 (m110) cc_final: 0.6970 (m110) REVERT: C 381 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7698 (mttp) REVERT: D 42 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6841 (ttmm) REVERT: D 108 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6168 (mm-30) REVERT: D 358 ASN cc_start: 0.7166 (m110) cc_final: 0.6910 (m110) REVERT: D 381 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7574 (mttp) REVERT: D 383 ASP cc_start: 0.7551 (m-30) cc_final: 0.7297 (m-30) REVERT: D 458 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8697 (mt) outliers start: 50 outliers final: 28 residues processed: 393 average time/residue: 1.4754 time to fit residues: 648.5929 Evaluate side-chains 376 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 342 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 224 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7978 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20768 Z= 0.182 Angle : 0.605 8.756 28000 Z= 0.293 Chirality : 0.040 0.207 3116 Planarity : 0.005 0.061 3416 Dihedral : 14.503 168.145 4119 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.13 % Allowed : 16.57 % Favored : 81.30 % 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: 1.52 (0.18), residues: 2360 helix: 1.64 (0.14), residues: 1472 sheet: -0.32 (0.58), residues: 88 loop : 0.11 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 583 HIS 0.003 0.001 HIS A 122 PHE 0.011 0.001 PHE D 537 TYR 0.019 0.002 TYR D 324 ARG 0.010 0.000 ARG C 606 *********************** 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 394 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 350 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6739 (ttmm) REVERT: A 322 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (mtmt) REVERT: A 381 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7682 (mttp) REVERT: A 458 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8774 (mt) REVERT: B 42 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6900 (ttmm) REVERT: B 108 GLU cc_start: 0.6312 (mm-30) cc_final: 0.6098 (mm-30) REVERT: B 260 MET cc_start: 0.7681 (tpt) cc_final: 0.7425 (tpt) REVERT: B 358 ASN cc_start: 0.7169 (m110) cc_final: 0.6953 (m110) REVERT: B 381 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7702 (mttp) REVERT: B 606 ARG cc_start: 0.7243 (ttm-80) cc_final: 0.6996 (ttm-80) REVERT: C 42 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6910 (ttmm) REVERT: C 358 ASN cc_start: 0.7185 (m110) cc_final: 0.6965 (m110) REVERT: C 381 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7697 (mttp) REVERT: D 42 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6814 (ttmm) REVERT: D 108 GLU cc_start: 0.6440 (mm-30) cc_final: 0.6111 (mm-30) REVERT: D 358 ASN cc_start: 0.7157 (m110) cc_final: 0.6879 (m110) REVERT: D 381 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7571 (mttp) REVERT: D 383 ASP cc_start: 0.7543 (m-30) cc_final: 0.7287 (m-30) REVERT: D 458 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8708 (mt) REVERT: D 606 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.7162 (ttm-80) outliers start: 44 outliers final: 28 residues processed: 381 average time/residue: 1.5020 time to fit residues: 639.0941 Evaluate side-chains 377 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 342 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 chunk 155 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 187 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 206 GLN A 257 GLN A 374 GLN B 257 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20768 Z= 0.167 Angle : 0.604 10.676 28000 Z= 0.289 Chirality : 0.039 0.202 3116 Planarity : 0.005 0.061 3416 Dihedral : 14.072 167.390 4117 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.89 % Allowed : 16.91 % Favored : 81.20 % 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: 1.58 (0.18), residues: 2360 helix: 1.71 (0.14), residues: 1472 sheet: -0.36 (0.57), residues: 88 loop : 0.07 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 583 HIS 0.002 0.001 HIS A 258 PHE 0.010 0.001 PHE B 537 TYR 0.018 0.002 TYR A 324 ARG 0.007 0.000 ARG B 606 ********************** 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 387 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 348 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6715 (ttmm) REVERT: A 90 ASP cc_start: 0.6079 (t70) cc_final: 0.5875 (t70) REVERT: A 177 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6875 (mm-30) REVERT: A 322 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7986 (mtmt) REVERT: A 381 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7681 (mttp) REVERT: A 458 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8778 (mt) REVERT: B 42 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6868 (ttmm) REVERT: B 108 GLU cc_start: 0.6291 (mm-30) cc_final: 0.6076 (mm-30) REVERT: B 381 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7703 (mttp) REVERT: B 606 ARG cc_start: 0.7243 (ttm-80) cc_final: 0.7006 (ttm-80) REVERT: C 42 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6872 (ttmm) REVERT: C 108 GLU cc_start: 0.6317 (mm-30) cc_final: 0.6096 (mm-30) REVERT: C 358 ASN cc_start: 0.7200 (m110) cc_final: 0.6961 (m110) REVERT: C 381 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7693 (mttp) REVERT: D 42 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6760 (ttmm) REVERT: D 108 GLU cc_start: 0.6483 (mm-30) cc_final: 0.6102 (mm-30) REVERT: D 358 ASN cc_start: 0.7082 (m110) cc_final: 0.6820 (m110) REVERT: D 381 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7584 (mttp) REVERT: D 383 ASP cc_start: 0.7546 (m-30) cc_final: 0.7290 (m-30) REVERT: D 458 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8705 (mt) REVERT: D 606 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.7125 (ttm-80) outliers start: 39 outliers final: 23 residues processed: 377 average time/residue: 1.4560 time to fit residues: 613.1513 Evaluate side-chains 371 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 341 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** ** C 546 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.167741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120860 restraints weight = 20441.706| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.55 r_work: 0.3101 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3355 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= 0.208 Angle : 0.643 12.578 28000 Z= 0.307 Chirality : 0.041 0.210 3116 Planarity : 0.005 0.061 3416 Dihedral : 14.056 167.688 4117 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.65 % Allowed : 17.49 % Favored : 80.86 % 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: 1.53 (0.18), residues: 2360 helix: 1.66 (0.14), residues: 1472 sheet: -0.45 (0.57), residues: 88 loop : 0.10 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 583 HIS 0.003 0.001 HIS D 201 PHE 0.012 0.001 PHE D 537 TYR 0.019 0.002 TYR D 324 ARG 0.007 0.000 ARG A 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10050.11 seconds wall clock time: 178 minutes 6.14 seconds (10686.14 seconds total)