Starting phenix.real_space_refine on Sun Dec 10 20:37:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg9_27419/12_2023/8dg9_27419.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg9_27419/12_2023/8dg9_27419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg9_27419/12_2023/8dg9_27419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg9_27419/12_2023/8dg9_27419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg9_27419/12_2023/8dg9_27419.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg9_27419/12_2023/8dg9_27419.pdb" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.368 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9762 2.51 5 N 2568 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ASP 489": "OD1" <-> "OD2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15450 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "B" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "C" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.52, per 1000 atoms: 0.55 Number of scatterers: 15450 At special positions: 0 Unit cell: (146.097, 140.952, 125.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3036 8.00 N 2568 7.00 C 9762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.04 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.04 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.07 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A5001 " - " ASN A 500 " " NAG A5002 " - " ASN A 27 " " NAG B 601 " - " ASN B 500 " " NAG B 602 " - " ASN B 27 " " NAG C 601 " - " ASN C 500 " " NAG C 602 " - " ASN C 27 " Time building additional restraints: 5.97 Conformation dependent library (CDL) restraints added in 3.2 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3714 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 36 sheets defined 24.9% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.503A pdb=" N HIS A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 217 through 239 removed outlier: 4.439A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.932A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.530A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 513 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.601A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 97 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 217 through 239 removed outlier: 4.325A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.974A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.553A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'C' and resid 74 through 97 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 217 through 239 removed outlier: 4.464A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.945A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.613A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 513 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 361 removed outlier: 8.316A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361 removed outlier: 8.316A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 10.733A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.445A pdb=" N ILE A 395 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A 489 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.268A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.903A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.416A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.528A pdb=" N GLY L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 358 through 361 removed outlier: 8.323A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 361 removed outlier: 8.323A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 176 through 180 removed outlier: 10.802A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.181A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.956A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.468A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AC6, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'C' and resid 358 through 361 removed outlier: 8.263A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 361 removed outlier: 8.263A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 176 through 180 removed outlier: 10.767A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AD2, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AD3, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.719A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.901A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AD7, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.625A pdb=" N VAL E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.625A pdb=" N VAL E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 19 through 24 768 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2571 1.30 - 1.43: 3856 1.43 - 1.56: 9169 1.56 - 1.69: 1 1.69 - 1.82: 111 Bond restraints: 15708 Sorted by residual: bond pdb=" C VAL C 349 " pdb=" O VAL C 349 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.04e-02 9.25e+03 4.38e+01 bond pdb=" C PRO E 7 " pdb=" O PRO E 7 " ideal model delta sigma weight residual 1.240 1.175 0.065 1.12e-02 7.97e+03 3.37e+01 bond pdb=" C GLY C 347 " pdb=" O GLY C 347 " ideal model delta sigma weight residual 1.237 1.188 0.048 9.40e-03 1.13e+04 2.66e+01 bond pdb=" C PRO E 8 " pdb=" O PRO E 8 " ideal model delta sigma weight residual 1.238 1.178 0.060 1.24e-02 6.50e+03 2.31e+01 bond pdb=" C ALA C 346 " pdb=" N GLY C 347 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.24e-02 6.50e+03 1.07e+01 ... (remaining 15703 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.05: 353 107.05 - 113.81: 8986 113.81 - 120.57: 5785 120.57 - 127.32: 6043 127.32 - 134.08: 115 Bond angle restraints: 21282 Sorted by residual: angle pdb=" C ASP C 344 " pdb=" CA ASP C 344 " pdb=" CB ASP C 344 " ideal model delta sigma weight residual 109.72 118.77 -9.05 1.66e+00 3.63e-01 2.97e+01 angle pdb=" C ALA C 346 " pdb=" N GLY C 347 " pdb=" CA GLY C 347 " ideal model delta sigma weight residual 122.83 114.60 8.23 1.80e+00 3.09e-01 2.09e+01 angle pdb=" C ASP E 50 " pdb=" N ASN E 51 " pdb=" CA ASN E 51 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N ILE C 432 " pdb=" CA ILE C 432 " pdb=" C ILE C 432 " ideal model delta sigma weight residual 112.96 109.26 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" N VAL E 11 " pdb=" CA VAL E 11 " pdb=" C VAL E 11 " ideal model delta sigma weight residual 108.45 103.04 5.41 1.48e+00 4.57e-01 1.33e+01 ... (remaining 21277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 8578 21.44 - 42.88: 824 42.88 - 64.32: 151 64.32 - 85.75: 34 85.75 - 107.19: 10 Dihedral angle restraints: 9597 sinusoidal: 3813 harmonic: 5784 Sorted by residual: dihedral pdb=" CB CYS B 37 " pdb=" SG CYS B 37 " pdb=" SG CYS B 439 " pdb=" CB CYS B 439 " ideal model delta sinusoidal sigma weight residual 93.00 145.99 -52.99 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CA ASN A 27 " pdb=" C ASN A 27 " pdb=" N ILE A 28 " pdb=" CA ILE A 28 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ARG D 98 " pdb=" C ARG D 98 " pdb=" N GLU D 99 " pdb=" CA GLU D 99 " ideal model delta harmonic sigma weight residual 180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 9594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2501 0.149 - 0.298: 5 0.298 - 0.447: 1 0.447 - 0.596: 0 0.596 - 0.745: 1 Chirality restraints: 2508 Sorted by residual: chirality pdb=" C1 NAG A5001 " pdb=" ND2 ASN A 500 " pdb=" C2 NAG A5001 " pdb=" O5 NAG A5001 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 500 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 500 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2505 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO L 8 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER E 9 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER E 9 " 0.042 2.00e-02 2.50e+03 pdb=" O SER E 9 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL E 11 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 344 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ASP C 344 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP C 344 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN C 345 " -0.014 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 223 2.67 - 3.23: 13860 3.23 - 3.79: 24569 3.79 - 4.34: 35667 4.34 - 4.90: 56600 Nonbonded interactions: 130919 Sorted by model distance: nonbonded pdb=" N GLN B 26 " pdb=" OD1 ASN B 363 " model vdw 2.116 2.520 nonbonded pdb=" OE2 GLU C 30 " pdb=" OG1 THR C 408 " model vdw 2.211 2.440 nonbonded pdb=" O PRO E 7 " pdb=" OG1 THR E 102 " model vdw 2.253 2.440 nonbonded pdb=" N GLN A 26 " pdb=" O GLY A 43 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG F 66 " pdb=" OD2 ASP F 86 " model vdw 2.266 2.520 ... (remaining 130914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.950 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: 0.000 Extract box with map and model: 14.210 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.610 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:15.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.004 0.093 15708 Z= 0.239 Angle : 0.635 9.050 21282 Z= 0.350 Chirality : 0.048 0.745 2508 Planarity : 0.005 0.104 2685 Dihedral : 17.358 107.193 5811 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.91 % Allowed : 23.76 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 1971 helix: 0.60 (0.25), residues: 432 sheet: 0.27 (0.21), residues: 594 loop : -0.61 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 96 HIS 0.003 0.001 HIS C 317 PHE 0.017 0.002 PHE H 67 TYR 0.019 0.002 TYR A 457 ARG 0.004 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 242 time to evaluate : 1.969 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 253 average time/residue: 1.2929 time to fit residues: 360.9744 Evaluate side-chains 227 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.1346 time to fit residues: 3.7310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 155 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN F 76 ASN F 81 GLN C 81 GLN C 197 ASN C 428 ASN D 76 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15708 Z= 0.198 Angle : 0.594 9.191 21282 Z= 0.313 Chirality : 0.047 0.574 2508 Planarity : 0.004 0.064 2685 Dihedral : 6.059 54.306 2253 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.36 % Allowed : 20.74 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.28 (0.18), residues: 1971 helix: 1.78 (0.25), residues: 420 sheet: 0.21 (0.21), residues: 597 loop : -0.51 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 103 HIS 0.003 0.001 HIS C 317 PHE 0.014 0.002 PHE F 29 TYR 0.019 0.002 TYR B 457 ARG 0.004 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 27 residues processed: 275 average time/residue: 1.1418 time to fit residues: 350.6335 Evaluate side-chains 243 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 16 residues processed: 11 average time/residue: 0.1454 time to fit residues: 5.4965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 39 GLN F 76 ASN F 81 GLN G 38 GLN C 197 ASN D 76 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 15708 Z= 0.333 Angle : 0.698 9.858 21282 Z= 0.370 Chirality : 0.050 0.551 2508 Planarity : 0.005 0.052 2685 Dihedral : 5.645 52.937 2253 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.65 % Allowed : 19.43 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.15 (0.18), residues: 1971 helix: 1.84 (0.24), residues: 414 sheet: 0.21 (0.21), residues: 546 loop : -0.67 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP D 103 HIS 0.006 0.002 HIS C 317 PHE 0.018 0.002 PHE A 387 TYR 0.024 0.003 TYR B 457 ARG 0.006 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 217 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 40 residues processed: 259 average time/residue: 1.2147 time to fit residues: 349.9534 Evaluate side-chains 244 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 24 residues processed: 16 average time/residue: 0.4289 time to fit residues: 11.4495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 0.0270 chunk 85 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 191 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27BASN F 39 GLN F 81 GLN C 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15708 Z= 0.134 Angle : 0.514 8.834 21282 Z= 0.271 Chirality : 0.044 0.523 2508 Planarity : 0.004 0.045 2685 Dihedral : 5.047 54.153 2253 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.13 % Allowed : 20.11 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.47 (0.18), residues: 1971 helix: 2.39 (0.25), residues: 414 sheet: 0.24 (0.21), residues: 567 loop : -0.51 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 103 HIS 0.003 0.001 HIS A 317 PHE 0.013 0.001 PHE B 190 TYR 0.016 0.001 TYR B 457 ARG 0.006 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 36 residues processed: 266 average time/residue: 1.1873 time to fit residues: 352.5691 Evaluate side-chains 246 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 27 residues processed: 10 average time/residue: 0.1564 time to fit residues: 5.1635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 81 GLN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 15708 Z= 0.384 Angle : 0.725 9.503 21282 Z= 0.385 Chirality : 0.052 0.527 2508 Planarity : 0.005 0.042 2685 Dihedral : 5.595 52.025 2253 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.48 % Allowed : 18.92 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.22 (0.18), residues: 1971 helix: 1.94 (0.24), residues: 414 sheet: 0.25 (0.21), residues: 558 loop : -0.66 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP F 47 HIS 0.006 0.003 HIS A 317 PHE 0.016 0.003 PHE F 29 TYR 0.025 0.003 TYR C 457 ARG 0.007 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 216 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 42 residues processed: 257 average time/residue: 1.1646 time to fit residues: 334.4183 Evaluate side-chains 247 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 28 residues processed: 14 average time/residue: 0.2435 time to fit residues: 7.6030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 0.0370 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15708 Z= 0.155 Angle : 0.536 9.030 21282 Z= 0.285 Chirality : 0.045 0.506 2508 Planarity : 0.004 0.044 2685 Dihedral : 5.017 53.792 2253 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.62 % Allowed : 20.17 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 1971 helix: 2.37 (0.25), residues: 414 sheet: 0.30 (0.21), residues: 537 loop : -0.57 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.012 0.001 PHE C 190 TYR 0.017 0.001 TYR B 457 ARG 0.003 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 219 time to evaluate : 1.950 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 38 residues processed: 257 average time/residue: 1.2000 time to fit residues: 342.8543 Evaluate side-chains 245 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 7 average time/residue: 0.1857 time to fit residues: 4.6809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 0.0040 chunk 88 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 216 ASN F 76 ASN F 81 GLN C 197 ASN D 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15708 Z= 0.238 Angle : 0.786 59.199 21282 Z= 0.433 Chirality : 0.047 0.575 2508 Planarity : 0.004 0.043 2685 Dihedral : 5.173 53.540 2253 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.85 % Allowed : 20.11 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.43 (0.18), residues: 1971 helix: 2.34 (0.25), residues: 414 sheet: 0.30 (0.21), residues: 537 loop : -0.57 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 103 HIS 0.005 0.002 HIS A 317 PHE 0.014 0.002 PHE C 190 TYR 0.019 0.002 TYR B 457 ARG 0.006 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 208 time to evaluate : 1.804 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 44 residues processed: 244 average time/residue: 1.1849 time to fit residues: 323.3778 Evaluate side-chains 251 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 32 residues processed: 13 average time/residue: 0.1759 time to fit residues: 6.5297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN F 76 ASN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 15708 Z= 0.343 Angle : 0.830 59.181 21282 Z= 0.458 Chirality : 0.049 0.404 2508 Planarity : 0.004 0.043 2685 Dihedral : 5.302 53.207 2253 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.62 % Allowed : 20.06 % Favored : 77.32 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.35 % 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: 0.41 (0.18), residues: 1971 helix: 2.26 (0.25), residues: 414 sheet: 0.32 (0.21), residues: 537 loop : -0.57 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 52 HIS 0.006 0.002 HIS A 317 PHE 0.018 0.002 PHE C 190 TYR 0.021 0.002 TYR A 457 ARG 0.007 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 1.986 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 39 residues processed: 241 average time/residue: 1.2467 time to fit residues: 334.6661 Evaluate side-chains 241 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 33 residues processed: 6 average time/residue: 0.1713 time to fit residues: 4.9911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 177 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN F 76 ASN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15708 Z= 0.189 Angle : 0.824 59.199 21282 Z= 0.443 Chirality : 0.069 2.578 2508 Planarity : 0.004 0.048 2685 Dihedral : 5.265 52.144 2253 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.22 % Allowed : 20.34 % Favored : 77.44 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.35 % 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: 0.43 (0.18), residues: 1971 helix: 2.34 (0.25), residues: 414 sheet: 0.28 (0.21), residues: 537 loop : -0.57 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 103 HIS 0.005 0.001 HIS A 317 PHE 0.016 0.002 PHE C 190 TYR 0.020 0.002 TYR B 457 ARG 0.003 0.000 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 2.310 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 37 residues processed: 237 average time/residue: 1.2353 time to fit residues: 325.1269 Evaluate side-chains 238 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 5 average time/residue: 0.1891 time to fit residues: 4.3158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN F 76 ASN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15708 Z= 0.189 Angle : 0.824 59.199 21282 Z= 0.443 Chirality : 0.069 2.578 2508 Planarity : 0.004 0.048 2685 Dihedral : 5.265 52.144 2253 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.88 % Allowed : 20.74 % Favored : 77.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.35 % 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: 0.43 (0.18), residues: 1971 helix: 2.34 (0.25), residues: 414 sheet: 0.28 (0.21), residues: 537 loop : -0.57 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 103 HIS 0.005 0.001 HIS A 317 PHE 0.016 0.002 PHE C 190 TYR 0.020 0.002 TYR B 457 ARG 0.003 0.000 ARG F 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 1.804 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 33 residues processed: 233 average time/residue: 1.2944 time to fit residues: 335.3051 Evaluate side-chains 233 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 33 residues processed: 1 average time/residue: 0.3362 time to fit residues: 3.1087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN F 76 ASN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118467 restraints weight = 13671.230| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.21 r_work: 0.3204 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15708 Z= 0.189 Angle : 0.824 59.199 21282 Z= 0.443 Chirality : 0.069 2.578 2508 Planarity : 0.004 0.048 2685 Dihedral : 5.265 52.144 2253 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.88 % Allowed : 20.74 % Favored : 77.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.35 % 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: 0.43 (0.18), residues: 1971 helix: 2.34 (0.25), residues: 414 sheet: 0.28 (0.21), residues: 537 loop : -0.57 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 103 HIS 0.005 0.001 HIS A 317 PHE 0.016 0.002 PHE C 190 TYR 0.020 0.002 TYR B 457 ARG 0.003 0.000 ARG F 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.63 seconds wall clock time: 114 minutes 37.01 seconds (6877.01 seconds total)