Starting phenix.real_space_refine on Mon Jul 22 21:51:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e84_31010/07_2024/7e84_31010.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e84_31010/07_2024/7e84_31010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e84_31010/07_2024/7e84_31010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e84_31010/07_2024/7e84_31010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e84_31010/07_2024/7e84_31010.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e84_31010/07_2024/7e84_31010.cif" } resolution = 3.1 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= 0.001 sd= 0.008 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 124 5.16 5 C 13228 2.51 5 N 3488 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 323": "OE1" <-> "OE2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H ASP 156": "OD1" <-> "OD2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H ASP 176": "OD1" <-> "OD2" Residue "H PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J ASP 156": "OD1" <-> "OD2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "J ASP 176": "OD1" <-> "OD2" Residue "J ASP 193": "OD1" <-> "OD2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L ASP 156": "OD1" <-> "OD2" Residue "L ASP 176": "OD1" <-> "OD2" Residue "L ASP 193": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20580 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "B" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "D" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "G" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "H" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "J" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "L" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Time building chain proxies: 10.27, per 1000 atoms: 0.50 Number of scatterers: 20580 At special positions: 0 Unit cell: (143.323, 143.323, 126.285, 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 124 16.00 O 3740 8.00 N 3488 7.00 C 13228 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: 8.20 Conformation dependent library (CDL) restraints added in 4.0 seconds 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 69.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 23 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.585A pdb=" N ARG A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.539A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.617A pdb=" N GLU A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 134 through 152 Processing helix chain 'A' and resid 166 through 177 removed outlier: 4.326A pdb=" N ARG A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 207 Processing helix chain 'A' and resid 227 through 249 removed outlier: 3.707A pdb=" N CYS A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix removed outlier: 3.826A pdb=" N ASN A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 4.006A pdb=" N VAL A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.772A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.848A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.227A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.607A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 450 removed outlier: 4.583A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.809A pdb=" N GLN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 23 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.586A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.537A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.623A pdb=" N GLU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 152 Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.371A pdb=" N ARG B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 207 Processing helix chain 'B' and resid 228 through 249 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix removed outlier: 3.803A pdb=" N ASN B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.074A pdb=" N VAL B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.774A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.779A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 346 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.130A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.594A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 450 removed outlier: 4.586A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.809A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 23 Proline residue: D 21 - end of helix Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.583A pdb=" N ARG D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.620A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.620A pdb=" N GLU D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 133 Processing helix chain 'D' and resid 134 through 152 Processing helix chain 'D' and resid 166 through 177 removed outlier: 4.412A pdb=" N ARG D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 207 Processing helix chain 'D' and resid 228 through 249 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix removed outlier: 3.791A pdb=" N ASN D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 4.002A pdb=" N VAL D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.783A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.773A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 346 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.072A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 removed outlier: 3.617A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 450 removed outlier: 4.591A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 421 " --> pdb=" O GLN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 488 removed outlier: 3.808A pdb=" N GLN D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 16 Processing helix chain 'G' and resid 17 through 23 Proline residue: G 21 - end of helix Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.581A pdb=" N ARG G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 91 through 101 removed outlier: 3.625A pdb=" N ILE G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 123 removed outlier: 3.621A pdb=" N GLU G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 133 Processing helix chain 'G' and resid 134 through 152 Processing helix chain 'G' and resid 166 through 177 removed outlier: 4.324A pdb=" N ARG G 170 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 207 Processing helix chain 'G' and resid 226 through 249 removed outlier: 3.702A pdb=" N PHE G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS G 231 " --> pdb=" O VAL G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 260 Processing helix chain 'G' and resid 260 through 282 Proline residue: G 272 - end of helix removed outlier: 3.814A pdb=" N ASN G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 297 through 305 removed outlier: 3.788A pdb=" N ARG G 305 " --> pdb=" O LYS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 320 removed outlier: 3.788A pdb=" N ARG G 311 " --> pdb=" O SER G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 346 Processing helix chain 'G' and resid 356 through 369 removed outlier: 4.050A pdb=" N TRP G 362 " --> pdb=" O PRO G 358 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR G 363 " --> pdb=" O ALA G 359 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 369 " --> pdb=" O ILE G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 399 removed outlier: 3.579A pdb=" N ILE G 385 " --> pdb=" O ILE G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 450 removed outlier: 4.592A pdb=" N VAL G 404 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP G 420 " --> pdb=" O ASN G 416 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS G 421 " --> pdb=" O GLN G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 488 removed outlier: 3.809A pdb=" N GLN G 477 " --> pdb=" O SER G 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.800A pdb=" N GLU E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.698A pdb=" N GLN E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.748A pdb=" N TYR E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.829A pdb=" N THR E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.872A pdb=" N THR E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 169 through 180 Processing helix chain 'E' and resid 192 through 202 removed outlier: 3.507A pdb=" N GLN E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.806A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 64 removed outlier: 3.799A pdb=" N GLU H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.641A pdb=" N GLN H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE H 82 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.728A pdb=" N TYR H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 removed outlier: 3.841A pdb=" N THR H 103 " --> pdb=" O THR H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100 through 103' Processing helix chain 'H' and resid 108 through 121 removed outlier: 3.692A pdb=" N THR H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA H 114 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 169 through 180 Processing helix chain 'H' and resid 192 through 202 Processing helix chain 'H' and resid 202 through 210 removed outlier: 3.776A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN H 210 " --> pdb=" O MET H 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 64 removed outlier: 3.728A pdb=" N GLU J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.698A pdb=" N GLN J 76 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR J 78 " --> pdb=" O PHE J 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN J 80 " --> pdb=" O GLN J 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE J 81 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE J 82 " --> pdb=" O TYR J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 99 removed outlier: 3.722A pdb=" N TYR J 93 " --> pdb=" O THR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 103 removed outlier: 3.827A pdb=" N THR J 103 " --> pdb=" O THR J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 100 through 103' Processing helix chain 'J' and resid 108 through 121 removed outlier: 3.808A pdb=" N THR J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 114 " --> pdb=" O ASP J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'J' and resid 147 through 157 Processing helix chain 'J' and resid 169 through 180 Processing helix chain 'J' and resid 192 through 202 removed outlier: 3.625A pdb=" N ASP J 202 " --> pdb=" O SER J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 210 removed outlier: 3.811A pdb=" N MET J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN J 210 " --> pdb=" O MET J 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 64 removed outlier: 3.732A pdb=" N GLU L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.667A pdb=" N GLN L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR L 78 " --> pdb=" O PHE L 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN L 80 " --> pdb=" O GLN L 76 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE L 81 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE L 82 " --> pdb=" O TYR L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR L 93 " --> pdb=" O THR L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 103 removed outlier: 3.837A pdb=" N THR L 103 " --> pdb=" O THR L 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 103' Processing helix chain 'L' and resid 108 through 121 removed outlier: 3.823A pdb=" N THR L 113 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA L 114 " --> pdb=" O ASP L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 147 through 157 Processing helix chain 'L' and resid 169 through 180 Processing helix chain 'L' and resid 192 through 202 removed outlier: 3.507A pdb=" N GLN L 200 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP L 202 " --> pdb=" O SER L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 210 removed outlier: 3.887A pdb=" N MET L 206 " --> pdb=" O ASP L 202 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN L 210 " --> pdb=" O MET L 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N TYR A 83 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 44 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 85 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 46 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N TYR B 83 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 44 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE B 85 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN B 46 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.813A pdb=" N THR D 50 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N TYR D 83 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 44 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE D 85 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN D 46 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 50 through 55 removed outlier: 3.808A pdb=" N THR G 50 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N TYR G 83 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 44 " --> pdb=" O TYR G 83 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE G 85 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN G 46 " --> pdb=" O PHE G 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA7, first strand: chain 'J' and resid 68 through 70 Processing sheet with id=AA8, first strand: chain 'L' and resid 68 through 70 1176 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6616 1.34 - 1.46: 5127 1.46 - 1.58: 9137 1.58 - 1.70: 0 1.70 - 1.81: 200 Bond restraints: 21080 Sorted by residual: bond pdb=" CB MET A 27 " pdb=" CG MET A 27 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB MET D 27 " pdb=" CG MET D 27 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB GLU G 346 " pdb=" CG GLU G 346 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.99e-01 bond pdb=" CA ASP E 86 " pdb=" CB ASP E 86 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.82e-02 3.02e+03 8.75e-01 bond pdb=" CB GLU B 346 " pdb=" CG GLU B 346 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.75e-01 ... (remaining 21075 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.49: 565 106.49 - 113.37: 11022 113.37 - 120.26: 7862 120.26 - 127.14: 8845 127.14 - 134.02: 218 Bond angle restraints: 28512 Sorted by residual: angle pdb=" N ILE D 91 " pdb=" CA ILE D 91 " pdb=" C ILE D 91 " ideal model delta sigma weight residual 112.96 108.11 4.85 1.00e+00 1.00e+00 2.36e+01 angle pdb=" N ILE B 91 " pdb=" CA ILE B 91 " pdb=" C ILE B 91 " ideal model delta sigma weight residual 113.42 108.04 5.38 1.17e+00 7.31e-01 2.11e+01 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 113.42 108.10 5.32 1.17e+00 7.31e-01 2.07e+01 angle pdb=" CB MET A 27 " pdb=" CG MET A 27 " pdb=" SD MET A 27 " ideal model delta sigma weight residual 112.70 125.46 -12.76 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CB MET D 27 " pdb=" CG MET D 27 " pdb=" SD MET D 27 " ideal model delta sigma weight residual 112.70 125.26 -12.56 3.00e+00 1.11e-01 1.75e+01 ... (remaining 28507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11164 17.84 - 35.68: 1079 35.68 - 53.51: 217 53.51 - 71.35: 34 71.35 - 89.19: 14 Dihedral angle restraints: 12508 sinusoidal: 5020 harmonic: 7488 Sorted by residual: dihedral pdb=" CB GLU G 136 " pdb=" CG GLU G 136 " pdb=" CD GLU G 136 " pdb=" OE1 GLU G 136 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA HIS G 77 " pdb=" C HIS G 77 " pdb=" N PRO G 78 " pdb=" CA PRO G 78 " ideal model delta harmonic sigma weight residual -180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA SER A 69 " pdb=" C SER A 69 " pdb=" N SER A 70 " pdb=" CA SER A 70 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 12505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2005 0.029 - 0.058: 677 0.058 - 0.087: 323 0.087 - 0.115: 102 0.115 - 0.144: 13 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA THR L 170 " pdb=" N THR L 170 " pdb=" C THR L 170 " pdb=" CB THR L 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR J 170 " pdb=" N THR J 170 " pdb=" C THR J 170 " pdb=" CB THR J 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA THR H 170 " pdb=" N THR H 170 " pdb=" C THR H 170 " pdb=" CB THR H 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3117 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 207 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO G 208 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 208 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 208 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 207 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO B 208 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 27 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C MET D 27 " 0.031 2.00e-02 2.50e+03 pdb=" O MET D 27 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO D 28 " -0.011 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5068 2.79 - 3.32: 20373 3.32 - 3.85: 33296 3.85 - 4.37: 39567 4.37 - 4.90: 67330 Nonbonded interactions: 165634 Sorted by model distance: nonbonded pdb=" OG1 THR D 65 " pdb=" OH TYR D 99 " model vdw 2.263 2.440 nonbonded pdb=" OE2 GLU B 71 " pdb=" OH TYR H 57 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR G 65 " pdb=" OH TYR G 99 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR A 65 " pdb=" OH TYR A 99 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" OH TYR B 99 " model vdw 2.266 2.440 ... (remaining 165629 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 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' 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: 2.480 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: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 52.750 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 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 : 0.002 0.031 21080 Z= 0.141 Angle : 0.534 12.756 28512 Z= 0.275 Chirality : 0.038 0.144 3120 Planarity : 0.003 0.053 3644 Dihedral : 14.852 89.189 7660 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.03 (0.17), residues: 2492 helix: 1.07 (0.13), residues: 1612 sheet: -2.41 (0.53), residues: 40 loop : -2.09 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 362 HIS 0.003 0.000 HIS B 94 PHE 0.016 0.001 PHE D 493 TYR 0.009 0.001 TYR G 188 ARG 0.004 0.000 ARG J 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 2.275 Fit side-chains REVERT: A 27 MET cc_start: 0.2190 (tmm) cc_final: 0.1011 (pmm) REVERT: A 46 ASN cc_start: 0.8648 (t0) cc_final: 0.8191 (t0) REVERT: B 27 MET cc_start: 0.1926 (tmm) cc_final: 0.0801 (pmm) REVERT: B 46 ASN cc_start: 0.8659 (t0) cc_final: 0.8212 (t0) REVERT: B 429 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6602 (mmt90) REVERT: D 27 MET cc_start: 0.1941 (tmm) cc_final: 0.0816 (pmm) REVERT: D 46 ASN cc_start: 0.8650 (t0) cc_final: 0.8205 (t0) REVERT: D 429 ARG cc_start: 0.6987 (ttm-80) cc_final: 0.6632 (mmt90) REVERT: G 27 MET cc_start: 0.1967 (tmm) cc_final: 0.0811 (pmm) REVERT: G 46 ASN cc_start: 0.8647 (t0) cc_final: 0.8196 (t0) REVERT: G 429 ARG cc_start: 0.6928 (ttm-80) cc_final: 0.6533 (mmt90) REVERT: E 168 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6572 (tm-30) REVERT: H 148 MET cc_start: 0.5449 (tpp) cc_final: 0.5233 (tpt) REVERT: J 168 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6615 (tm-30) REVERT: L 148 MET cc_start: 0.5826 (tpp) cc_final: 0.5605 (tpt) REVERT: L 168 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6601 (tm-30) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.3765 time to fit residues: 219.0924 Evaluate side-chains 302 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 228 optimal weight: 0.0470 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS A 416 ASN B 414 HIS D 414 HIS D 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21080 Z= 0.268 Angle : 0.574 7.299 28512 Z= 0.303 Chirality : 0.041 0.167 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.078 15.406 2804 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.06 % Favored : 92.78 % Rotamer: Outliers : 0.59 % Allowed : 8.86 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2492 helix: 1.40 (0.13), residues: 1592 sheet: -1.11 (0.76), residues: 40 loop : -1.97 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 362 HIS 0.005 0.001 HIS D 94 PHE 0.017 0.002 PHE G 122 TYR 0.012 0.001 TYR D 188 ARG 0.006 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 291 time to evaluate : 2.077 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: B 429 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6828 (mmt180) REVERT: B 475 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: D 429 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6825 (mmt180) REVERT: D 475 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: G 429 ARG cc_start: 0.7164 (ttm-80) cc_final: 0.6843 (mmt180) REVERT: G 475 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7287 (mt-10) outliers start: 13 outliers final: 7 residues processed: 299 average time/residue: 0.3469 time to fit residues: 153.9291 Evaluate side-chains 285 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21080 Z= 0.253 Angle : 0.548 8.412 28512 Z= 0.290 Chirality : 0.041 0.179 3120 Planarity : 0.004 0.052 3644 Dihedral : 4.132 15.858 2804 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.26 % Favored : 92.58 % Rotamer: Outliers : 1.58 % Allowed : 10.44 % Favored : 87.97 % 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: 0.47 (0.17), residues: 2492 helix: 1.52 (0.13), residues: 1600 sheet: -1.24 (0.66), residues: 40 loop : -2.04 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.003 0.001 HIS G 491 PHE 0.023 0.002 PHE E 131 TYR 0.015 0.001 TYR G 188 ARG 0.007 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 2.291 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: B 429 ARG cc_start: 0.7165 (ttm-80) cc_final: 0.6952 (mmt180) REVERT: B 475 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: D 429 ARG cc_start: 0.7150 (ttm-80) cc_final: 0.6931 (mmt180) REVERT: D 475 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: G 429 ARG cc_start: 0.7183 (ttm-80) cc_final: 0.6960 (mmt180) REVERT: G 475 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: H 106 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8214 (p) REVERT: J 102 GLN cc_start: 0.7522 (mm110) cc_final: 0.7298 (mm110) REVERT: J 106 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8272 (p) REVERT: L 106 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8254 (p) outliers start: 35 outliers final: 16 residues processed: 295 average time/residue: 0.3196 time to fit residues: 144.3805 Evaluate side-chains 280 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 230 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS D 416 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS E 84 HIS H 84 HIS J 84 HIS L 84 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 21080 Z= 0.602 Angle : 0.757 9.393 28512 Z= 0.390 Chirality : 0.049 0.206 3120 Planarity : 0.006 0.051 3644 Dihedral : 4.866 19.023 2804 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.59 % Favored : 91.25 % Rotamer: Outliers : 2.76 % Allowed : 13.43 % Favored : 83.82 % 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: -0.23 (0.16), residues: 2492 helix: 0.88 (0.12), residues: 1640 sheet: None (None), residues: 0 loop : -2.24 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 362 HIS 0.008 0.002 HIS G 491 PHE 0.023 0.003 PHE D 122 TYR 0.019 0.002 TYR B 188 ARG 0.007 0.001 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 287 time to evaluate : 2.225 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: B 90 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: B 429 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6941 (mmt180) REVERT: B 475 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: D 329 PHE cc_start: 0.7586 (t80) cc_final: 0.7385 (t80) REVERT: D 429 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.7013 (mmt180) REVERT: D 475 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: G 429 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.7001 (mmt180) REVERT: G 475 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7462 (mt-10) outliers start: 61 outliers final: 32 residues processed: 335 average time/residue: 0.3193 time to fit residues: 164.9561 Evaluate side-chains 302 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 185 ASN Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 185 ASN Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN H 132 ASN H 213 GLN J 132 ASN L 132 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21080 Z= 0.198 Angle : 0.556 8.648 28512 Z= 0.292 Chirality : 0.040 0.142 3120 Planarity : 0.004 0.054 3644 Dihedral : 4.457 17.893 2804 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 1.54 % Allowed : 14.78 % Favored : 83.68 % 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: 0.29 (0.17), residues: 2492 helix: 1.33 (0.13), residues: 1628 sheet: -0.98 (0.75), residues: 40 loop : -2.15 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 362 HIS 0.005 0.001 HIS D 94 PHE 0.027 0.002 PHE H 131 TYR 0.014 0.001 TYR D 188 ARG 0.003 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 2.349 Fit side-chains REVERT: A 475 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: B 429 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.7004 (mmt180) REVERT: B 475 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: D 429 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.7008 (mmt180) REVERT: D 475 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: G 475 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7340 (mt-10) outliers start: 34 outliers final: 20 residues processed: 302 average time/residue: 0.3282 time to fit residues: 150.8622 Evaluate side-chains 284 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain L residue 149 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 202 optimal weight: 0.3980 chunk 112 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN H 132 ASN J 132 ASN L 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21080 Z= 0.181 Angle : 0.527 9.398 28512 Z= 0.276 Chirality : 0.039 0.139 3120 Planarity : 0.004 0.054 3644 Dihedral : 4.252 16.503 2804 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.94 % Favored : 92.90 % Rotamer: Outliers : 1.72 % Allowed : 15.05 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2492 helix: 1.53 (0.13), residues: 1616 sheet: -0.75 (0.77), residues: 40 loop : -2.24 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.004 0.001 HIS B 94 PHE 0.030 0.002 PHE J 178 TYR 0.013 0.001 TYR G 188 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 275 time to evaluate : 2.207 Fit side-chains REVERT: A 27 MET cc_start: 0.2417 (tmm) cc_final: 0.2191 (tmm) REVERT: A 475 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: B 429 ARG cc_start: 0.7272 (ttm-80) cc_final: 0.7042 (mmt180) REVERT: B 475 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: D 429 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.7043 (mmt180) REVERT: D 475 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: G 475 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7342 (mt-10) outliers start: 38 outliers final: 30 residues processed: 305 average time/residue: 0.3248 time to fit residues: 151.3027 Evaluate side-chains 293 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 259 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 149 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 138 optimal weight: 0.0020 chunk 178 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 148 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN G 416 ASN E 132 ASN H 132 ASN J 132 ASN L 132 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21080 Z= 0.158 Angle : 0.530 11.522 28512 Z= 0.274 Chirality : 0.039 0.167 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.116 16.356 2804 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 1.81 % Allowed : 15.73 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2492 helix: 1.61 (0.13), residues: 1636 sheet: -0.73 (0.76), residues: 40 loop : -2.19 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 362 HIS 0.004 0.001 HIS B 94 PHE 0.028 0.002 PHE E 131 TYR 0.012 0.001 TYR G 188 ARG 0.001 0.000 ARG H 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 271 time to evaluate : 2.866 Fit side-chains REVERT: A 475 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: B 27 MET cc_start: 0.2339 (tmm) cc_final: 0.2064 (tmm) REVERT: B 475 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: D 429 ARG cc_start: 0.7176 (ttm-80) cc_final: 0.6954 (mmt180) REVERT: D 475 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: G 90 ASP cc_start: 0.7530 (m-30) cc_final: 0.7322 (m-30) REVERT: G 475 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7340 (mt-10) outliers start: 40 outliers final: 21 residues processed: 305 average time/residue: 0.3351 time to fit residues: 155.5131 Evaluate side-chains 288 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 263 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 416 ASN Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain L residue 64 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN H 132 ASN H 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21080 Z= 0.302 Angle : 0.600 12.273 28512 Z= 0.305 Chirality : 0.042 0.149 3120 Planarity : 0.004 0.052 3644 Dihedral : 4.259 16.711 2804 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.42 % Favored : 92.42 % Rotamer: Outliers : 1.90 % Allowed : 15.87 % Favored : 82.23 % 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: 0.50 (0.17), residues: 2492 helix: 1.49 (0.13), residues: 1656 sheet: -1.12 (0.75), residues: 40 loop : -2.17 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 362 HIS 0.003 0.001 HIS G 94 PHE 0.031 0.002 PHE H 178 TYR 0.014 0.001 TYR G 188 ARG 0.003 0.000 ARG G 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 267 time to evaluate : 2.298 Fit side-chains REVERT: A 475 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: B 27 MET cc_start: 0.2386 (tmm) cc_final: 0.2109 (tmm) REVERT: B 475 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: D 429 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6993 (mmt180) REVERT: D 475 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: G 475 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7404 (mt-10) outliers start: 42 outliers final: 34 residues processed: 300 average time/residue: 0.3302 time to fit residues: 149.8189 Evaluate side-chains 299 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 261 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 185 ASN Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.0670 chunk 212 optimal weight: 0.8980 chunk 226 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 204 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN E 132 ASN H 132 ASN H 213 GLN J 132 ASN L 132 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21080 Z= 0.163 Angle : 0.545 12.118 28512 Z= 0.278 Chirality : 0.039 0.167 3120 Planarity : 0.004 0.054 3644 Dihedral : 4.095 16.216 2804 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.30 % Favored : 92.54 % Rotamer: Outliers : 1.58 % Allowed : 16.50 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2492 helix: 1.70 (0.13), residues: 1632 sheet: -1.04 (0.76), residues: 40 loop : -2.22 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 362 HIS 0.003 0.001 HIS A 94 PHE 0.031 0.002 PHE H 131 TYR 0.012 0.001 TYR G 188 ARG 0.002 0.000 ARG G 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 2.068 Fit side-chains REVERT: A 475 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: B 475 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: D 429 ARG cc_start: 0.7194 (ttm-80) cc_final: 0.6972 (mmt180) REVERT: D 475 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: G 475 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7343 (mt-10) outliers start: 35 outliers final: 28 residues processed: 289 average time/residue: 0.3367 time to fit residues: 146.3679 Evaluate side-chains 291 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 259 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 185 ASN Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 193 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 113 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 154 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 158 optimal weight: 0.0040 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21080 Z= 0.232 Angle : 0.582 13.455 28512 Z= 0.293 Chirality : 0.040 0.154 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.132 16.522 2804 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.94 % Favored : 92.90 % Rotamer: Outliers : 1.63 % Allowed : 16.41 % Favored : 81.96 % 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: 0.63 (0.17), residues: 2492 helix: 1.68 (0.13), residues: 1632 sheet: -1.00 (0.79), residues: 40 loop : -2.22 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.004 0.001 HIS G 94 PHE 0.026 0.002 PHE H 178 TYR 0.013 0.001 TYR G 188 ARG 0.001 0.000 ARG D 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 270 time to evaluate : 2.249 Fit side-chains REVERT: A 475 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: B 475 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: D 429 ARG cc_start: 0.7204 (ttm-80) cc_final: 0.6970 (mmt180) REVERT: D 475 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: G 90 ASP cc_start: 0.7558 (m-30) cc_final: 0.7350 (m-30) REVERT: G 475 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7366 (mt-10) outliers start: 36 outliers final: 30 residues processed: 299 average time/residue: 0.3413 time to fit residues: 153.1521 Evaluate side-chains 296 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 262 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 185 ASN Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain L residue 213 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.208764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.185977 restraints weight = 22418.016| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.02 r_work: 0.3785 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21080 Z= 0.234 Angle : 0.581 13.072 28512 Z= 0.294 Chirality : 0.040 0.155 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.170 16.762 2804 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.42 % Favored : 92.42 % Rotamer: Outliers : 1.67 % Allowed : 16.37 % Favored : 81.96 % 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: 0.61 (0.17), residues: 2492 helix: 1.67 (0.13), residues: 1632 sheet: -1.06 (0.80), residues: 40 loop : -2.26 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.004 0.001 HIS A 94 PHE 0.027 0.002 PHE H 178 TYR 0.013 0.001 TYR G 188 ARG 0.001 0.000 ARG D 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.79 seconds wall clock time: 73 minutes 36.48 seconds (4416.48 seconds total)