Starting phenix.real_space_refine on Mon Jul 22 22:13:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3f_31433/07_2024/7f3f_31433.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3f_31433/07_2024/7f3f_31433.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/7f3f_31433/07_2024/7f3f_31433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3f_31433/07_2024/7f3f_31433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3f_31433/07_2024/7f3f_31433.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3f_31433/07_2024/7f3f_31433.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 GLU 136": "OE1" <-> "OE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 60": "OE1" <-> "OE2" 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" 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: 10.75, per 1000 atoms: 0.52 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: 7.83 Conformation dependent library (CDL) restraints added in 3.6 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: 125 helices and 8 sheets defined 69.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 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: 3.579A 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 91 through 101 removed outlier: 3.574A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.672A 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: 4.265A pdb=" N ARG A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.126A 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: 3.616A 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: 3.754A pdb=" N ASN A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 4.021A pdb=" N VAL A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.714A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.768A 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: 4.126A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.659A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 450 removed outlier: 4.605A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.936A pdb=" N GLN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.579A 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 91 through 101 removed outlier: 3.570A pdb=" N ILE B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.679A 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: 4.290A pdb=" N ARG B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.117A 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: 3.738A pdb=" N ASN B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.739A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.764A 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: 4.094A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.660A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 450 removed outlier: 4.607A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.937A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.825A 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: 3.580A 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: 3.574A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.675A 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: 4.293A pdb=" N ARG D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 4.119A 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 227 through 249 removed outlier: 3.968A pdb=" N CYS D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) 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: 3.737A pdb=" N ASN D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.996A pdb=" N VAL D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.545A pdb=" N PHE D 301 " --> pdb=" O PHE D 298 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.776A 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: 4.126A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.653A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 450 removed outlier: 4.600A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS D 421 " --> pdb=" O GLN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 488 removed outlier: 3.938A 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: 3.573A 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: 3.571A pdb=" N ILE G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 123 removed outlier: 3.674A pdb=" N GLU G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 133 removed outlier: 3.506A pdb=" N CYS G 133 " --> pdb=" O GLY G 130 " (cutoff:3.500A) No H-bonds generated for '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: 4.267A pdb=" N ARG G 170 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 4.099A 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 227 through 249 removed outlier: 3.652A 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: 3.742A pdb=" N ASN G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 297 removed outlier: 4.056A pdb=" N VAL G 297 " --> pdb=" O ARG G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 removed outlier: 3.732A pdb=" N ARG G 305 " --> pdb=" O LYS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 320 removed outlier: 3.812A 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: 4.150A pdb=" N TRP G 362 " --> pdb=" O PRO G 358 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR G 363 " --> pdb=" O ALA G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 400 removed outlier: 3.644A pdb=" N ILE G 385 " --> pdb=" O ILE G 381 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G 386 " --> pdb=" O ALA G 382 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 400 " --> pdb=" O LEU G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 417 removed outlier: 4.609A pdb=" N VAL G 404 " --> pdb=" O LEU G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 450 Processing helix chain 'G' and resid 473 through 489 removed outlier: 3.936A pdb=" N GLN G 477 " --> pdb=" O SER G 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR G 489 " --> pdb=" O LEU G 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.668A pdb=" N GLU E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.829A pdb=" N GLN E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.756A 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: 3.792A pdb=" N THR E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 3.590A 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 Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.660A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 64 removed outlier: 3.667A pdb=" N GLU H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.826A pdb=" N GLN H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE H 82 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 removed outlier: 3.756A 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: 3.822A pdb=" N THR H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.700A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN H 210 " --> pdb=" O MET H 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 64 removed outlier: 3.667A pdb=" N GLU J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.826A pdb=" N GLN J 76 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR J 78 " --> pdb=" O PHE J 74 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE J 81 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE J 82 " --> pdb=" O TYR J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR J 93 " --> pdb=" O THR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 103 removed outlier: 3.756A 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: 3.822A pdb=" N THR J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 3.595A 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 Processing helix chain 'J' and resid 202 through 210 removed outlier: 3.637A pdb=" N MET J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN J 210 " --> pdb=" O MET J 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 64 removed outlier: 3.681A pdb=" N GLU L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.828A pdb=" N GLN L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR L 78 " --> pdb=" O PHE L 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE L 81 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.759A 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: 3.793A pdb=" N THR L 113 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 3.590A 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 Processing helix chain 'L' and resid 202 through 210 removed outlier: 3.661A pdb=" N MET L 206 " --> pdb=" O ASP L 202 " (cutoff:3.500A) removed outlier: 3.710A 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: 3.523A pdb=" N GLN A 82 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.810A pdb=" N THR B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 82 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR D 50 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 82 " --> pdb=" O HIS D 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR G 50 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN G 82 " --> pdb=" O HIS G 77 " (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 1185 hydrogen bonds defined for protein. 3462 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: 5.67 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3919 1.33 - 1.45: 5510 1.45 - 1.57: 11451 1.57 - 1.70: 0 1.70 - 1.82: 200 Bond restraints: 21080 Sorted by residual: bond pdb=" C ARG G 418 " pdb=" O ARG G 418 " ideal model delta sigma weight residual 1.234 1.205 0.029 1.17e-02 7.31e+03 6.14e+00 bond pdb=" C GLN A 417 " pdb=" O GLN A 417 " ideal model delta sigma weight residual 1.236 1.208 0.029 1.22e-02 6.72e+03 5.47e+00 bond pdb=" C GLN D 417 " pdb=" O GLN D 417 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.28e-02 6.10e+03 5.15e+00 bond pdb=" C ASN A 416 " pdb=" O ASN A 416 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.32e-02 5.74e+03 4.36e+00 bond pdb=" C ASN D 416 " pdb=" O ASN D 416 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.32e-02 5.74e+03 4.08e+00 ... (remaining 21075 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.80: 444 105.80 - 112.86: 10869 112.86 - 119.91: 7257 119.91 - 126.97: 9718 126.97 - 134.03: 224 Bond angle restraints: 28512 Sorted by residual: angle pdb=" N GLN B 417 " pdb=" CA GLN B 417 " pdb=" C GLN B 417 " ideal model delta sigma weight residual 113.12 104.25 8.87 1.25e+00 6.40e-01 5.03e+01 angle pdb=" N GLN G 417 " pdb=" CA GLN G 417 " pdb=" C GLN G 417 " ideal model delta sigma weight residual 113.38 105.52 7.86 1.23e+00 6.61e-01 4.08e+01 angle pdb=" N GLN A 417 " pdb=" CA GLN A 417 " pdb=" C GLN A 417 " ideal model delta sigma weight residual 111.69 104.26 7.43 1.23e+00 6.61e-01 3.65e+01 angle pdb=" N GLN D 417 " pdb=" CA GLN D 417 " pdb=" C GLN D 417 " ideal model delta sigma weight residual 112.45 104.47 7.98 1.39e+00 5.18e-01 3.30e+01 angle pdb=" CB ARG D 418 " pdb=" CG ARG D 418 " pdb=" CD ARG D 418 " ideal model delta sigma weight residual 111.30 98.74 12.56 2.30e+00 1.89e-01 2.98e+01 ... (remaining 28507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11161 17.77 - 35.54: 1092 35.54 - 53.31: 203 53.31 - 71.08: 36 71.08 - 88.85: 16 Dihedral angle restraints: 12508 sinusoidal: 5020 harmonic: 7488 Sorted by residual: 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 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA HIS D 77 " pdb=" C HIS D 77 " pdb=" N PRO D 78 " pdb=" CA PRO D 78 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 12505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2881 0.071 - 0.142: 228 0.142 - 0.213: 5 0.213 - 0.284: 3 0.284 - 0.355: 3 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA GLN B 417 " pdb=" N GLN B 417 " pdb=" C GLN B 417 " pdb=" CB GLN B 417 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA GLN A 417 " pdb=" N GLN A 417 " pdb=" C GLN A 417 " pdb=" CB GLN A 417 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA GLN D 417 " pdb=" N GLN D 417 " pdb=" C GLN D 417 " pdb=" CB GLN D 417 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3117 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 207 " 0.036 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO B 208 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 207 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO G 208 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 208 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 208 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C GLN B 417 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN B 417 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG B 418 " -0.012 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5217 2.79 - 3.32: 20446 3.32 - 3.85: 33262 3.85 - 4.37: 39351 4.37 - 4.90: 67309 Nonbonded interactions: 165585 Sorted by model distance: nonbonded pdb=" OE2 GLU B 71 " pdb=" OH TYR H 57 " model vdw 2.268 2.440 nonbonded pdb=" OE2 GLU D 71 " pdb=" OH TYR J 57 " model vdw 2.271 2.440 nonbonded pdb=" OE2 GLU G 71 " pdb=" OH TYR L 57 " model vdw 2.271 2.440 nonbonded pdb=" OE2 GLU A 71 " pdb=" OH TYR E 57 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR A 65 " pdb=" OH TYR A 99 " model vdw 2.280 2.440 ... (remaining 165580 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.360 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 0.038 21080 Z= 0.160 Angle : 0.617 12.558 28512 Z= 0.329 Chirality : 0.040 0.355 3120 Planarity : 0.003 0.056 3644 Dihedral : 14.673 88.848 7660 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.34 % Favored : 92.34 % Rotamer: Outliers : 0.14 % Allowed : 0.45 % Favored : 99.41 % Cbeta Deviations : 0.08 % 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: 0.02 (0.17), residues: 2492 helix: 1.16 (0.13), residues: 1584 sheet: -2.35 (0.54), residues: 40 loop : -2.08 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 362 HIS 0.004 0.001 HIS G 77 PHE 0.009 0.001 PHE D 493 TYR 0.009 0.001 TYR B 188 ARG 0.008 0.000 ARG B 142 *********************** 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 385 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 382 time to evaluate : 2.325 Fit side-chains REVERT: A 46 ASN cc_start: 0.8604 (t0) cc_final: 0.8117 (t0) REVERT: A 183 MET cc_start: 0.2445 (mmm) cc_final: 0.2057 (tpt) REVERT: A 429 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6608 (mmt180) REVERT: B 46 ASN cc_start: 0.8600 (t0) cc_final: 0.8114 (t0) REVERT: B 183 MET cc_start: 0.2406 (mmm) cc_final: 0.2029 (tpt) REVERT: B 429 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6631 (mmt90) REVERT: D 46 ASN cc_start: 0.8600 (t0) cc_final: 0.8116 (t0) REVERT: D 183 MET cc_start: 0.2480 (mmm) cc_final: 0.2068 (tpt) REVERT: D 429 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6621 (mmt90) REVERT: G 46 ASN cc_start: 0.8595 (t0) cc_final: 0.8109 (t0) REVERT: G 183 MET cc_start: 0.2419 (mmm) cc_final: 0.2008 (tpt) REVERT: G 299 ARG cc_start: 0.7114 (ptp-170) cc_final: 0.6871 (mtt180) REVERT: G 429 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6603 (mmt90) REVERT: E 109 GLU cc_start: 0.7339 (mp0) cc_final: 0.7100 (mp0) REVERT: H 109 GLU cc_start: 0.7243 (mp0) cc_final: 0.7035 (mp0) REVERT: H 168 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7129 (tm-30) REVERT: J 109 GLU cc_start: 0.7259 (mp0) cc_final: 0.7046 (mp0) REVERT: J 210 GLN cc_start: 0.7415 (mp10) cc_final: 0.7209 (mp10) REVERT: L 109 GLU cc_start: 0.7335 (mp0) cc_final: 0.7088 (mp0) REVERT: L 168 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7166 (tm-30) outliers start: 3 outliers final: 0 residues processed: 382 average time/residue: 0.3453 time to fit residues: 202.0328 Evaluate side-chains 294 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 2.183 ------------------------------------------------------------------------------- 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: 0.9980 chunk 191 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN B 417 GLN D 144 ASN D 417 GLN E 210 GLN H 210 GLN J 210 GLN L 210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21080 Z= 0.319 Angle : 0.615 7.397 28512 Z= 0.322 Chirality : 0.043 0.163 3120 Planarity : 0.005 0.059 3644 Dihedral : 4.233 20.943 2804 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 1.81 % Allowed : 6.42 % Favored : 91.77 % 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: 0.15 (0.17), residues: 2492 helix: 1.23 (0.13), residues: 1628 sheet: -0.86 (0.76), residues: 40 loop : -2.22 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 362 HIS 0.005 0.001 HIS A 94 PHE 0.018 0.002 PHE B 122 TYR 0.013 0.001 TYR A 188 ARG 0.007 0.001 ARG G 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 347 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 307 time to evaluate : 2.277 Fit side-chains REVERT: A 42 LEU cc_start: 0.8985 (pt) cc_final: 0.8738 (pt) REVERT: A 429 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6914 (mmt180) REVERT: A 475 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: B 42 LEU cc_start: 0.8968 (pt) cc_final: 0.8727 (pt) REVERT: B 429 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6882 (mmt180) REVERT: B 475 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: D 42 LEU cc_start: 0.8952 (pt) cc_final: 0.8704 (pt) REVERT: D 429 ARG cc_start: 0.7186 (ttm-80) cc_final: 0.6906 (mmt180) REVERT: D 475 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: G 42 LEU cc_start: 0.8952 (pt) cc_final: 0.8711 (pt) REVERT: G 411 ARG cc_start: 0.7573 (ttp-170) cc_final: 0.7351 (ptt90) REVERT: G 429 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6826 (mmt180) REVERT: G 475 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: E 109 GLU cc_start: 0.7283 (mp0) cc_final: 0.7056 (mp0) REVERT: H 109 GLU cc_start: 0.7244 (mp0) cc_final: 0.7027 (mp0) REVERT: J 109 GLU cc_start: 0.7255 (mp0) cc_final: 0.7040 (mp0) REVERT: L 109 GLU cc_start: 0.7298 (mp0) cc_final: 0.7069 (mp0) outliers start: 40 outliers final: 19 residues processed: 334 average time/residue: 0.3504 time to fit residues: 175.0421 Evaluate side-chains 306 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 283 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN 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 E residue 106 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 193 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.0770 chunk 227 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 144 ASN J 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21080 Z= 0.207 Angle : 0.534 7.137 28512 Z= 0.281 Chirality : 0.040 0.157 3120 Planarity : 0.004 0.055 3644 Dihedral : 4.130 19.101 2804 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.30 % Favored : 92.54 % Rotamer: Outliers : 1.13 % Allowed : 9.90 % Favored : 88.97 % 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: 0.36 (0.17), residues: 2492 helix: 1.48 (0.13), residues: 1612 sheet: -0.79 (0.75), residues: 40 loop : -2.28 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 362 HIS 0.004 0.001 HIS A 94 PHE 0.022 0.002 PHE E 131 TYR 0.014 0.001 TYR G 188 ARG 0.008 0.000 ARG D 51 *********************** 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 323 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 2.299 Fit side-chains REVERT: A 42 LEU cc_start: 0.8910 (pt) cc_final: 0.8690 (pt) REVERT: A 183 MET cc_start: 0.3254 (mmp) cc_final: 0.2087 (tpt) REVERT: A 429 ARG cc_start: 0.7197 (ttm-80) cc_final: 0.6974 (mmt180) REVERT: A 475 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: B 42 LEU cc_start: 0.8895 (pt) cc_final: 0.8679 (pt) REVERT: B 183 MET cc_start: 0.3307 (mmp) cc_final: 0.2085 (tpt) REVERT: B 475 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: D 42 LEU cc_start: 0.8877 (pt) cc_final: 0.8659 (pt) REVERT: D 183 MET cc_start: 0.3288 (mmp) cc_final: 0.2080 (tpt) REVERT: D 475 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: G 42 LEU cc_start: 0.8877 (pt) cc_final: 0.8663 (pt) REVERT: G 183 MET cc_start: 0.3299 (mmp) cc_final: 0.2110 (tpt) REVERT: G 429 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6899 (mmt180) REVERT: G 475 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: E 109 GLU cc_start: 0.7291 (mp0) cc_final: 0.7066 (mp0) REVERT: H 109 GLU cc_start: 0.7186 (mp0) cc_final: 0.6974 (mp0) REVERT: J 109 GLU cc_start: 0.7223 (mp0) cc_final: 0.7008 (mp0) REVERT: L 109 GLU cc_start: 0.7284 (mp0) cc_final: 0.7053 (mp0) outliers start: 25 outliers final: 13 residues processed: 315 average time/residue: 0.3403 time to fit residues: 161.3186 Evaluate side-chains 300 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 283 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 208 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: 10.0000 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 230 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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** B 414 HIS ** 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: 0.7434 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 21080 Z= 0.464 Angle : 0.669 8.470 28512 Z= 0.345 Chirality : 0.046 0.191 3120 Planarity : 0.005 0.054 3644 Dihedral : 4.554 20.346 2804 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.03 % Favored : 91.81 % Rotamer: Outliers : 2.12 % Allowed : 12.75 % Favored : 85.13 % 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: 0.08 (0.17), residues: 2492 helix: 1.20 (0.12), residues: 1636 sheet: -0.76 (0.77), residues: 40 loop : -2.35 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 362 HIS 0.007 0.001 HIS D 491 PHE 0.023 0.002 PHE J 131 TYR 0.017 0.002 TYR G 188 ARG 0.007 0.001 ARG G 305 *********************** 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 334 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 287 time to evaluate : 2.264 Fit side-chains REVERT: A 183 MET cc_start: 0.3139 (mmp) cc_final: 0.1593 (tpt) REVERT: A 429 ARG cc_start: 0.7261 (ttm-80) cc_final: 0.7013 (mmt180) REVERT: A 475 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: B 183 MET cc_start: 0.3087 (mmp) cc_final: 0.1703 (tpt) REVERT: B 475 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: D 183 MET cc_start: 0.3008 (mmp) cc_final: 0.1728 (tpt) REVERT: D 475 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: G 183 MET cc_start: 0.3162 (mmp) cc_final: 0.1612 (tpt) REVERT: G 429 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6993 (mmt180) REVERT: G 475 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7597 (mt-10) outliers start: 47 outliers final: 32 residues processed: 319 average time/residue: 0.3225 time to fit residues: 157.6750 Evaluate side-chains 294 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 258 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 332 THR 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 70 SER Chi-restraints excluded: chain B residue 221 CYS 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 B residue 490 ASN Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 221 CYS 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 D residue 490 ASN Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL 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: 4.9990 chunk 138 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 213 GLN J 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2555 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= 0.172 Angle : 0.540 8.945 28512 Z= 0.282 Chirality : 0.040 0.178 3120 Planarity : 0.004 0.055 3644 Dihedral : 4.268 17.267 2804 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.30 % Favored : 92.54 % Rotamer: Outliers : 1.63 % Allowed : 13.70 % Favored : 84.67 % 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: 0.39 (0.17), residues: 2492 helix: 1.49 (0.13), residues: 1632 sheet: -0.39 (0.82), residues: 40 loop : -2.36 (0.20), residues: 820 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 0.019 0.001 PHE E 131 TYR 0.014 0.001 TYR G 188 ARG 0.005 0.000 ARG A 51 *********************** 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 312 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 2.484 Fit side-chains REVERT: A 183 MET cc_start: 0.3087 (mmp) cc_final: 0.1687 (tpt) REVERT: A 429 ARG cc_start: 0.7164 (ttm-80) cc_final: 0.6931 (mmt180) REVERT: A 475 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: B 475 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: D 475 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: G 475 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7525 (mt-10) outliers start: 36 outliers final: 16 residues processed: 305 average time/residue: 0.3197 time to fit residues: 150.4401 Evaluate side-chains 285 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 265 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR 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 368 MET 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 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 208 SER 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: 1.9990 chunk 48 optimal weight: 0.4980 chunk 143 optimal weight: 0.0000 chunk 60 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 80 optimal weight: 0.0270 chunk 128 optimal weight: 0.4980 overall best weight: 0.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21080 Z= 0.145 Angle : 0.519 10.945 28512 Z= 0.271 Chirality : 0.039 0.209 3120 Planarity : 0.004 0.054 3644 Dihedral : 4.037 15.912 2804 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.46 % Favored : 92.38 % Rotamer: Outliers : 1.36 % Allowed : 14.29 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2492 helix: 1.71 (0.13), residues: 1624 sheet: -0.05 (0.84), residues: 40 loop : -2.35 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 362 HIS 0.004 0.001 HIS G 94 PHE 0.032 0.002 PHE E 178 TYR 0.012 0.001 TYR G 188 ARG 0.007 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 310 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 2.302 Fit side-chains REVERT: A 475 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: B 183 MET cc_start: 0.2961 (mmp) cc_final: 0.1686 (tpt) REVERT: B 475 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: D 183 MET cc_start: 0.2952 (mmp) cc_final: 0.1687 (tpt) REVERT: D 475 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: G 90 ASP cc_start: 0.7633 (m-30) cc_final: 0.7423 (m-30) REVERT: G 183 MET cc_start: 0.2960 (mmp) cc_final: 0.1703 (tpt) REVERT: G 475 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: H 210 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7385 (mm-40) outliers start: 30 outliers final: 15 residues processed: 306 average time/residue: 0.3341 time to fit residues: 155.2350 Evaluate side-chains 291 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE 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 475 GLU Chi-restraints excluded: chain B residue 490 ASN 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 332 THR Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 138 optimal weight: 0.0020 chunk 178 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 overall best weight: 2.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS D 414 HIS ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21080 Z= 0.267 Angle : 0.573 10.768 28512 Z= 0.295 Chirality : 0.041 0.154 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.176 16.008 2804 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.87 % Favored : 91.97 % Rotamer: Outliers : 1.54 % Allowed : 13.70 % Favored : 84.76 % 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: 1.76 (0.13), residues: 1612 sheet: -0.41 (0.79), residues: 40 loop : -2.34 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 362 HIS 0.003 0.001 HIS D 94 PHE 0.027 0.002 PHE E 178 TYR 0.020 0.001 TYR A 134 ARG 0.004 0.000 ARG A 296 *********************** 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 307 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 273 time to evaluate : 2.179 Fit side-chains REVERT: A 183 MET cc_start: 0.2888 (mmp) cc_final: 0.1549 (tpt) REVERT: A 475 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: B 183 MET cc_start: 0.2822 (mmp) cc_final: 0.1927 (mmm) REVERT: B 475 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: D 183 MET cc_start: 0.2822 (mmp) cc_final: 0.1933 (mmm) REVERT: D 475 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: G 183 MET cc_start: 0.2833 (mmp) cc_final: 0.1431 (tpt) REVERT: G 475 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: H 210 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7357 (mm-40) outliers start: 34 outliers final: 30 residues processed: 297 average time/residue: 0.3206 time to fit residues: 145.9923 Evaluate side-chains 301 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 393 SER 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 393 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 144 ASN 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 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL 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: 0.9990 chunk 145 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2760 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= 0.201 Angle : 0.563 11.881 28512 Z= 0.287 Chirality : 0.040 0.158 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.117 15.913 2804 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 1.31 % Allowed : 15.14 % Favored : 83.54 % 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: 0.69 (0.17), residues: 2492 helix: 1.75 (0.13), residues: 1628 sheet: -0.47 (0.80), residues: 40 loop : -2.27 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 362 HIS 0.004 0.001 HIS G 94 PHE 0.026 0.002 PHE H 178 TYR 0.014 0.001 TYR G 188 ARG 0.004 0.000 ARG A 296 *********************** 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 299 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 270 time to evaluate : 2.129 Fit side-chains REVERT: A 183 MET cc_start: 0.2609 (mmp) cc_final: 0.1262 (tpt) REVERT: A 475 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: B 183 MET cc_start: 0.2662 (mmp) cc_final: 0.1783 (mmm) REVERT: B 475 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: D 183 MET cc_start: 0.2661 (mmp) cc_final: 0.1274 (tpt) REVERT: D 475 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: G 183 MET cc_start: 0.2670 (mmp) cc_final: 0.1286 (tpt) REVERT: G 475 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: H 210 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7596 (mm-40) outliers start: 29 outliers final: 25 residues processed: 289 average time/residue: 0.3172 time to fit residues: 139.9985 Evaluate side-chains 293 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE 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 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 B residue 490 ASN Chi-restraints excluded: chain D residue 144 ASN 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 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 chunk 214 optimal weight: 0.4980 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21080 Z= 0.247 Angle : 0.588 11.752 28512 Z= 0.298 Chirality : 0.041 0.156 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.183 16.299 2804 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.30 % Favored : 92.54 % Rotamer: Outliers : 1.81 % Allowed : 15.24 % Favored : 82.96 % 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: 1.70 (0.13), residues: 1632 sheet: -0.64 (0.76), residues: 40 loop : -2.35 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 362 HIS 0.004 0.001 HIS D 94 PHE 0.034 0.002 PHE L 131 TYR 0.015 0.001 TYR G 188 ARG 0.003 0.000 ARG A 296 *********************** 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 304 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 264 time to evaluate : 2.233 Fit side-chains REVERT: A 183 MET cc_start: 0.2572 (mmp) cc_final: 0.1202 (tpt) REVERT: A 475 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: B 183 MET cc_start: 0.2674 (mmp) cc_final: 0.1251 (tpt) REVERT: B 475 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: D 183 MET cc_start: 0.2683 (mmp) cc_final: 0.1264 (tpt) REVERT: D 475 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: G 183 MET cc_start: 0.2653 (mmp) cc_final: 0.1238 (tpt) REVERT: G 475 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: H 210 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7628 (mm-40) outliers start: 40 outliers final: 29 residues processed: 292 average time/residue: 0.3132 time to fit residues: 141.0412 Evaluate side-chains 292 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 259 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 300 ILE 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 70 SER 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 B residue 490 ASN Chi-restraints excluded: chain D residue 144 ASN 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 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 158 optimal weight: 0.2980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21080 Z= 0.209 Angle : 0.580 12.971 28512 Z= 0.293 Chirality : 0.040 0.155 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.136 15.968 2804 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 1.45 % Allowed : 15.69 % Favored : 82.87 % 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: 0.68 (0.17), residues: 2492 helix: 1.75 (0.13), residues: 1628 sheet: -0.55 (0.78), residues: 40 loop : -2.29 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 362 HIS 0.004 0.001 HIS G 94 PHE 0.027 0.002 PHE J 131 TYR 0.014 0.001 TYR G 188 ARG 0.003 0.000 ARG A 296 ********************** 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 296 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 264 time to evaluate : 2.222 Fit side-chains REVERT: A 183 MET cc_start: 0.2544 (mmp) cc_final: 0.1172 (tpt) REVERT: A 475 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: B 183 MET cc_start: 0.2598 (mmp) cc_final: 0.1169 (tpt) REVERT: B 475 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: D 183 MET cc_start: 0.2626 (mmp) cc_final: 0.1208 (tpt) REVERT: D 475 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: G 90 ASP cc_start: 0.7710 (m-30) cc_final: 0.7493 (m-30) REVERT: G 183 MET cc_start: 0.2603 (mmp) cc_final: 0.1198 (tpt) REVERT: G 475 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: H 210 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7633 (mm-40) outliers start: 32 outliers final: 28 residues processed: 285 average time/residue: 0.3259 time to fit residues: 144.8059 Evaluate side-chains 296 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 264 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 393 SER 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 B residue 490 ASN Chi-restraints excluded: chain D residue 144 ASN 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 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.205783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.181701 restraints weight = 22415.145| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.04 r_work: 0.3737 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21080 Z= 0.398 Angle : 0.675 13.039 28512 Z= 0.340 Chirality : 0.045 0.168 3120 Planarity : 0.005 0.051 3644 Dihedral : 4.461 17.084 2804 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.03 % Favored : 91.81 % Rotamer: Outliers : 1.63 % Allowed : 15.64 % Favored : 82.73 % 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: 0.34 (0.17), residues: 2492 helix: 1.45 (0.13), residues: 1640 sheet: -0.97 (0.74), residues: 40 loop : -2.36 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 362 HIS 0.005 0.001 HIS B 491 PHE 0.026 0.002 PHE J 131 TYR 0.017 0.002 TYR G 188 ARG 0.005 0.000 ARG D 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4088.15 seconds wall clock time: 74 minutes 9.39 seconds (4449.39 seconds total)