Starting phenix.real_space_refine on Tue Mar 19 16:16:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlz_34886/03_2024/8hlz_34886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlz_34886/03_2024/8hlz_34886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlz_34886/03_2024/8hlz_34886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlz_34886/03_2024/8hlz_34886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlz_34886/03_2024/8hlz_34886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlz_34886/03_2024/8hlz_34886.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 132 5.16 5 C 15842 2.51 5 N 4098 2.21 5 O 4646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 288": "OE1" <-> "OE2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F GLU 401": "OE1" <-> "OE2" Residue "F GLU 426": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D GLU 529": "OE1" <-> "OE2" Residue "D GLU 579": "OE1" <-> "OE2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 769": "OE1" <-> "OE2" Residue "D GLU 790": "OE1" <-> "OE2" Residue "D GLU 856": "OE1" <-> "OE2" Residue "D GLU 879": "OE1" <-> "OE2" Residue "D PHE 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 969": "OE1" <-> "OE2" Residue "D GLU 978": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A PHE 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24718 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3020 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 7, 'TRANS': 362} Chain breaks: 1 Chain: "E" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "D" Number of atoms: 7567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7567 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 895} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3020 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 7, 'TRANS': 362} Chain breaks: 1 Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "A" Number of atoms: 7567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7567 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 895} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 12.53, per 1000 atoms: 0.51 Number of scatterers: 24718 At special positions: 0 Unit cell: (111.69, 114.975, 215.715, 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 132 16.00 O 4646 8.00 N 4098 7.00 C 15842 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: 9.48 Conformation dependent library (CDL) restraints added in 4.4 seconds 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5820 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 38 sheets defined 38.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'F' and resid 4 through 18 removed outlier: 4.572A pdb=" N LYS F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 40 removed outlier: 3.980A pdb=" N SER F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 118 removed outlier: 3.521A pdb=" N ARG F 111 " --> pdb=" O PRO F 107 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 removed outlier: 4.064A pdb=" N LYS F 153 " --> pdb=" O VAL F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 189 removed outlier: 4.864A pdb=" N MET F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.709A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 298 removed outlier: 3.622A pdb=" N VAL F 289 " --> pdb=" O THR F 285 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 323 Processing helix chain 'F' and resid 330 through 341 Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'F' and resid 352 through 360 Processing helix chain 'F' and resid 366 through 373 removed outlier: 3.702A pdb=" N THR F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 397 through 406 removed outlier: 4.107A pdb=" N ILE F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN F 406 " --> pdb=" O THR F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 425 removed outlier: 4.080A pdb=" N PHE F 410 " --> pdb=" O ASN F 406 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 19 through 38 removed outlier: 4.376A pdb=" N SER E 24 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TRP E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 54 removed outlier: 4.607A pdb=" N GLN E 52 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 54 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 removed outlier: 4.210A pdb=" N LEU E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 152 removed outlier: 3.556A pdb=" N TRP E 137 " --> pdb=" O HIS E 133 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE E 140 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 150 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS E 151 " --> pdb=" O HIS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 197 through 205 removed outlier: 3.639A pdb=" N GLU E 203 " --> pdb=" O ASN E 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 108 through 116 removed outlier: 3.628A pdb=" N PHE D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 240 through 253 Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.692A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.534A pdb=" N PHE D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 439 through 446 removed outlier: 3.592A pdb=" N MET D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 474 removed outlier: 3.686A pdb=" N ARG D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS D 461 " --> pdb=" O ARG D 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP D 470 " --> pdb=" O CYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 485 removed outlier: 4.243A pdb=" N ASP D 480 " --> pdb=" O GLU D 476 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.512A pdb=" N GLU D 512 " --> pdb=" O LYS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.692A pdb=" N LEU D 588 " --> pdb=" O ASN D 584 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 643 removed outlier: 3.778A pdb=" N LYS D 639 " --> pdb=" O ALA D 635 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 642 " --> pdb=" O LYS D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 666 removed outlier: 3.960A pdb=" N ASP D 654 " --> pdb=" O LYS D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 673 removed outlier: 3.796A pdb=" N GLY D 672 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 673 " --> pdb=" O GLY D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 687 Processing helix chain 'D' and resid 688 through 701 removed outlier: 3.522A pdb=" N VAL D 701 " --> pdb=" O TYR D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 782 removed outlier: 3.530A pdb=" N ALA D 771 " --> pdb=" O SER D 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 773 " --> pdb=" O GLU D 769 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN D 779 " --> pdb=" O GLU D 775 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER D 780 " --> pdb=" O ARG D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 854 removed outlier: 4.099A pdb=" N THR D 845 " --> pdb=" O ASN D 841 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 854 " --> pdb=" O LEU D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 882 removed outlier: 4.136A pdb=" N GLN D 863 " --> pdb=" O MET D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 979 removed outlier: 3.620A pdb=" N TYR D 971 " --> pdb=" O PHE D 967 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 972 " --> pdb=" O TYR D 968 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 973 " --> pdb=" O GLU D 969 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR D 976 " --> pdb=" O PHE D 972 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 996 removed outlier: 3.571A pdb=" N CYS D 989 " --> pdb=" O ASN D 985 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 990 " --> pdb=" O LYS D 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 removed outlier: 4.572A pdb=" N LYS C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.979A pdb=" N SER C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 118 removed outlier: 3.522A pdb=" N ARG C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 removed outlier: 4.065A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 4.865A pdb=" N MET C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.711A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.620A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'C' and resid 366 through 373 removed outlier: 3.702A pdb=" N THR C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 406 removed outlier: 4.106A pdb=" N ILE C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 4.080A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.378A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.688A pdb=" N LEU B 53 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 54 " --> pdb=" O ILE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 54' Processing helix chain 'B' and resid 86 through 101 removed outlier: 4.210A pdb=" N LEU B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 removed outlier: 3.554A pdb=" N TRP B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.640A pdb=" N GLU B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.627A pdb=" N PHE A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.692A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.533A pdb=" N PHE A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.592A pdb=" N MET A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.686A pdb=" N ARG A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP A 470 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 485 removed outlier: 4.244A pdb=" N ASP A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.512A pdb=" N GLU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 579 through 590 removed outlier: 3.694A pdb=" N LEU A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 643 removed outlier: 3.777A pdb=" N LYS A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.960A pdb=" N ASP A 654 " --> pdb=" O LYS A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 removed outlier: 3.796A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 673 " --> pdb=" O GLY A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 687 Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.523A pdb=" N VAL A 701 " --> pdb=" O TYR A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 782 removed outlier: 3.800A pdb=" N ILE A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 854 removed outlier: 4.099A pdb=" N THR A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 882 removed outlier: 4.137A pdb=" N GLN A 863 " --> pdb=" O MET A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 979 removed outlier: 3.621A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 972 " --> pdb=" O TYR A 968 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 996 removed outlier: 3.572A pdb=" N CYS A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 126 through 132 removed outlier: 6.667A pdb=" N PHE F 126 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA F 141 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG F 128 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 197 through 199 Processing sheet with id=AA3, first strand: chain 'F' and resid 244 through 245 removed outlier: 7.146A pdb=" N ILE F 238 " --> pdb=" O GLU F 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'F' and resid 301 through 304 Processing sheet with id=AA6, first strand: chain 'F' and resid 375 through 380 removed outlier: 6.773A pdb=" N ARG F 376 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE F 387 " --> pdb=" O ARG F 376 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS F 378 " --> pdb=" O VAL F 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AA8, first strand: chain 'E' and resid 42 through 43 removed outlier: 3.861A pdb=" N CYS E 125 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 116 through 120 removed outlier: 6.754A pdb=" N CYS E 63 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU E 158 " --> pdb=" O CYS E 63 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS E 65 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU E 155 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY E 179 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N CYS E 157 " --> pdb=" O GLY E 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 126 removed outlier: 6.948A pdb=" N LYS D 21 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP D 8 " --> pdb=" O TYR D 19 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR D 19 " --> pdb=" O TRP D 8 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU D 10 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE D 17 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR D 140 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE D 31 " --> pdb=" O TYR D 140 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 38 through 43 removed outlier: 6.514A pdb=" N SER D 84 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG D 64 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA D 86 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 62 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET D 88 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ILE D 516 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG D 64 " --> pdb=" O ILE D 516 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL D 518 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 66 " --> pdb=" O VAL D 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 72 through 73 removed outlier: 6.422A pdb=" N LEU D 568 " --> pdb=" O ASP D 616 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP D 616 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY D 570 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 162 through 169 removed outlier: 3.808A pdb=" N ILE D 191 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 166 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER D 184 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N VAL D 237 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR D 201 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N CYS D 239 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE D 203 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AB6, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AB7, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AB8, first strand: chain 'D' and resid 355 through 360 removed outlier: 6.531A pdb=" N LYS D 416 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 408 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL D 418 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 548 through 549 Processing sheet with id=AC1, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.551A pdb=" N PHE D 743 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 126 through 132 removed outlier: 6.667A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AC4, first strand: chain 'C' and resid 244 through 245 removed outlier: 7.146A pdb=" N ILE C 238 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AC7, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.773A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AC9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.862A pdb=" N CYS B 125 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.754A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY B 179 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 157 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.947A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.514A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.422A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 162 through 169 removed outlier: 3.807A pdb=" N ILE A 191 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 166 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AD7, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AD8, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AD9, first strand: chain 'A' and resid 355 through 360 removed outlier: 6.530A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 545 through 549 Processing sheet with id=AE2, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.552A pdb=" N PHE A 743 " --> pdb=" O GLU A 706 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2520 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: 8.57 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7613 1.33 - 1.45: 4227 1.45 - 1.57: 13188 1.57 - 1.69: 4 1.69 - 1.81: 198 Bond restraints: 25230 Sorted by residual: bond pdb=" N PRO D 606 " pdb=" CD PRO D 606 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO A 606 " pdb=" CD PRO A 606 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CA PHE C 215 " pdb=" CB PHE C 215 " ideal model delta sigma weight residual 1.534 1.588 -0.054 1.78e-02 3.16e+03 9.27e+00 bond pdb=" CA PHE F 215 " pdb=" CB PHE F 215 " ideal model delta sigma weight residual 1.534 1.586 -0.052 1.78e-02 3.16e+03 8.66e+00 bond pdb=" CB GLN A 657 " pdb=" CG GLN A 657 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.03e+00 ... (remaining 25225 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.87: 455 105.87 - 114.06: 14431 114.06 - 122.25: 15256 122.25 - 130.44: 3870 130.44 - 138.63: 66 Bond angle restraints: 34078 Sorted by residual: angle pdb=" N LYS A 788 " pdb=" CA LYS A 788 " pdb=" C LYS A 788 " ideal model delta sigma weight residual 108.19 118.25 -10.06 1.29e+00 6.01e-01 6.08e+01 angle pdb=" N LYS D 788 " pdb=" CA LYS D 788 " pdb=" C LYS D 788 " ideal model delta sigma weight residual 108.19 118.24 -10.05 1.29e+00 6.01e-01 6.06e+01 angle pdb=" N ASP B 192 " pdb=" CA ASP B 192 " pdb=" C ASP B 192 " ideal model delta sigma weight residual 107.80 118.69 -10.89 1.73e+00 3.34e-01 3.96e+01 angle pdb=" C ILE B 67 " pdb=" N ASP B 68 " pdb=" CA ASP B 68 " ideal model delta sigma weight residual 122.45 110.01 12.44 2.03e+00 2.43e-01 3.75e+01 angle pdb=" C ILE E 67 " pdb=" N ASP E 68 " pdb=" CA ASP E 68 " ideal model delta sigma weight residual 122.45 110.02 12.43 2.03e+00 2.43e-01 3.75e+01 ... (remaining 34073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 12530 17.63 - 35.26: 1508 35.26 - 52.88: 821 52.88 - 70.51: 405 70.51 - 88.14: 32 Dihedral angle restraints: 15296 sinusoidal: 6298 harmonic: 8998 Sorted by residual: dihedral pdb=" CA PHE D 175 " pdb=" C PHE D 175 " pdb=" N PRO D 176 " pdb=" CA PRO D 176 " ideal model delta harmonic sigma weight residual 180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PHE A 175 " pdb=" C PHE A 175 " pdb=" N PRO A 176 " pdb=" CA PRO A 176 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG A 823 " pdb=" C ARG A 823 " pdb=" N ILE A 824 " pdb=" CA ILE A 824 " ideal model delta harmonic sigma weight residual 180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 15293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2857 0.065 - 0.129: 820 0.129 - 0.194: 99 0.194 - 0.258: 17 0.258 - 0.323: 3 Chirality restraints: 3796 Sorted by residual: chirality pdb=" CA ILE D 547 " pdb=" N ILE D 547 " pdb=" C ILE D 547 " pdb=" CB ILE D 547 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE E 198 " pdb=" CA ILE E 198 " pdb=" CG1 ILE E 198 " pdb=" CG2 ILE E 198 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 198 " pdb=" CA ILE B 198 " pdb=" CG1 ILE B 198 " pdb=" CG2 ILE B 198 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3793 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 688 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C THR D 688 " 0.075 2.00e-02 2.50e+03 pdb=" O THR D 688 " -0.028 2.00e-02 2.50e+03 pdb=" N SER D 689 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 688 " 0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C THR A 688 " -0.074 2.00e-02 2.50e+03 pdb=" O THR A 688 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 689 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 215 " 0.017 2.00e-02 2.50e+03 1.93e-02 6.53e+00 pdb=" CG PHE C 215 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 215 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 215 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 215 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 215 " 0.001 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 401 2.55 - 3.13: 20391 3.13 - 3.72: 36900 3.72 - 4.31: 51822 4.31 - 4.90: 83823 Nonbonded interactions: 193337 Sorted by model distance: nonbonded pdb=" O ASN A 716 " pdb=" OG1 THR A 717 " model vdw 1.958 2.440 nonbonded pdb=" N GLU C 109 " pdb=" OE1 GLU C 109 " model vdw 2.023 2.520 nonbonded pdb=" N GLU F 109 " pdb=" OE1 GLU F 109 " model vdw 2.026 2.520 nonbonded pdb=" O ASN D 544 " pdb=" ND2 ASN D 544 " model vdw 2.117 2.520 nonbonded pdb=" O ASN A 544 " pdb=" ND2 ASN A 544 " model vdw 2.117 2.520 ... (remaining 193332 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.460 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 64.010 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4135 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 : 0.010 0.085 25230 Z= 0.617 Angle : 1.148 13.629 34078 Z= 0.654 Chirality : 0.059 0.323 3796 Planarity : 0.006 0.057 4332 Dihedral : 21.958 88.137 9476 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 1.77 % Allowed : 11.66 % Favored : 86.58 % Rotamer: Outliers : 25.98 % Allowed : 16.15 % Favored : 57.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.55 % 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: -4.60 (0.12), residues: 3002 helix: -3.13 (0.11), residues: 1064 sheet: -2.45 (0.20), residues: 566 loop : -3.19 (0.14), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 470 HIS 0.008 0.002 HIS D 461 PHE 0.045 0.003 PHE C 215 TYR 0.028 0.003 TYR A 140 ARG 0.029 0.002 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 727 poor density : 494 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 150 ASN cc_start: 0.6897 (OUTLIER) cc_final: 0.6657 (p0) REVERT: F 234 ILE cc_start: 0.6822 (pt) cc_final: 0.6440 (mm) REVERT: F 279 ASP cc_start: -0.1371 (OUTLIER) cc_final: -0.1616 (p0) REVERT: F 294 ILE cc_start: 0.4723 (mm) cc_final: 0.3359 (mm) REVERT: F 373 ASN cc_start: 0.6887 (m-40) cc_final: 0.6669 (m110) REVERT: F 380 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: E 1 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.3156 (tpp) REVERT: E 50 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4817 (m-80) REVERT: E 88 SER cc_start: 0.4430 (OUTLIER) cc_final: 0.4068 (p) REVERT: E 109 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6544 (p0) REVERT: E 148 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7185 (tt) REVERT: E 167 ARG cc_start: 0.6776 (tpt170) cc_final: 0.6530 (mmm160) REVERT: D 177 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7405 (t) REVERT: D 271 TYR cc_start: 0.4228 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: D 492 MET cc_start: 0.7975 (mmt) cc_final: 0.7490 (mmt) REVERT: D 522 THR cc_start: 0.4840 (OUTLIER) cc_final: 0.4610 (p) REVERT: D 528 TYR cc_start: 0.2872 (OUTLIER) cc_final: 0.0506 (p90) REVERT: D 544 ASN cc_start: 0.4183 (OUTLIER) cc_final: 0.3101 (m-40) REVERT: D 558 CYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6603 (t) REVERT: D 656 MET cc_start: 0.8562 (mmm) cc_final: 0.8254 (mmt) REVERT: D 765 ASP cc_start: 0.4675 (OUTLIER) cc_final: 0.4466 (t0) REVERT: D 828 THR cc_start: 0.6774 (OUTLIER) cc_final: 0.6553 (m) REVERT: D 853 MET cc_start: 0.3503 (OUTLIER) cc_final: 0.3094 (tpp) REVERT: D 858 ARG cc_start: -0.0434 (OUTLIER) cc_final: -0.2692 (ptp90) REVERT: C 33 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7997 (p) REVERT: C 202 LEU cc_start: -0.0749 (OUTLIER) cc_final: -0.2180 (tt) REVERT: C 330 THR cc_start: 0.5935 (OUTLIER) cc_final: 0.5268 (m) REVERT: C 339 ASN cc_start: 0.6954 (t0) cc_final: 0.6595 (m-40) REVERT: B 1 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.3853 (mmt) REVERT: B 90 LYS cc_start: -0.1836 (OUTLIER) cc_final: -0.3195 (tttm) REVERT: B 178 VAL cc_start: -0.0413 (OUTLIER) cc_final: -0.0651 (p) REVERT: A 15 ASN cc_start: 0.1285 (OUTLIER) cc_final: 0.0954 (p0) REVERT: A 63 MET cc_start: -0.1508 (mtt) cc_final: -0.1881 (ttm) REVERT: A 142 CYS cc_start: 0.1883 (OUTLIER) cc_final: 0.1452 (t) REVERT: A 189 CYS cc_start: -0.1480 (OUTLIER) cc_final: -0.2204 (t) REVERT: A 191 ILE cc_start: -0.1742 (mt) cc_final: -0.2082 (mp) REVERT: A 219 ARG cc_start: -0.1345 (OUTLIER) cc_final: -0.4214 (ttp80) REVERT: A 223 ARG cc_start: -0.0074 (OUTLIER) cc_final: -0.0385 (mtt90) REVERT: A 368 MET cc_start: 0.0496 (mtp) cc_final: 0.0039 (mmt) REVERT: A 428 ILE cc_start: 0.0285 (OUTLIER) cc_final: 0.0008 (mp) REVERT: A 488 LEU cc_start: 0.3277 (OUTLIER) cc_final: 0.2706 (tp) REVERT: A 655 SER cc_start: -0.1507 (OUTLIER) cc_final: -0.2415 (t) REVERT: A 758 GLU cc_start: -0.2961 (OUTLIER) cc_final: -0.4045 (pt0) REVERT: A 799 ILE cc_start: 0.5362 (OUTLIER) cc_final: 0.4838 (mt) REVERT: A 819 SER cc_start: -0.0834 (OUTLIER) cc_final: -0.1497 (p) REVERT: A 837 LYS cc_start: -0.3887 (OUTLIER) cc_final: -0.4724 (mptt) REVERT: A 842 MET cc_start: 0.1359 (mmp) cc_final: 0.1073 (tpt) REVERT: A 847 LYS cc_start: -0.1304 (OUTLIER) cc_final: -0.2158 (tptt) REVERT: A 873 GLU cc_start: -0.1757 (OUTLIER) cc_final: -0.2344 (mt-10) REVERT: A 966 ILE cc_start: 0.3904 (OUTLIER) cc_final: 0.3611 (pt) REVERT: A 996 MET cc_start: -0.2381 (tpt) cc_final: -0.2623 (tpt) outliers start: 727 outliers final: 103 residues processed: 1089 average time/residue: 0.3894 time to fit residues: 649.7673 Evaluate side-chains 424 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 282 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 526 PHE Chi-restraints excluded: chain D residue 528 TYR Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 686 SER Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 819 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 855 SER Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 147 ASN ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 225 GLN D 274 ASN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN D 585 GLN D 600 HIS D 797 ASN D 937 ASN C 146 GLN C 208 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS A 147 ASN A 211 GLN A 336 GLN A 413 ASN A 720 ASN A 797 ASN A 816 ASN A 937 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4443 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25230 Z= 0.257 Angle : 0.806 12.730 34078 Z= 0.421 Chirality : 0.049 0.261 3796 Planarity : 0.006 0.147 4332 Dihedral : 11.344 102.667 3621 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.89 % Favored : 91.44 % Rotamer: Outliers : 8.68 % Allowed : 24.34 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.14), residues: 3002 helix: -1.56 (0.14), residues: 1080 sheet: -1.45 (0.22), residues: 522 loop : -2.77 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 470 HIS 0.007 0.001 HIS C 252 PHE 0.024 0.002 PHE D 756 TYR 0.026 0.002 TYR A 681 ARG 0.023 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 291 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.2413 (tpp) cc_final: 0.1988 (tpp) REVERT: F 294 ILE cc_start: 0.6062 (mm) cc_final: 0.5704 (mm) REVERT: F 380 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: E 88 SER cc_start: 0.4703 (OUTLIER) cc_final: 0.4458 (p) REVERT: E 109 ASN cc_start: 0.7103 (OUTLIER) cc_final: 0.6738 (p0) REVERT: E 142 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6909 (mmmt) REVERT: E 167 ARG cc_start: 0.6710 (tpt170) cc_final: 0.6282 (mmm160) REVERT: D 271 TYR cc_start: 0.4205 (OUTLIER) cc_final: 0.3298 (m-80) REVERT: D 492 MET cc_start: 0.7839 (mmt) cc_final: 0.7596 (mmt) REVERT: D 656 MET cc_start: 0.8314 (mmm) cc_final: 0.8043 (mmt) REVERT: D 828 THR cc_start: 0.6705 (OUTLIER) cc_final: 0.6446 (m) REVERT: D 858 ARG cc_start: -0.1087 (OUTLIER) cc_final: -0.2322 (ptp90) REVERT: D 932 TYR cc_start: 0.4666 (OUTLIER) cc_final: 0.3933 (m-80) REVERT: C 122 ASN cc_start: 0.4223 (m-40) cc_final: 0.3838 (p0) REVERT: C 183 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6842 (pp) REVERT: C 339 ASN cc_start: 0.6762 (t0) cc_final: 0.6452 (m-40) REVERT: C 422 LYS cc_start: 0.2950 (OUTLIER) cc_final: 0.2705 (ttmt) REVERT: B 1 MET cc_start: 0.5562 (mmp) cc_final: 0.5348 (tpp) REVERT: B 23 MET cc_start: 0.3371 (ppp) cc_final: 0.3028 (ptp) REVERT: A 63 MET cc_start: -0.0597 (mtt) cc_final: -0.0875 (mtt) REVERT: A 158 ILE cc_start: -0.5050 (OUTLIER) cc_final: -0.5289 (mm) REVERT: A 189 CYS cc_start: -0.0739 (OUTLIER) cc_final: -0.1170 (t) REVERT: A 219 ARG cc_start: -0.0782 (OUTLIER) cc_final: -0.4257 (ttp80) REVERT: A 223 ARG cc_start: 0.1068 (OUTLIER) cc_final: -0.0610 (mmt90) REVERT: A 228 MET cc_start: 0.3575 (pmm) cc_final: 0.3292 (pmm) REVERT: A 416 LYS cc_start: -0.0596 (OUTLIER) cc_final: -0.1392 (tptp) REVERT: A 428 ILE cc_start: 0.0605 (OUTLIER) cc_final: 0.0391 (mp) REVERT: A 511 LEU cc_start: 0.1352 (OUTLIER) cc_final: 0.1015 (mm) REVERT: A 640 MET cc_start: 0.0718 (ptm) cc_final: 0.0418 (ptp) REVERT: A 809 MET cc_start: 0.2930 (OUTLIER) cc_final: 0.2624 (mtp) REVERT: A 811 TYR cc_start: -0.0037 (OUTLIER) cc_final: -0.1996 (m-80) REVERT: A 819 SER cc_start: -0.0334 (OUTLIER) cc_final: -0.0988 (p) REVERT: A 837 LYS cc_start: -0.4845 (OUTLIER) cc_final: -0.5854 (mttt) REVERT: A 842 MET cc_start: 0.1827 (mmp) cc_final: 0.0607 (tpt) REVERT: A 859 MET cc_start: 0.7114 (tpp) cc_final: 0.6105 (tmm) outliers start: 243 outliers final: 131 residues processed: 502 average time/residue: 0.3651 time to fit residues: 292.8165 Evaluate side-chains 375 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 224 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 736 SER Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 855 SER Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 970 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 226 optimal weight: 30.0000 chunk 185 optimal weight: 0.8980 chunk 75 optimal weight: 0.0470 chunk 272 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 218 optimal weight: 0.0010 overall best weight: 1.5886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 146 GLN ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN D 141 HIS ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 274 ASN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN D 985 ASN ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 HIS A 336 GLN A 448 ASN A 963 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4538 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25230 Z= 0.209 Angle : 0.693 10.508 34078 Z= 0.363 Chirality : 0.047 0.244 3796 Planarity : 0.005 0.056 4332 Dihedral : 9.122 97.546 3468 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.13 % Favored : 91.21 % Rotamer: Outliers : 6.93 % Allowed : 25.13 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -2.58 (0.14), residues: 3002 helix: -0.98 (0.15), residues: 1074 sheet: -1.08 (0.23), residues: 504 loop : -2.55 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 470 HIS 0.015 0.001 HIS D 141 PHE 0.021 0.002 PHE F 152 TYR 0.018 0.002 TYR C 181 ARG 0.008 0.001 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 247 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 294 ILE cc_start: 0.5965 (mm) cc_final: 0.5661 (mm) REVERT: E 109 ASN cc_start: 0.6866 (OUTLIER) cc_final: 0.6307 (p0) REVERT: E 142 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6680 (mmmt) REVERT: D 656 MET cc_start: 0.8189 (mmm) cc_final: 0.7331 (mmt) REVERT: D 828 THR cc_start: 0.7024 (OUTLIER) cc_final: 0.5926 (m) REVERT: D 858 ARG cc_start: -0.1113 (OUTLIER) cc_final: -0.2600 (ptp90) REVERT: D 891 MET cc_start: 0.4371 (mpp) cc_final: 0.4039 (mpp) REVERT: D 932 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.4208 (m-80) REVERT: C 1 MET cc_start: 0.4038 (tmm) cc_final: 0.3755 (mmm) REVERT: C 122 ASN cc_start: 0.4138 (m-40) cc_final: 0.3845 (p0) REVERT: C 177 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5847 (m-30) REVERT: C 183 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6708 (pp) REVERT: C 339 ASN cc_start: 0.6516 (t0) cc_final: 0.6196 (m-40) REVERT: C 376 ARG cc_start: 0.2434 (mmt180) cc_final: 0.1649 (tpt170) REVERT: B 23 MET cc_start: 0.3380 (ppp) cc_final: 0.3122 (ptp) REVERT: A 158 ILE cc_start: -0.4868 (OUTLIER) cc_final: -0.5432 (pt) REVERT: A 223 ARG cc_start: 0.0965 (OUTLIER) cc_final: -0.0734 (mmt90) REVERT: A 230 MET cc_start: -0.0822 (ttp) cc_final: -0.1331 (ttm) REVERT: A 640 MET cc_start: 0.0411 (ptm) cc_final: 0.0183 (ptp) REVERT: A 811 TYR cc_start: -0.0299 (OUTLIER) cc_final: -0.2052 (m-80) REVERT: A 837 LYS cc_start: -0.5107 (OUTLIER) cc_final: -0.6166 (mttt) REVERT: A 842 MET cc_start: 0.1591 (mmp) cc_final: 0.0414 (tpt) REVERT: A 859 MET cc_start: 0.7161 (tpp) cc_final: 0.6267 (tmm) REVERT: A 892 LEU cc_start: 0.0285 (OUTLIER) cc_final: -0.0100 (tt) outliers start: 194 outliers final: 109 residues processed: 412 average time/residue: 0.3448 time to fit residues: 227.0310 Evaluate side-chains 344 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 224 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 736 SER Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 963 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.5980 chunk 205 optimal weight: 0.0970 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 289 optimal weight: 50.0000 chunk 143 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 ASN F 146 GLN ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4588 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25230 Z= 0.197 Angle : 0.658 10.516 34078 Z= 0.345 Chirality : 0.045 0.233 3796 Planarity : 0.004 0.052 4332 Dihedral : 7.662 61.734 3417 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.03 % Favored : 91.44 % Rotamer: Outliers : 6.18 % Allowed : 25.77 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -2.30 (0.14), residues: 3002 helix: -0.70 (0.15), residues: 1072 sheet: -1.10 (0.22), residues: 528 loop : -2.36 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 19 HIS 0.006 0.001 HIS C 252 PHE 0.023 0.002 PHE F 152 TYR 0.044 0.002 TYR E 15 ARG 0.009 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 239 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 TRP cc_start: 0.4291 (t-100) cc_final: 0.4057 (t-100) REVERT: F 294 ILE cc_start: 0.6041 (mm) cc_final: 0.5758 (mm) REVERT: E 109 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6454 (p0) REVERT: E 142 LYS cc_start: 0.7064 (mmmt) cc_final: 0.6790 (mmmt) REVERT: D 299 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6876 (mm) REVERT: D 492 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7413 (mtt) REVERT: D 656 MET cc_start: 0.8090 (mmm) cc_final: 0.7202 (mmt) REVERT: D 828 THR cc_start: 0.6257 (OUTLIER) cc_final: 0.5800 (m) REVERT: D 842 MET cc_start: 0.7124 (tpp) cc_final: 0.6698 (tpt) REVERT: D 858 ARG cc_start: -0.1345 (OUTLIER) cc_final: -0.3129 (ptp90) REVERT: D 932 TYR cc_start: 0.4961 (OUTLIER) cc_final: 0.4390 (m-80) REVERT: C 177 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: C 183 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6700 (pp) REVERT: C 255 ARG cc_start: 0.5458 (OUTLIER) cc_final: 0.4297 (ptm-80) REVERT: C 376 ARG cc_start: 0.2561 (mmt180) cc_final: 0.1729 (tpt170) REVERT: B 23 MET cc_start: 0.3548 (ppp) cc_final: 0.2975 (ptp) REVERT: A 158 ILE cc_start: -0.4741 (OUTLIER) cc_final: -0.5305 (pt) REVERT: A 207 MET cc_start: -0.2213 (ttt) cc_final: -0.2457 (ttt) REVERT: A 223 ARG cc_start: 0.1065 (OUTLIER) cc_final: -0.0798 (mmt90) REVERT: A 230 MET cc_start: -0.0751 (ttp) cc_final: -0.1242 (ttm) REVERT: A 842 MET cc_start: 0.1150 (mmp) cc_final: 0.0275 (tpt) REVERT: A 859 MET cc_start: 0.7132 (tpp) cc_final: 0.6331 (tmm) REVERT: A 892 LEU cc_start: 0.0144 (OUTLIER) cc_final: -0.0179 (tt) REVERT: A 996 MET cc_start: -0.2628 (tpt) cc_final: -0.2913 (ttm) outliers start: 173 outliers final: 115 residues processed: 393 average time/residue: 0.3559 time to fit residues: 223.3739 Evaluate side-chains 341 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 214 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 381 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 736 SER Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.0270 chunk 164 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 247 optimal weight: 0.0370 chunk 200 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 148 optimal weight: 6.9990 chunk 260 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 146 GLN ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4583 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25230 Z= 0.165 Angle : 0.634 11.912 34078 Z= 0.330 Chirality : 0.045 0.255 3796 Planarity : 0.004 0.048 4332 Dihedral : 7.134 61.901 3408 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.50 % Favored : 92.01 % Rotamer: Outliers : 6.15 % Allowed : 26.20 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -2.00 (0.15), residues: 3002 helix: -0.43 (0.15), residues: 1072 sheet: -0.80 (0.23), residues: 486 loop : -2.23 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 470 HIS 0.005 0.001 HIS C 252 PHE 0.022 0.002 PHE F 152 TYR 0.019 0.001 TYR E 15 ARG 0.009 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 229 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.1859 (tpp) cc_final: -0.0988 (tmm) REVERT: F 43 TRP cc_start: 0.4393 (t-100) cc_final: 0.4170 (t-100) REVERT: F 129 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5574 (m-80) REVERT: F 373 ASN cc_start: 0.7008 (m-40) cc_final: 0.6654 (m110) REVERT: E 177 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6510 (mp) REVERT: D 299 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6833 (mm) REVERT: D 492 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7489 (mtt) REVERT: D 611 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6031 (tt0) REVERT: D 656 MET cc_start: 0.8013 (mmm) cc_final: 0.7143 (mmt) REVERT: D 828 THR cc_start: 0.6220 (OUTLIER) cc_final: 0.5820 (m) REVERT: D 842 MET cc_start: 0.7111 (tpp) cc_final: 0.6707 (tpt) REVERT: D 858 ARG cc_start: -0.1315 (OUTLIER) cc_final: -0.3156 (ptp90) REVERT: D 932 TYR cc_start: 0.4997 (OUTLIER) cc_final: 0.4458 (m-80) REVERT: C 177 ASP cc_start: 0.6579 (OUTLIER) cc_final: 0.6216 (m-30) REVERT: C 183 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6860 (tp) REVERT: C 376 ARG cc_start: 0.2680 (mmt180) cc_final: 0.1745 (tpt170) REVERT: B 23 MET cc_start: 0.4208 (ppp) cc_final: 0.3373 (ptp) REVERT: A 88 MET cc_start: 0.4159 (OUTLIER) cc_final: 0.0213 (mmt) REVERT: A 158 ILE cc_start: -0.4769 (OUTLIER) cc_final: -0.5216 (pt) REVERT: A 207 MET cc_start: -0.2344 (ttt) cc_final: -0.2892 (ttt) REVERT: A 223 ARG cc_start: 0.1015 (OUTLIER) cc_final: -0.0688 (mmt90) REVERT: A 230 MET cc_start: -0.0778 (ttp) cc_final: -0.1293 (ttm) REVERT: A 842 MET cc_start: 0.1155 (mmp) cc_final: 0.0313 (tpt) REVERT: A 859 MET cc_start: 0.7062 (tpp) cc_final: 0.6474 (tmm) REVERT: A 891 MET cc_start: 0.2499 (mtt) cc_final: 0.0935 (ptt) outliers start: 172 outliers final: 112 residues processed: 376 average time/residue: 0.3641 time to fit residues: 213.6705 Evaluate side-chains 334 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 209 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 736 SER Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN A 204 ASN A 985 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4679 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25230 Z= 0.212 Angle : 0.655 9.820 34078 Z= 0.343 Chirality : 0.046 0.396 3796 Planarity : 0.004 0.046 4332 Dihedral : 6.730 59.845 3387 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.66 % Favored : 91.84 % Rotamer: Outliers : 5.83 % Allowed : 26.09 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 3002 helix: -0.38 (0.15), residues: 1072 sheet: -0.89 (0.23), residues: 484 loop : -2.19 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 470 HIS 0.006 0.001 HIS D 170 PHE 0.027 0.002 PHE C 410 TYR 0.017 0.002 TYR F 181 ARG 0.008 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 221 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.1809 (tpp) cc_final: -0.1115 (tmm) REVERT: F 43 TRP cc_start: 0.4523 (t-100) cc_final: 0.4287 (t-100) REVERT: F 106 ILE cc_start: -0.1740 (OUTLIER) cc_final: -0.2062 (tp) REVERT: F 129 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5615 (m-80) REVERT: F 306 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6699 (mtmm) REVERT: F 373 ASN cc_start: 0.7074 (m-40) cc_final: 0.6697 (m110) REVERT: E 177 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6619 (mp) REVERT: D 492 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7502 (mtt) REVERT: D 605 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7134 (tt) REVERT: D 611 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6278 (tt0) REVERT: D 656 MET cc_start: 0.8162 (mmm) cc_final: 0.7283 (mmt) REVERT: D 828 THR cc_start: 0.6375 (OUTLIER) cc_final: 0.5927 (m) REVERT: D 842 MET cc_start: 0.7313 (tpp) cc_final: 0.7050 (tpt) REVERT: D 858 ARG cc_start: -0.1539 (OUTLIER) cc_final: -0.3612 (ptp-110) REVERT: C 177 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6041 (m-30) REVERT: C 376 ARG cc_start: 0.3209 (mmt180) cc_final: 0.1930 (tpt170) REVERT: B 23 MET cc_start: 0.4604 (ppp) cc_final: 0.3191 (ptp) REVERT: A 158 ILE cc_start: -0.4987 (OUTLIER) cc_final: -0.5334 (pt) REVERT: A 180 ILE cc_start: -0.0891 (OUTLIER) cc_final: -0.1206 (mm) REVERT: A 207 MET cc_start: -0.2140 (ttt) cc_final: -0.2605 (ttt) REVERT: A 223 ARG cc_start: 0.1271 (OUTLIER) cc_final: -0.0592 (mmt90) REVERT: A 230 MET cc_start: -0.0935 (ttp) cc_final: -0.1641 (ttm) REVERT: A 842 MET cc_start: 0.1104 (mmp) cc_final: 0.0314 (tpt) REVERT: A 859 MET cc_start: 0.7076 (tpp) cc_final: 0.6538 (tmm) REVERT: A 891 MET cc_start: 0.2444 (mtt) cc_final: 0.1421 (ptp) REVERT: A 996 MET cc_start: -0.1121 (ttm) cc_final: -0.2457 (mmt) outliers start: 163 outliers final: 120 residues processed: 362 average time/residue: 0.3727 time to fit residues: 210.5971 Evaluate side-chains 333 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 200 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 306 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 381 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 736 SER Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 289 optimal weight: 30.0000 chunk 180 optimal weight: 1.9990 chunk 176 optimal weight: 30.0000 chunk 133 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 146 GLN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4812 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25230 Z= 0.279 Angle : 0.711 9.563 34078 Z= 0.375 Chirality : 0.047 0.279 3796 Planarity : 0.005 0.046 4332 Dihedral : 6.658 59.429 3381 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.63 % Favored : 90.87 % Rotamer: Outliers : 5.86 % Allowed : 26.88 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -2.06 (0.15), residues: 3002 helix: -0.50 (0.15), residues: 1080 sheet: -0.84 (0.24), residues: 490 loop : -2.26 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 470 HIS 0.007 0.002 HIS E 181 PHE 0.034 0.002 PHE D 787 TYR 0.051 0.002 TYR E 15 ARG 0.011 0.001 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 211 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.1927 (tpp) cc_final: -0.1079 (tmm) REVERT: F 43 TRP cc_start: 0.5017 (t-100) cc_final: 0.4770 (t-100) REVERT: F 106 ILE cc_start: -0.1331 (OUTLIER) cc_final: -0.1675 (tp) REVERT: F 129 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: F 373 ASN cc_start: 0.7365 (m-40) cc_final: 0.7151 (m-40) REVERT: E 177 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6845 (mp) REVERT: D 110 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7741 (tp) REVERT: D 492 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7588 (mtt) REVERT: D 605 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7295 (tt) REVERT: D 611 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6210 (tt0) REVERT: D 656 MET cc_start: 0.8245 (mmm) cc_final: 0.7276 (mmt) REVERT: D 828 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.5952 (m) REVERT: D 842 MET cc_start: 0.7339 (tpp) cc_final: 0.6777 (tpt) REVERT: D 858 ARG cc_start: -0.1241 (OUTLIER) cc_final: -0.3796 (ptp-110) REVERT: C 1 MET cc_start: 0.5581 (tmm) cc_final: 0.5065 (tmm) REVERT: C 25 SER cc_start: 0.5993 (t) cc_final: 0.5668 (p) REVERT: C 255 ARG cc_start: 0.5575 (OUTLIER) cc_final: 0.4633 (ptm-80) REVERT: C 376 ARG cc_start: 0.2897 (mmt180) cc_final: 0.1782 (tpt170) REVERT: B 23 MET cc_start: 0.4837 (ppp) cc_final: 0.3412 (ptp) REVERT: A 180 ILE cc_start: -0.0940 (OUTLIER) cc_final: -0.1291 (mm) REVERT: A 207 MET cc_start: -0.1999 (ttt) cc_final: -0.2702 (ttt) REVERT: A 223 ARG cc_start: 0.1821 (OUTLIER) cc_final: -0.0583 (mmt90) REVERT: A 230 MET cc_start: -0.0759 (ttp) cc_final: -0.1625 (ttm) REVERT: A 640 MET cc_start: -0.0970 (ptt) cc_final: -0.2082 (ppp) REVERT: A 842 MET cc_start: 0.0892 (mmp) cc_final: 0.0135 (tpt) REVERT: A 859 MET cc_start: 0.7010 (tpp) cc_final: 0.6624 (tmm) REVERT: A 996 MET cc_start: -0.0956 (ttm) cc_final: -0.2600 (mmt) outliers start: 164 outliers final: 126 residues processed: 357 average time/residue: 0.3793 time to fit residues: 212.7012 Evaluate side-chains 330 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 192 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 381 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 736 SER Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 815 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 963 ASN Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 263 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 HIS ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4744 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25230 Z= 0.177 Angle : 0.646 9.636 34078 Z= 0.337 Chirality : 0.045 0.240 3796 Planarity : 0.004 0.083 4332 Dihedral : 6.362 59.362 3378 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.10 % Favored : 92.44 % Rotamer: Outliers : 5.22 % Allowed : 27.98 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 3002 helix: -0.17 (0.16), residues: 1068 sheet: -0.67 (0.24), residues: 480 loop : -2.16 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 470 HIS 0.004 0.001 HIS D 170 PHE 0.024 0.002 PHE F 152 TYR 0.020 0.001 TYR F 199 ARG 0.012 0.000 ARG F 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 215 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.2076 (tpp) cc_final: -0.0981 (tmm) REVERT: F 106 ILE cc_start: -0.1370 (OUTLIER) cc_final: -0.1580 (tp) REVERT: D 251 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7621 (tt) REVERT: D 368 MET cc_start: 0.5980 (mpp) cc_final: 0.5449 (mtm) REVERT: D 486 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7967 (m-10) REVERT: D 492 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7518 (mtt) REVERT: D 605 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7090 (tt) REVERT: D 611 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: D 656 MET cc_start: 0.8154 (mmm) cc_final: 0.7188 (mmt) REVERT: D 828 THR cc_start: 0.6564 (OUTLIER) cc_final: 0.6057 (m) REVERT: D 842 MET cc_start: 0.7226 (tpp) cc_final: 0.6981 (tpt) REVERT: D 858 ARG cc_start: -0.1251 (OUTLIER) cc_final: -0.3923 (ptp-110) REVERT: D 891 MET cc_start: 0.3263 (OUTLIER) cc_final: 0.3013 (tpp) REVERT: C 1 MET cc_start: 0.5702 (tmm) cc_final: 0.5349 (tmm) REVERT: C 25 SER cc_start: 0.5861 (t) cc_final: 0.5570 (p) REVERT: C 177 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.6012 (m-30) REVERT: C 376 ARG cc_start: 0.2906 (mmt180) cc_final: 0.1668 (tpt170) REVERT: B 23 MET cc_start: 0.4904 (ppp) cc_final: 0.3450 (ptp) REVERT: A 180 ILE cc_start: -0.1081 (OUTLIER) cc_final: -0.1402 (mm) REVERT: A 207 MET cc_start: -0.2057 (ttt) cc_final: -0.2730 (ttt) REVERT: A 223 ARG cc_start: 0.2033 (OUTLIER) cc_final: -0.0430 (mmt90) REVERT: A 230 MET cc_start: -0.0762 (ttp) cc_final: -0.1593 (ttm) REVERT: A 533 VAL cc_start: 0.1492 (t) cc_final: 0.1070 (t) REVERT: A 640 MET cc_start: -0.0629 (OUTLIER) cc_final: -0.1543 (ppp) REVERT: A 842 MET cc_start: 0.0808 (mmp) cc_final: 0.0110 (tpt) REVERT: A 996 MET cc_start: -0.0510 (ttm) cc_final: -0.2080 (mmt) outliers start: 146 outliers final: 117 residues processed: 343 average time/residue: 0.3537 time to fit residues: 192.8029 Evaluate side-chains 320 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 190 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 815 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 891 MET Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 963 ASN Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 chunk 276 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 274 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4756 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25230 Z= 0.182 Angle : 0.649 11.963 34078 Z= 0.335 Chirality : 0.045 0.206 3796 Planarity : 0.004 0.045 4332 Dihedral : 6.100 58.905 3376 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.83 % Favored : 91.71 % Rotamer: Outliers : 5.25 % Allowed : 27.98 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3002 helix: -0.06 (0.16), residues: 1072 sheet: -0.56 (0.24), residues: 480 loop : -2.08 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 470 HIS 0.005 0.001 HIS D 185 PHE 0.023 0.002 PHE F 152 TYR 0.023 0.001 TYR E 15 ARG 0.008 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 210 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.2298 (tpp) cc_final: -0.0924 (tmm) REVERT: F 106 ILE cc_start: -0.1072 (OUTLIER) cc_final: -0.1319 (tp) REVERT: E 23 MET cc_start: 0.5245 (tpt) cc_final: 0.4986 (mmm) REVERT: D 251 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7709 (tt) REVERT: D 283 LYS cc_start: 0.3873 (OUTLIER) cc_final: 0.3309 (mttp) REVERT: D 303 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7730 (p0) REVERT: D 486 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: D 492 MET cc_start: 0.7789 (mmt) cc_final: 0.7491 (mtt) REVERT: D 605 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6931 (tt) REVERT: D 611 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6110 (tt0) REVERT: D 656 MET cc_start: 0.8192 (mmm) cc_final: 0.7850 (mmt) REVERT: D 716 ASN cc_start: 0.5988 (OUTLIER) cc_final: 0.5512 (p0) REVERT: D 800 MET cc_start: 0.4901 (tpt) cc_final: 0.4499 (tpt) REVERT: D 828 THR cc_start: 0.6469 (OUTLIER) cc_final: 0.5974 (m) REVERT: D 842 MET cc_start: 0.7196 (tpp) cc_final: 0.6959 (tpt) REVERT: D 858 ARG cc_start: -0.1284 (OUTLIER) cc_final: -0.3916 (ptp-110) REVERT: C 1 MET cc_start: 0.5751 (tmm) cc_final: 0.5388 (tmm) REVERT: C 25 SER cc_start: 0.6122 (t) cc_final: 0.5815 (p) REVERT: C 255 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.4463 (ptm-80) REVERT: C 376 ARG cc_start: 0.2709 (mmt180) cc_final: 0.1801 (tpt170) REVERT: B 23 MET cc_start: 0.5271 (ppp) cc_final: 0.3415 (ptp) REVERT: A 180 ILE cc_start: -0.1022 (OUTLIER) cc_final: -0.1322 (mm) REVERT: A 207 MET cc_start: -0.1914 (ttt) cc_final: -0.2879 (ttt) REVERT: A 230 MET cc_start: -0.0779 (ttp) cc_final: -0.1581 (ttm) REVERT: A 533 VAL cc_start: 0.1682 (t) cc_final: 0.1231 (t) REVERT: A 640 MET cc_start: -0.0944 (OUTLIER) cc_final: -0.2334 (ppp) REVERT: A 842 MET cc_start: 0.0915 (mmp) cc_final: 0.0236 (tpt) REVERT: A 859 MET cc_start: 0.6482 (tmm) cc_final: 0.6114 (tmm) REVERT: A 996 MET cc_start: -0.0292 (ttm) cc_final: -0.1892 (mmt) outliers start: 147 outliers final: 116 residues processed: 340 average time/residue: 0.3592 time to fit residues: 193.8297 Evaluate side-chains 324 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 195 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 381 ASN Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 815 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 963 ASN Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 470 TRP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 20.0000 chunk 284 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 298 optimal weight: 0.0970 chunk 275 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 overall best weight: 2.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 231 ASN ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS A 75 ASN A 170 HIS A 274 ASN A 304 GLN A 413 ASN ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4851 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25230 Z= 0.257 Angle : 0.718 14.328 34078 Z= 0.375 Chirality : 0.047 0.235 3796 Planarity : 0.005 0.060 4332 Dihedral : 6.211 59.056 3371 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.63 % Favored : 90.91 % Rotamer: Outliers : 5.18 % Allowed : 28.45 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 3002 helix: -0.41 (0.15), residues: 1084 sheet: -0.59 (0.25), residues: 476 loop : -2.18 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 470 HIS 0.006 0.001 HIS D 185 PHE 0.026 0.002 PHE F 152 TYR 0.035 0.002 TYR B 121 ARG 0.010 0.001 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 202 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.2145 (tpp) cc_final: -0.1128 (tmm) REVERT: F 106 ILE cc_start: -0.0979 (OUTLIER) cc_final: -0.1238 (tp) REVERT: F 284 GLU cc_start: 0.4275 (OUTLIER) cc_final: 0.1483 (mt-10) REVERT: E 177 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7644 (mp) REVERT: D 492 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7583 (mtt) REVERT: D 605 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7092 (tt) REVERT: D 611 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6124 (mt-10) REVERT: D 716 ASN cc_start: 0.6249 (OUTLIER) cc_final: 0.5676 (p0) REVERT: D 828 THR cc_start: 0.6413 (OUTLIER) cc_final: 0.6145 (p) REVERT: D 842 MET cc_start: 0.7446 (tpp) cc_final: 0.6949 (tpt) REVERT: D 853 MET cc_start: 0.5154 (ptp) cc_final: 0.4870 (tpp) REVERT: D 858 ARG cc_start: -0.0714 (OUTLIER) cc_final: -0.3703 (ptp-110) REVERT: D 960 LEU cc_start: 0.1202 (OUTLIER) cc_final: 0.0957 (pp) REVERT: C 1 MET cc_start: 0.5899 (tmm) cc_final: 0.5523 (tmm) REVERT: C 25 SER cc_start: 0.6697 (t) cc_final: 0.6393 (p) REVERT: C 255 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.4561 (ptm-80) REVERT: C 376 ARG cc_start: 0.2718 (mmt180) cc_final: 0.1474 (tpt170) REVERT: C 414 PHE cc_start: 0.4333 (OUTLIER) cc_final: 0.3839 (m-80) REVERT: B 23 MET cc_start: 0.5343 (ppp) cc_final: 0.3416 (ptp) REVERT: A 180 ILE cc_start: -0.1271 (OUTLIER) cc_final: -0.1557 (mm) REVERT: A 207 MET cc_start: -0.1770 (ttt) cc_final: -0.2768 (ttt) REVERT: A 230 MET cc_start: -0.0702 (ttp) cc_final: -0.1511 (ttm) REVERT: A 640 MET cc_start: -0.0933 (OUTLIER) cc_final: -0.2317 (ppp) REVERT: A 837 LYS cc_start: -0.4803 (OUTLIER) cc_final: -0.5565 (mptt) REVERT: A 842 MET cc_start: 0.0920 (mmp) cc_final: 0.0238 (tpt) REVERT: A 859 MET cc_start: 0.6361 (tmm) cc_final: 0.5793 (tmm) REVERT: A 996 MET cc_start: -0.0238 (ttm) cc_final: -0.1831 (mmt) outliers start: 145 outliers final: 114 residues processed: 329 average time/residue: 0.3624 time to fit residues: 187.6613 Evaluate side-chains 319 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 190 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 815 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 963 ASN Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 470 TRP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 72 optimal weight: 0.0270 chunk 219 optimal weight: 30.0000 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 244 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 HIS ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 274 ASN A 413 ASN ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.179887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.142740 restraints weight = 83985.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.141843 restraints weight = 50774.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.141564 restraints weight = 35962.556| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.7833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25230 Z= 0.173 Angle : 0.664 13.304 34078 Z= 0.344 Chirality : 0.045 0.231 3796 Planarity : 0.004 0.057 4332 Dihedral : 5.932 56.544 3369 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.13 % Favored : 92.44 % Rotamer: Outliers : 4.54 % Allowed : 29.16 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 3002 helix: -0.11 (0.16), residues: 1076 sheet: -0.63 (0.25), residues: 460 loop : -2.07 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 43 HIS 0.009 0.001 HIS D 600 PHE 0.037 0.002 PHE F 188 TYR 0.023 0.001 TYR B 121 ARG 0.007 0.000 ARG A 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5731.53 seconds wall clock time: 104 minutes 14.96 seconds (6254.96 seconds total)