Starting phenix.real_space_refine on Thu Feb 15 10:52:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/02_2024/6ppj_20440_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/02_2024/6ppj_20440.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/6ppj_20440/02_2024/6ppj_20440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/02_2024/6ppj_20440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/02_2024/6ppj_20440_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/02_2024/6ppj_20440_updated.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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 3 5.49 5 S 37 5.16 5 C 7621 2.51 5 N 2230 2.21 5 O 2109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 59": "NH1" <-> "NH2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 600": "NH1" <-> "NH2" Residue "B ARG 996": "NH1" <-> "NH2" Residue "B PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 681": "NH1" <-> "NH2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A ARG 918": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12004 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 5756 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 222} Link IDs: {'PTRANS': 37, 'TRANS': 810} Chain breaks: 22 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 901 Unresolved non-hydrogen dihedrals: 503 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'ASP:plan': 29, 'UNK:plan-1': 77, 'HIS:plan': 7, 'PHE:plan': 2, 'GLU:plan': 36, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 466 Chain: "A" Number of atoms: 6248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 6248 Unusual residues: {'ANP': 1, 'SF4': 1} Classifications: {'peptide': 901, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 54, 'TRANS': 846, None: 2} Not linked: pdbres="GLN A1039 " pdbres="SF4 A1101 " Not linked: pdbres="SF4 A1101 " pdbres="ANP A1102 " Chain breaks: 25 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 40, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 34, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 465 Time building chain proxies: 7.24, per 1000 atoms: 0.60 Number of scatterers: 12004 At special positions: 0 Unit cell: (144.698, 99.9108, 109.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 37 16.00 P 3 15.00 O 2109 8.00 N 2230 7.00 C 7621 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: 4.59 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1027 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A 807 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1036 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1030 " Number of angles added : 12 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 8 sheets defined 43.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'B' and resid 32 through 35 No H-bonds generated for 'chain 'B' and resid 32 through 35' Processing helix chain 'B' and resid 52 through 55 No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.690A pdb=" N VAL B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 66 " --> pdb=" O TRP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 3.670A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 4.326A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 No H-bonds generated for 'chain 'B' and resid 149 through 152' Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.575A pdb=" N LEU B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.517A pdb=" N UNK B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N UNK B 201 " --> pdb=" O UNK B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.687A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 278 removed outlier: 3.580A pdb=" N LEU B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 292 through 295 No H-bonds generated for 'chain 'B' and resid 292 through 295' Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 336 through 339 No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 362 through 375 removed outlier: 3.607A pdb=" N UNK B 370 " --> pdb=" O UNK B 366 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N UNK B 371 " --> pdb=" O UNK B 367 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N UNK B 374 " --> pdb=" O UNK B 370 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK B 375 " --> pdb=" O UNK B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 418 removed outlier: 4.023A pdb=" N ASP B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 417 " --> pdb=" O HIS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 442 through 449 removed outlier: 3.766A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.965A pdb=" N MET B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.523A pdb=" N MET B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.554A pdb=" N ALA B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 506 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 555 through 576 removed outlier: 4.224A pdb=" N GLU B 559 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 589 removed outlier: 3.888A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 589 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.538A pdb=" N ALA B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 597' Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 745 through 748 No H-bonds generated for 'chain 'B' and resid 745 through 748' Processing helix chain 'B' and resid 753 through 760 removed outlier: 3.519A pdb=" N THR B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 793 removed outlier: 4.180A pdb=" N THR B 791 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 792 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 852 removed outlier: 3.648A pdb=" N GLY B 843 " --> pdb=" O HIS B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 875 removed outlier: 3.620A pdb=" N ASP B 869 " --> pdb=" O ALA B 865 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 897 No H-bonds generated for 'chain 'B' and resid 894 through 897' Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 922 through 934 removed outlier: 3.644A pdb=" N PHE B 927 " --> pdb=" O LEU B 923 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP B 930 " --> pdb=" O THR B 926 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 932 " --> pdb=" O HIS B 928 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 971 Processing helix chain 'B' and resid 973 through 976 No H-bonds generated for 'chain 'B' and resid 973 through 976' Processing helix chain 'B' and resid 1030 through 1042 removed outlier: 3.783A pdb=" N LEU B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B1036 " --> pdb=" O VAL B1032 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B1037 " --> pdb=" O GLN B1033 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP B1041 " --> pdb=" O TYR B1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.808A pdb=" N VAL A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.759A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.838A pdb=" N ALA A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.513A pdb=" N ASP A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.539A pdb=" N THR A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.582A pdb=" N GLN A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.705A pdb=" N GLU A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 4.258A pdb=" N VAL A 228 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 229 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 232 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 233 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 236 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 237 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 238 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.780A pdb=" N THR A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.768A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 420 through 434 removed outlier: 4.403A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 No H-bonds generated for 'chain 'A' and resid 443 through 446' Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.867A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 removed outlier: 4.171A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 509 removed outlier: 3.981A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.718A pdb=" N ASP A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 569 removed outlier: 3.815A pdb=" N ASP A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 Processing helix chain 'A' and resid 641 through 644 No H-bonds generated for 'chain 'A' and resid 641 through 644' Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.980A pdb=" N SER A 708 " --> pdb=" O CYS A 704 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 709' Processing helix chain 'A' and resid 728 through 735 removed outlier: 3.546A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 762 removed outlier: 3.547A pdb=" N ALA A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 806 Processing helix chain 'A' and resid 808 through 815 removed outlier: 3.671A pdb=" N LEU A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 removed outlier: 3.751A pdb=" N HIS A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 855 removed outlier: 3.751A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 886 removed outlier: 3.944A pdb=" N ASP A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 867 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 884 " --> pdb=" O THR A 880 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 885 " --> pdb=" O ARG A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 1001 through 1014 removed outlier: 4.154A pdb=" N THR A1006 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 42 through 46 removed outlier: 7.920A pdb=" N ILE B 45 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 351 " --> pdb=" O ILE B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.665A pdb=" N THR B 115 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 76 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 78 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 281 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU B 77 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 283 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 311 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU B 284 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR B 313 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 394 through 399 removed outlier: 3.531A pdb=" N ALA B 398 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 769 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B 768 " --> pdb=" O VAL B 677 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 660 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 984 through 989 removed outlier: 3.731A pdb=" N PHE B 986 " --> pdb=" O GLY B 997 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 997 " --> pdb=" O PHE B 986 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= F, first strand: chain 'A' and resid 26 through 29 Processing sheet with id= G, first strand: chain 'A' and resid 348 through 354 removed outlier: 3.505A pdb=" N ALA A 688 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 604 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 386 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 606 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 921 through 923 removed outlier: 3.582A pdb=" N GLU A 923 " --> pdb=" O VAL A 931 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 861 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: 3.21 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4858 1.43 - 1.64: 7272 1.64 - 1.85: 53 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 12195 Sorted by residual: bond pdb=" N3B ANP A1102 " pdb=" PG ANP A1102 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" O3A ANP A1102 " pdb=" PB ANP A1102 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" N VAL B 970 " pdb=" CA VAL B 970 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.83e+01 bond pdb=" N VAL B 677 " pdb=" CA VAL B 677 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.50e-03 1.78e+04 1.74e+01 bond pdb=" N TRP B 830 " pdb=" CA TRP B 830 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.22e+01 ... (remaining 12190 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.73: 12 85.73 - 97.86: 1 97.86 - 110.00: 2768 110.00 - 122.14: 11578 122.14 - 134.27: 2367 Bond angle restraints: 16726 Sorted by residual: angle pdb=" N ARG A 918 " pdb=" CA ARG A 918 " pdb=" C ARG A 918 " ideal model delta sigma weight residual 111.17 121.42 -10.25 1.41e+00 5.03e-01 5.28e+01 angle pdb=" N PRO B 678 " pdb=" CA PRO B 678 " pdb=" C PRO B 678 " ideal model delta sigma weight residual 113.47 123.53 -10.06 1.43e+00 4.89e-01 4.95e+01 angle pdb=" C GLY A 917 " pdb=" N ARG A 918 " pdb=" CA ARG A 918 " ideal model delta sigma weight residual 122.82 129.74 -6.92 1.42e+00 4.96e-01 2.37e+01 angle pdb=" CA ARG A 918 " pdb=" C ARG A 918 " pdb=" O ARG A 918 " ideal model delta sigma weight residual 122.27 116.71 5.56 1.16e+00 7.43e-01 2.30e+01 angle pdb=" N VAL A 960 " pdb=" CA VAL A 960 " pdb=" C VAL A 960 " ideal model delta sigma weight residual 110.42 105.92 4.50 9.60e-01 1.09e+00 2.20e+01 ... (remaining 16721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 7130 35.78 - 71.56: 58 71.56 - 107.34: 6 107.34 - 143.12: 0 143.12 - 178.90: 2 Dihedral angle restraints: 7196 sinusoidal: 2204 harmonic: 4992 Sorted by residual: dihedral pdb=" C LEU B 701 " pdb=" N LEU B 701 " pdb=" CA LEU B 701 " pdb=" CB LEU B 701 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" CA VAL B 982 " pdb=" C VAL B 982 " pdb=" N GLU B 983 " pdb=" CA GLU B 983 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLY A 274 " pdb=" C GLY A 274 " pdb=" N THR A 275 " pdb=" CA THR A 275 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1899 0.098 - 0.196: 200 0.196 - 0.294: 16 0.294 - 0.392: 5 0.392 - 0.490: 1 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA LEU B 701 " pdb=" N LEU B 701 " pdb=" C LEU B 701 " pdb=" CB LEU B 701 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA PRO B 678 " pdb=" N PRO B 678 " pdb=" C PRO B 678 " pdb=" CB PRO B 678 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ARG A 918 " pdb=" N ARG A 918 " pdb=" C ARG A 918 " pdb=" CB ARG A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 2118 not shown) Planarity restraints: 2117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 917 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C GLY A 917 " -0.068 2.00e-02 2.50e+03 pdb=" O GLY A 917 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 918 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 113 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C SER B 113 " -0.054 2.00e-02 2.50e+03 pdb=" O SER B 113 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 114 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 576 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.65e+00 pdb=" C GLY B 576 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY B 576 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS B 577 " 0.019 2.00e-02 2.50e+03 ... (remaining 2114 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1303 2.74 - 3.28: 10681 3.28 - 3.82: 17832 3.82 - 4.36: 20931 4.36 - 4.90: 35772 Nonbonded interactions: 86519 Sorted by model distance: nonbonded pdb=" NE1 TRP A 787 " pdb=" CA ALA A1015 " model vdw 2.202 3.550 nonbonded pdb=" OG SER A 312 " pdb=" O THR A 340 " model vdw 2.243 2.440 nonbonded pdb=" O THR A 33 " pdb=" O2A ANP A1102 " model vdw 2.272 3.040 nonbonded pdb=" O THR B 165 " pdb=" ND2 ASN A 867 " model vdw 2.294 2.520 nonbonded pdb=" O GLY B 863 " pdb=" NH2 ARG A 724 " model vdw 2.356 2.520 ... (remaining 86514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.150 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.050 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.009 0.168 12195 Z= 0.593 Angle : 1.152 10.357 16726 Z= 0.667 Chirality : 0.065 0.490 2121 Planarity : 0.008 0.072 2117 Dihedral : 11.631 178.898 3924 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.82 % Allowed : 6.16 % Favored : 92.03 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.15), residues: 1580 helix: -4.55 (0.09), residues: 801 sheet: -1.61 (0.43), residues: 151 loop : -3.22 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 616 HIS 0.014 0.002 HIS B 243 PHE 0.024 0.003 PHE A 477 TYR 0.030 0.003 TYR A 864 ARG 0.020 0.001 ARG B 597 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 249 time to evaluate : 1.297 Fit side-chains REVERT: B 225 MET cc_start: 0.7703 (tmt) cc_final: 0.7409 (tmm) REVERT: B 612 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8908 (mt) REVERT: B 1013 LEU cc_start: 0.9034 (tm) cc_final: 0.8703 (tp) REVERT: A 284 PRO cc_start: 0.9030 (Cg_endo) cc_final: 0.8685 (Cg_exo) REVERT: A 313 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: A 568 TYR cc_start: 0.8268 (t80) cc_final: 0.7937 (t80) REVERT: A 964 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5077 (tp) REVERT: A 1000 ARG cc_start: 0.7035 (tmm-80) cc_final: 0.6685 (tpp-160) outliers start: 18 outliers final: 7 residues processed: 262 average time/residue: 0.3644 time to fit residues: 122.2794 Evaluate side-chains 155 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS B 332 ASN ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 HIS A 46 HIS A 259 HIS A 263 GLN A 311 GLN A 342 ASN A 816 HIS A 848 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12195 Z= 0.223 Angle : 0.638 15.167 16726 Z= 0.314 Chirality : 0.042 0.141 2121 Planarity : 0.005 0.054 2117 Dihedral : 9.159 175.180 1876 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.83 % Allowed : 10.90 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.17), residues: 1580 helix: -3.57 (0.13), residues: 792 sheet: -1.12 (0.46), residues: 132 loop : -2.65 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 497 HIS 0.007 0.001 HIS A 259 PHE 0.012 0.001 PHE A 618 TYR 0.018 0.002 TYR B 755 ARG 0.006 0.001 ARG B 842 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7911 (tmt) cc_final: 0.7486 (tmm) REVERT: B 679 HIS cc_start: 0.6921 (p90) cc_final: 0.6671 (p-80) REVERT: A 126 ILE cc_start: 0.8899 (mm) cc_final: 0.8679 (mm) REVERT: A 313 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7706 (m-10) REVERT: A 568 TYR cc_start: 0.8461 (t80) cc_final: 0.7997 (t80) REVERT: A 685 MET cc_start: 0.8549 (ttm) cc_final: 0.8148 (ttt) REVERT: A 964 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.4860 (tp) outliers start: 38 outliers final: 17 residues processed: 174 average time/residue: 0.3279 time to fit residues: 76.4542 Evaluate side-chains 144 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 0.0870 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS B 229 GLN B 332 ASN ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN A 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12195 Z= 0.187 Angle : 0.564 13.778 16726 Z= 0.276 Chirality : 0.040 0.132 2121 Planarity : 0.004 0.044 2117 Dihedral : 7.758 172.489 1868 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.15 % Allowed : 10.49 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.19), residues: 1580 helix: -2.66 (0.15), residues: 798 sheet: -1.02 (0.43), residues: 147 loop : -2.43 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS A 775 PHE 0.012 0.001 PHE A 618 TYR 0.013 0.001 TYR B 755 ARG 0.006 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 131 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7926 (tmt) cc_final: 0.7482 (tmm) REVERT: B 448 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 313 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7581 (m-10) REVERT: A 568 TYR cc_start: 0.8537 (t80) cc_final: 0.8013 (t80) REVERT: A 685 MET cc_start: 0.8532 (ttm) cc_final: 0.8238 (ttm) REVERT: A 964 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5013 (tp) outliers start: 51 outliers final: 26 residues processed: 169 average time/residue: 0.2879 time to fit residues: 67.9079 Evaluate side-chains 150 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.9980 chunk 119 optimal weight: 0.0010 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 75 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 150 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 chunk 140 optimal weight: 0.0010 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12195 Z= 0.122 Angle : 0.511 11.636 16726 Z= 0.250 Chirality : 0.039 0.177 2121 Planarity : 0.004 0.036 2117 Dihedral : 7.009 160.053 1868 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.43 % Allowed : 13.02 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.19), residues: 1580 helix: -1.97 (0.17), residues: 786 sheet: -0.84 (0.41), residues: 164 loop : -2.24 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 497 HIS 0.003 0.000 HIS B 243 PHE 0.010 0.001 PHE A 618 TYR 0.013 0.001 TYR B 755 ARG 0.007 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7887 (tmt) cc_final: 0.7459 (tmm) REVERT: B 290 THR cc_start: 0.8543 (m) cc_final: 0.8222 (p) REVERT: B 448 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 86 VAL cc_start: 0.8735 (p) cc_final: 0.8491 (m) REVERT: A 313 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: A 568 TYR cc_start: 0.8548 (t80) cc_final: 0.8253 (t80) REVERT: A 625 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: A 685 MET cc_start: 0.8524 (ttm) cc_final: 0.8279 (ttm) REVERT: A 964 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.4985 (tp) outliers start: 34 outliers final: 17 residues processed: 167 average time/residue: 0.2754 time to fit residues: 63.3777 Evaluate side-chains 147 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS B 332 ASN B 413 HIS ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 12195 Z= 0.530 Angle : 0.740 11.332 16726 Z= 0.365 Chirality : 0.049 0.174 2121 Planarity : 0.005 0.050 2117 Dihedral : 8.064 173.146 1866 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.46 % Allowed : 12.61 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.19), residues: 1580 helix: -2.11 (0.17), residues: 809 sheet: -1.16 (0.42), residues: 157 loop : -2.37 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 497 HIS 0.014 0.002 HIS A 775 PHE 0.019 0.003 PHE B 336 TYR 0.024 0.002 TYR A 864 ARG 0.007 0.001 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 120 time to evaluate : 1.219 Fit side-chains REVERT: B 225 MET cc_start: 0.8050 (tmt) cc_final: 0.7527 (tmm) REVERT: B 1038 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7202 (tpm170) REVERT: A 86 VAL cc_start: 0.8803 (p) cc_final: 0.8595 (m) REVERT: A 254 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8767 (t) REVERT: A 313 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7601 (m-10) REVERT: A 625 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: A 633 ILE cc_start: 0.9158 (mm) cc_final: 0.8941 (mm) REVERT: A 685 MET cc_start: 0.8566 (ttm) cc_final: 0.8168 (ttt) REVERT: A 787 TRP cc_start: 0.7405 (OUTLIER) cc_final: 0.6920 (p-90) outliers start: 64 outliers final: 43 residues processed: 173 average time/residue: 0.2849 time to fit residues: 66.6895 Evaluate side-chains 164 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 117 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12195 Z= 0.164 Angle : 0.559 10.451 16726 Z= 0.271 Chirality : 0.040 0.171 2121 Planarity : 0.004 0.042 2117 Dihedral : 7.125 163.603 1864 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.34 % Allowed : 14.73 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.20), residues: 1580 helix: -1.50 (0.18), residues: 799 sheet: -1.07 (0.41), residues: 165 loop : -2.12 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.003 0.000 HIS A 775 PHE 0.011 0.001 PHE A 618 TYR 0.020 0.001 TYR A 568 ARG 0.011 0.001 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7903 (tmt) cc_final: 0.7474 (tmm) REVERT: B 872 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8239 (mm) REVERT: A 86 VAL cc_start: 0.8752 (p) cc_final: 0.8504 (m) REVERT: A 313 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: A 390 PRO cc_start: 0.7409 (Cg_exo) cc_final: 0.6874 (Cg_endo) REVERT: A 685 MET cc_start: 0.8517 (ttm) cc_final: 0.8261 (ttm) outliers start: 43 outliers final: 33 residues processed: 157 average time/residue: 0.2993 time to fit residues: 64.7768 Evaluate side-chains 156 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS B 332 ASN ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12195 Z= 0.308 Angle : 0.616 10.603 16726 Z= 0.300 Chirality : 0.043 0.158 2121 Planarity : 0.004 0.056 2117 Dihedral : 7.234 165.295 1864 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.41 % Favored : 92.53 % Rotamer: Outliers : 5.65 % Allowed : 14.33 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.20), residues: 1580 helix: -1.42 (0.18), residues: 811 sheet: -1.01 (0.42), residues: 156 loop : -2.12 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 497 HIS 0.008 0.001 HIS A 775 PHE 0.029 0.002 PHE B 254 TYR 0.023 0.002 TYR A 568 ARG 0.012 0.001 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 116 time to evaluate : 1.326 Fit side-chains REVERT: B 225 MET cc_start: 0.8004 (tmt) cc_final: 0.7529 (tmm) REVERT: B 579 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8031 (tp) REVERT: B 872 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 86 VAL cc_start: 0.8723 (p) cc_final: 0.8488 (m) REVERT: A 313 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7418 (m-10) REVERT: A 390 PRO cc_start: 0.7671 (Cg_exo) cc_final: 0.7189 (Cg_endo) REVERT: A 787 TRP cc_start: 0.7371 (OUTLIER) cc_final: 0.6666 (p-90) outliers start: 56 outliers final: 45 residues processed: 158 average time/residue: 0.3051 time to fit residues: 67.2539 Evaluate side-chains 165 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12195 Z= 0.355 Angle : 0.652 10.932 16726 Z= 0.317 Chirality : 0.045 0.159 2121 Planarity : 0.005 0.058 2117 Dihedral : 7.483 168.275 1864 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 6.76 % Allowed : 13.72 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.20), residues: 1580 helix: -1.41 (0.18), residues: 806 sheet: -1.03 (0.42), residues: 156 loop : -2.13 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 525 HIS 0.009 0.001 HIS A 775 PHE 0.029 0.002 PHE B 254 TYR 0.026 0.002 TYR A 568 ARG 0.014 0.001 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 121 time to evaluate : 1.339 Fit side-chains REVERT: B 225 MET cc_start: 0.7968 (tmt) cc_final: 0.7503 (tmm) REVERT: B 579 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8101 (tp) REVERT: B 872 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 86 VAL cc_start: 0.8710 (p) cc_final: 0.8485 (m) REVERT: A 313 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7457 (m-10) REVERT: A 390 PRO cc_start: 0.7656 (Cg_exo) cc_final: 0.7176 (Cg_endo) REVERT: A 787 TRP cc_start: 0.7426 (OUTLIER) cc_final: 0.6690 (p-90) outliers start: 67 outliers final: 53 residues processed: 173 average time/residue: 0.2986 time to fit residues: 69.9434 Evaluate side-chains 174 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 117 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 141 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 165 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN B 679 HIS ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12195 Z= 0.146 Angle : 0.547 10.361 16726 Z= 0.263 Chirality : 0.040 0.168 2121 Planarity : 0.004 0.045 2117 Dihedral : 6.685 158.143 1864 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 4.64 % Allowed : 15.94 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.21), residues: 1580 helix: -0.87 (0.19), residues: 798 sheet: -0.84 (0.42), residues: 165 loop : -1.91 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 497 HIS 0.003 0.001 HIS A 372 PHE 0.028 0.001 PHE B 254 TYR 0.023 0.001 TYR A 568 ARG 0.013 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7914 (tmt) cc_final: 0.7493 (tmm) REVERT: B 872 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 86 VAL cc_start: 0.8724 (p) cc_final: 0.8451 (m) REVERT: A 390 PRO cc_start: 0.7718 (Cg_exo) cc_final: 0.7193 (Cg_endo) REVERT: A 685 MET cc_start: 0.8572 (ttm) cc_final: 0.8209 (ttt) outliers start: 46 outliers final: 35 residues processed: 161 average time/residue: 0.3071 time to fit residues: 67.4050 Evaluate side-chains 155 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1030 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 0.0770 chunk 147 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12195 Z= 0.159 Angle : 0.546 11.295 16726 Z= 0.260 Chirality : 0.040 0.167 2121 Planarity : 0.004 0.061 2117 Dihedral : 6.200 149.317 1862 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.11 % Rotamer: Outliers : 4.24 % Allowed : 15.74 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1580 helix: -0.52 (0.19), residues: 790 sheet: -0.39 (0.43), residues: 155 loop : -1.72 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 497 HIS 0.003 0.001 HIS A 775 PHE 0.029 0.001 PHE B 254 TYR 0.016 0.001 TYR B 755 ARG 0.014 0.000 ARG B 998 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 119 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7869 (tmt) cc_final: 0.7479 (tmm) REVERT: B 872 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8284 (mm) REVERT: A 86 VAL cc_start: 0.8644 (p) cc_final: 0.8379 (m) REVERT: A 390 PRO cc_start: 0.7757 (Cg_exo) cc_final: 0.7247 (Cg_endo) REVERT: A 625 GLN cc_start: 0.7961 (pt0) cc_final: 0.7669 (mt0) REVERT: A 685 MET cc_start: 0.8559 (ttm) cc_final: 0.8176 (ttt) outliers start: 42 outliers final: 39 residues processed: 150 average time/residue: 0.2998 time to fit residues: 60.8685 Evaluate side-chains 159 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1030 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.0060 chunk 57 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104887 restraints weight = 18349.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105099 restraints weight = 24663.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106114 restraints weight = 22609.003| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12195 Z= 0.319 Angle : 0.626 11.906 16726 Z= 0.302 Chirality : 0.044 0.154 2121 Planarity : 0.004 0.068 2117 Dihedral : 6.623 154.940 1862 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 4.84 % Allowed : 15.24 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1580 helix: -0.77 (0.18), residues: 803 sheet: -0.77 (0.43), residues: 156 loop : -1.84 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 497 HIS 0.008 0.001 HIS A 775 PHE 0.028 0.002 PHE B 254 TYR 0.018 0.002 TYR B 755 ARG 0.013 0.001 ARG B 998 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.74 seconds wall clock time: 44 minutes 47.73 seconds (2687.73 seconds total)