Starting phenix.real_space_refine on Sun Mar 17 06:06:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it0_35702/03_2024/8it0_35702.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it0_35702/03_2024/8it0_35702.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/8it0_35702/03_2024/8it0_35702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it0_35702/03_2024/8it0_35702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it0_35702/03_2024/8it0_35702.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it0_35702/03_2024/8it0_35702.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= 0.001 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 46 5.16 5 C 10602 2.51 5 N 2836 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "F GLU 398": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16922 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Time building chain proxies: 9.46, per 1000 atoms: 0.56 Number of scatterers: 16922 At special positions: 0 Unit cell: (173.68, 107.12, 142.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 90 15.00 O 3348 8.00 N 2836 7.00 C 10602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 2.6 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 19 sheets defined 38.7% alpha, 11.4% beta 2 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 5.50 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.547A pdb=" N ARG A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 131 removed outlier: 3.615A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.521A pdb=" N TYR A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.751A pdb=" N THR A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.560A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.564A pdb=" N TRP A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.749A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 28 removed outlier: 3.753A pdb=" N ARG B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 21 " --> pdb=" O PHE B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 46 through 56 removed outlier: 4.184A pdb=" N ARG B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.919A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.854A pdb=" N VAL B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 114' Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.742A pdb=" N GLN B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.584A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.554A pdb=" N GLU B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 238 " --> pdb=" O GLY B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 238' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 258 through 280 Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.871A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.829A pdb=" N TRP B 373 " --> pdb=" O TRP B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.784A pdb=" N GLU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.062A pdb=" N GLU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 removed outlier: 3.535A pdb=" N PHE E 30 " --> pdb=" O GLY E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 97 through 105 removed outlier: 4.222A pdb=" N ILE E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.512A pdb=" N ASP E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 205 through 214 removed outlier: 3.845A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.828A pdb=" N THR E 218 " --> pdb=" O LEU E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 263 removed outlier: 3.740A pdb=" N LEU E 252 " --> pdb=" O ILE E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 326 removed outlier: 3.614A pdb=" N GLY E 326 " --> pdb=" O PRO E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 351 Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.652A pdb=" N GLU E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 377 " --> pdb=" O PHE E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.777A pdb=" N ALA E 483 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS E 485 " --> pdb=" O ARG E 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.577A pdb=" N LEU F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 4.302A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 removed outlier: 3.608A pdb=" N ALA F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.527A pdb=" N THR F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 231' Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.608A pdb=" N GLU F 237 " --> pdb=" O ASN F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.736A pdb=" N ILE F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 280 Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.721A pdb=" N ASP F 303 " --> pdb=" O LEU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 366 removed outlier: 3.910A pdb=" N GLN F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS F 366 " --> pdb=" O ARG F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 385 Processing helix chain 'F' and resid 421 through 438 removed outlier: 4.293A pdb=" N GLU F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU F 438 " --> pdb=" O ASN F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.911A pdb=" N LYS A 270 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.687A pdb=" N LYS A 94 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 45 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.606A pdb=" N PHE A 304 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 280 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 447 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A 443 " --> pdb=" O THR A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 3.535A pdb=" N GLY A 318 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 removed outlier: 3.602A pdb=" N ASP B 172 " --> pdb=" O TYR A 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.968A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.134A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE B 95 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE B 60 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU B 97 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 62 " --> pdb=" O LEU B 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 328 removed outlier: 3.527A pdb=" N LEU B 402 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'E' and resid 92 through 94 removed outlier: 3.774A pdb=" N VAL E 92 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL E 141 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 301 through 302 removed outlier: 6.424A pdb=" N VAL E 357 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL E 386 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE E 359 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 388 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA E 361 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E 444 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 420 " --> pdb=" O ILE E 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 397 through 398 Processing sheet with id=AB6, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.792A pdb=" N SER E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.286A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS F 4 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS F 59 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 318 through 328 removed outlier: 3.526A pdb=" N MET F 336 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER F 404 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE F 403 " --> pdb=" O ILE F 391 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 186 through 189 Processing sheet with id=AC1, first strand: chain 'F' and resid 283 through 284 522 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3470 1.33 - 1.45: 4465 1.45 - 1.57: 9334 1.57 - 1.69: 177 1.69 - 1.81: 70 Bond restraints: 17516 Sorted by residual: bond pdb=" N ILE B 308 " pdb=" CA ILE B 308 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.28e-02 6.10e+03 9.76e+00 bond pdb=" N THR B 11 " pdb=" CA THR B 11 " ideal model delta sigma weight residual 1.462 1.491 -0.029 9.50e-03 1.11e+04 9.46e+00 bond pdb=" N GLU B 13 " pdb=" CA GLU B 13 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.20e+00 bond pdb=" N ARG B 186 " pdb=" CA ARG B 186 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.27e-02 6.20e+03 8.00e+00 bond pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.82e+00 ... (remaining 17511 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.58: 545 104.58 - 111.96: 8236 111.96 - 119.34: 6471 119.34 - 126.73: 8318 126.73 - 134.11: 510 Bond angle restraints: 24080 Sorted by residual: angle pdb=" C GLN B 314 " pdb=" N LYS B 315 " pdb=" CA LYS B 315 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.28e+01 angle pdb=" N ILE E 52 " pdb=" CA ILE E 52 " pdb=" C ILE E 52 " ideal model delta sigma weight residual 110.72 105.22 5.50 1.01e+00 9.80e-01 2.97e+01 angle pdb=" CA ARG B 209 " pdb=" CB ARG B 209 " pdb=" CG ARG B 209 " ideal model delta sigma weight residual 114.10 124.98 -10.88 2.00e+00 2.50e-01 2.96e+01 angle pdb=" CA GLU F 212 " pdb=" CB GLU F 212 " pdb=" CG GLU F 212 " ideal model delta sigma weight residual 114.10 124.51 -10.41 2.00e+00 2.50e-01 2.71e+01 angle pdb=" C3' DC D 33 " pdb=" O3' DC D 33 " pdb=" P DC D 34 " ideal model delta sigma weight residual 120.20 127.79 -7.59 1.50e+00 4.44e-01 2.56e+01 ... (remaining 24075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.18: 9198 22.18 - 44.37: 957 44.37 - 66.55: 307 66.55 - 88.73: 25 88.73 - 110.92: 1 Dihedral angle restraints: 10488 sinusoidal: 5098 harmonic: 5390 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ILE B 208 " pdb=" C ILE B 208 " pdb=" N ARG B 209 " pdb=" CA ARG B 209 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS F 211 " pdb=" C LYS F 211 " pdb=" N GLU F 212 " pdb=" CA GLU F 212 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2488 0.108 - 0.217: 140 0.217 - 0.325: 4 0.325 - 0.433: 3 0.433 - 0.541: 3 Chirality restraints: 2638 Sorted by residual: chirality pdb=" P DA D 36 " pdb=" OP1 DA D 36 " pdb=" OP2 DA D 36 " pdb=" O5' DA D 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" P DC D 34 " pdb=" OP1 DC D 34 " pdb=" OP2 DC D 34 " pdb=" O5' DC D 34 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" P A G 10 " pdb=" OP1 A G 10 " pdb=" OP2 A G 10 " pdb=" O5' A G 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 2635 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 320 " 0.021 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP A 320 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 320 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 320 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 320 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 320 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 320 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 320 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 384 " -0.017 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU F 384 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU F 384 " -0.025 2.00e-02 2.50e+03 pdb=" N SER F 385 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 67 " -0.018 2.00e-02 2.50e+03 2.61e-02 1.02e+01 pdb=" CG HIS E 67 " 0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS E 67 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS E 67 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS E 67 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 67 " 0.002 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1932 2.75 - 3.29: 16125 3.29 - 3.83: 28468 3.83 - 4.36: 32298 4.36 - 4.90: 53319 Nonbonded interactions: 132142 Sorted by model distance: nonbonded pdb=" O PHE A 373 " pdb=" OG1 THR A 377 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR B 233 " pdb=" OG SER B 238 " model vdw 2.221 2.440 nonbonded pdb=" O2 DT D 26 " pdb=" N2 G C 20 " model vdw 2.228 2.496 nonbonded pdb=" OG1 THR A 387 " pdb=" OE1 GLU A 444 " model vdw 2.236 2.440 nonbonded pdb=" O TYR A 321 " pdb=" OD1 ASN A 322 " model vdw 2.267 3.040 ... (remaining 132137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.390 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: 5.790 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 48.770 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 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 : 0.005 0.066 17516 Z= 0.286 Angle : 0.958 12.471 24080 Z= 0.529 Chirality : 0.057 0.541 2638 Planarity : 0.006 0.064 2744 Dihedral : 18.671 110.918 7004 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.12 % Allowed : 18.90 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.62 (0.18), residues: 1818 helix: -1.16 (0.18), residues: 614 sheet: -0.92 (0.34), residues: 225 loop : -2.38 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP A 320 HIS 0.034 0.002 HIS E 67 PHE 0.032 0.002 PHE F 187 TYR 0.037 0.002 TYR B 233 ARG 0.009 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.6939 (tpt) cc_final: 0.6707 (tpt) REVERT: F 414 MET cc_start: 0.5948 (ptt) cc_final: 0.4422 (ptt) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.3577 time to fit residues: 58.3177 Evaluate side-chains 59 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 57 optimal weight: 0.0270 chunk 90 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 430 GLN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17516 Z= 0.368 Angle : 0.715 12.713 24080 Z= 0.380 Chirality : 0.045 0.309 2638 Planarity : 0.005 0.062 2744 Dihedral : 19.618 91.839 3194 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.74 % Allowed : 17.68 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 (0.19), residues: 1818 helix: -0.51 (0.19), residues: 633 sheet: -0.76 (0.34), residues: 235 loop : -2.06 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 320 HIS 0.006 0.001 HIS F 340 PHE 0.024 0.002 PHE E 482 TYR 0.019 0.002 TYR F 416 ARG 0.009 0.001 ARG E 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 62 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.7973 (tpp) cc_final: 0.7694 (tpt) REVERT: E 1 MET cc_start: 0.7255 (tpt) cc_final: 0.6790 (tpt) outliers start: 45 outliers final: 17 residues processed: 103 average time/residue: 0.2755 time to fit residues: 44.8713 Evaluate side-chains 70 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17516 Z= 0.210 Angle : 0.604 9.336 24080 Z= 0.320 Chirality : 0.043 0.292 2638 Planarity : 0.004 0.047 2744 Dihedral : 19.554 93.947 3194 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.65 % Allowed : 18.11 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.60 (0.19), residues: 1818 helix: -0.11 (0.20), residues: 633 sheet: -0.68 (0.34), residues: 235 loop : -1.86 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 320 HIS 0.003 0.001 HIS F 340 PHE 0.013 0.001 PHE E 30 TYR 0.012 0.001 TYR E 285 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 57 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.7868 (tpp) cc_final: 0.7646 (tmm) REVERT: E 1 MET cc_start: 0.7412 (tpt) cc_final: 0.6888 (tpt) outliers start: 27 outliers final: 13 residues processed: 83 average time/residue: 0.2963 time to fit residues: 38.7950 Evaluate side-chains 63 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17516 Z= 0.347 Angle : 0.669 10.544 24080 Z= 0.356 Chirality : 0.043 0.315 2638 Planarity : 0.005 0.056 2744 Dihedral : 19.624 96.853 3194 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 26.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.80 % Allowed : 17.44 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.45 (0.19), residues: 1818 helix: 0.07 (0.20), residues: 625 sheet: -0.73 (0.34), residues: 219 loop : -1.75 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 33 HIS 0.006 0.001 HIS F 340 PHE 0.017 0.002 PHE B 217 TYR 0.017 0.002 TYR E 285 ARG 0.005 0.001 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 51 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 24 residues processed: 93 average time/residue: 0.2857 time to fit residues: 41.7751 Evaluate side-chains 71 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 47 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 302 GLN Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.0670 chunk 104 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17516 Z= 0.250 Angle : 0.606 8.159 24080 Z= 0.323 Chirality : 0.043 0.284 2638 Planarity : 0.004 0.044 2744 Dihedral : 19.635 98.432 3194 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.32 % Allowed : 17.87 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.33 (0.19), residues: 1818 helix: 0.19 (0.20), residues: 632 sheet: -0.59 (0.34), residues: 220 loop : -1.73 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 20 HIS 0.005 0.001 HIS B 320 PHE 0.014 0.001 PHE B 217 TYR 0.018 0.001 TYR B 293 ARG 0.005 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 46 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 81 average time/residue: 0.2770 time to fit residues: 36.3033 Evaluate side-chains 62 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17516 Z= 0.164 Angle : 0.585 9.133 24080 Z= 0.306 Chirality : 0.042 0.247 2638 Planarity : 0.004 0.044 2744 Dihedral : 19.510 97.793 3194 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.59 % Allowed : 18.48 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.16 (0.20), residues: 1818 helix: 0.36 (0.20), residues: 630 sheet: -0.53 (0.34), residues: 224 loop : -1.63 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 373 HIS 0.003 0.001 HIS B 188 PHE 0.010 0.001 PHE B 217 TYR 0.021 0.001 TYR B 293 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 49 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 75 average time/residue: 0.3061 time to fit residues: 36.4459 Evaluate side-chains 66 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 111 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 17516 Z= 0.339 Angle : 0.638 7.817 24080 Z= 0.340 Chirality : 0.043 0.253 2638 Planarity : 0.004 0.043 2744 Dihedral : 19.626 98.522 3194 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.83 % Allowed : 18.54 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.18 (0.20), residues: 1818 helix: 0.35 (0.20), residues: 631 sheet: -0.65 (0.34), residues: 225 loop : -1.63 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 254 HIS 0.006 0.001 HIS B 320 PHE 0.014 0.001 PHE B 217 TYR 0.017 0.002 TYR B 293 ARG 0.005 0.001 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 44 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.4918 (ttm-80) outliers start: 30 outliers final: 23 residues processed: 71 average time/residue: 0.3213 time to fit residues: 34.9917 Evaluate side-chains 65 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 41 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17516 Z= 0.277 Angle : 0.618 13.674 24080 Z= 0.327 Chirality : 0.043 0.228 2638 Planarity : 0.004 0.043 2744 Dihedral : 19.623 99.612 3194 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.71 % Allowed : 18.90 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.14 (0.20), residues: 1818 helix: 0.41 (0.20), residues: 631 sheet: -0.68 (0.34), residues: 226 loop : -1.60 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 20 HIS 0.004 0.001 HIS B 320 PHE 0.014 0.001 PHE B 217 TYR 0.020 0.001 TYR B 293 ARG 0.005 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 44 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 70 average time/residue: 0.3024 time to fit residues: 33.6178 Evaluate side-chains 65 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 44 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17516 Z= 0.339 Angle : 0.655 8.999 24080 Z= 0.348 Chirality : 0.043 0.216 2638 Planarity : 0.004 0.043 2744 Dihedral : 19.720 99.754 3194 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.59 % Allowed : 18.84 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.19 (0.20), residues: 1818 helix: 0.36 (0.20), residues: 631 sheet: -0.85 (0.35), residues: 225 loop : -1.58 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 319 HIS 0.006 0.001 HIS F 340 PHE 0.010 0.001 PHE F 217 TYR 0.022 0.002 TYR B 293 ARG 0.020 0.001 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 42 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 23 residues processed: 66 average time/residue: 0.3290 time to fit residues: 33.8089 Evaluate side-chains 64 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 41 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 174 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17516 Z= 0.177 Angle : 0.594 9.419 24080 Z= 0.312 Chirality : 0.042 0.166 2638 Planarity : 0.004 0.041 2744 Dihedral : 19.524 99.315 3194 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.46 % Allowed : 19.27 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.04 (0.20), residues: 1818 helix: 0.52 (0.20), residues: 630 sheet: -0.72 (0.35), residues: 227 loop : -1.54 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 373 HIS 0.003 0.001 HIS E 329 PHE 0.009 0.001 PHE A 403 TYR 0.020 0.001 TYR B 293 ARG 0.006 0.000 ARG A 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 71 average time/residue: 0.3106 time to fit residues: 34.7429 Evaluate side-chains 64 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 470 CYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 10.0000 chunk 138 optimal weight: 0.0050 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** 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 = 0.3061 r_free = 0.3061 target = 0.041619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035096 restraints weight = 183557.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035655 restraints weight = 121242.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036037 restraints weight = 89872.101| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17516 Z= 0.200 Angle : 0.592 12.577 24080 Z= 0.309 Chirality : 0.041 0.161 2638 Planarity : 0.004 0.041 2744 Dihedral : 19.518 98.433 3194 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.28 % Allowed : 19.51 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1818 helix: 0.54 (0.20), residues: 636 sheet: -0.72 (0.35), residues: 240 loop : -1.47 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.003 0.001 HIS F 340 PHE 0.010 0.001 PHE B 217 TYR 0.020 0.001 TYR B 293 ARG 0.006 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.23 seconds wall clock time: 47 minutes 59.01 seconds (2879.01 seconds total)