Starting phenix.real_space_refine on Wed Feb 14 12:07:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujb_20795/02_2024/6ujb_20795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujb_20795/02_2024/6ujb_20795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujb_20795/02_2024/6ujb_20795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujb_20795/02_2024/6ujb_20795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujb_20795/02_2024/6ujb_20795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujb_20795/02_2024/6ujb_20795.pdb" } resolution = 3.51 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= 0.003 sd= 0.060 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 Ca 5 9.91 5 Mg 1 5.21 5 S 43 5.16 5 C 5792 2.51 5 N 1549 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9193 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4387 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2812 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 898 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.27, per 1000 atoms: 0.57 Number of scatterers: 9193 At special positions: 0 Unit cell: (72.63, 100.875, 165.435, 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) Ca 5 19.99 S 43 16.00 Mg 1 11.99 O 1803 8.00 N 1549 7.00 C 5792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.02 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.06 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.05 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 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 Links applied ALPHA1-2 " MAN C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2005 " - " ASN A 260 " " NAG B2005 " - " ASN B 360 " " NAG B2010 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG D 1 " - " ASN A 44 " " NAG G 1 " - " ASN B 191 " " NAG H 1 " - " ASN B 389 " " NAG I 1 " - " ASN B 414 " Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.8 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 13.6% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.519A pdb=" N VAL B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.791A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.712A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 4.326A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 100 through 104 removed outlier: 4.313A pdb=" N ASP E 104 " --> pdb=" O TYR E 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.793A pdb=" N LEU F 89 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.200A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR A 412 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 423 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY A 410 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY A 425 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 408 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.071A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.010A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.710A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.516A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.441A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.328A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 471 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.328A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.661A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.298A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.414A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.508A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 345 hydrogen bonds defined for protein. 867 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: 3.08 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1827 1.32 - 1.45: 2418 1.45 - 1.58: 5059 1.58 - 1.71: 9 1.71 - 1.83: 66 Bond restraints: 9379 Sorted by residual: bond pdb=" CB HIS B 184 " pdb=" CG HIS B 184 " ideal model delta sigma weight residual 1.497 1.445 0.052 1.40e-02 5.10e+03 1.37e+01 bond pdb=" CB ASN B 332 " pdb=" CG ASN B 332 " ideal model delta sigma weight residual 1.516 1.430 0.086 2.50e-02 1.60e+03 1.17e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.455 -0.071 2.10e-02 2.27e+03 1.15e+01 bond pdb=" C5 NAG A2005 " pdb=" O5 NAG A2005 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 9374 not shown) Histogram of bond angle deviations from ideal: 98.48 - 111.47: 4162 111.47 - 124.45: 8351 124.45 - 137.43: 211 137.43 - 150.42: 0 150.42 - 163.40: 1 Bond angle restraints: 12725 Sorted by residual: angle pdb=" C2 NAG H 2 " pdb=" N2 NAG H 2 " pdb=" C7 NAG H 2 " ideal model delta sigma weight residual 124.56 163.40 -38.84 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.17 -8.61 1.02e+00 9.61e-01 7.12e+01 angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 127.81 -8.25 1.02e+00 9.61e-01 6.54e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.93e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.40 -7.84 1.02e+00 9.61e-01 5.91e+01 ... (remaining 12720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 5640 21.42 - 42.83: 122 42.83 - 64.25: 37 64.25 - 85.67: 17 85.67 - 107.08: 7 Dihedral angle restraints: 5823 sinusoidal: 2433 harmonic: 3390 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 40.72 52.28 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 94 " pdb=" CB CYS F 94 " ideal model delta sinusoidal sigma weight residual 93.00 52.10 40.90 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 5820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1000 0.071 - 0.141: 343 0.141 - 0.212: 61 0.212 - 0.283: 32 0.283 - 0.354: 18 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.44e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.07e+01 chirality pdb=" C1 MAN C 5 " pdb=" O2 MAN C 4 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 7.47e+00 ... (remaining 1451 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.12e-02 1.22e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 379 " -0.023 2.00e-02 2.50e+03 2.44e-02 7.46e+00 pdb=" CG ASN B 379 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 379 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 379 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B2010 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.021 2.00e-02 2.50e+03 2.26e-02 6.40e+00 pdb=" CG ASN A 44 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.028 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 25 2.41 - 3.03: 5542 3.03 - 3.65: 12893 3.65 - 4.28: 21698 4.28 - 4.90: 34934 Nonbonded interactions: 75092 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.782 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 1.955 2.170 nonbonded pdb=" OD2 ASP B 151 " pdb="CA CA B2001 " model vdw 2.095 2.510 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.099 2.510 nonbonded pdb=" OD1 ASP B 209 " pdb="CA CA B2001 " model vdw 2.104 2.510 ... (remaining 75087 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 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.120 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: 5.880 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.410 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.014 0.086 9379 Z= 0.952 Angle : 1.445 38.841 12725 Z= 0.955 Chirality : 0.084 0.354 1454 Planarity : 0.006 0.027 1645 Dihedral : 11.747 107.084 3628 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1170 helix: -1.33 (0.43), residues: 97 sheet: 1.03 (0.23), residues: 429 loop : 0.29 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.006 TRP A 179 HIS 0.003 0.001 HIS B 227 PHE 0.021 0.004 PHE A 276 TYR 0.034 0.005 TYR A 254 ARG 0.005 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7791 (t0) cc_final: 0.7580 (t0) REVERT: A 408 MET cc_start: 0.8061 (mtm) cc_final: 0.7859 (mtm) REVERT: B 117 MET cc_start: 0.9137 (mmm) cc_final: 0.8853 (mmm) REVERT: B 135 MET cc_start: 0.8005 (mmm) cc_final: 0.7786 (mmm) REVERT: E 43 LYS cc_start: 0.8264 (mttt) cc_final: 0.7990 (mppt) REVERT: E 50 ARG cc_start: 0.7997 (ptm-80) cc_final: 0.7745 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2890 time to fit residues: 66.7926 Evaluate side-chains 90 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 377 ASN B 166 HIS F 31 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9379 Z= 0.292 Angle : 0.633 8.543 12725 Z= 0.338 Chirality : 0.048 0.244 1454 Planarity : 0.004 0.039 1645 Dihedral : 7.900 89.850 1617 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 6.55 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1170 helix: -0.35 (0.51), residues: 96 sheet: 0.69 (0.23), residues: 463 loop : 0.27 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 230 HIS 0.004 0.001 HIS B 161 PHE 0.015 0.002 PHE F 68 TYR 0.013 0.002 TYR A 561 ARG 0.005 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8121 (t0) cc_final: 0.7909 (t0) REVERT: A 241 SER cc_start: 0.9273 (t) cc_final: 0.9055 (p) REVERT: A 408 MET cc_start: 0.7996 (mtm) cc_final: 0.7775 (mtm) REVERT: B 135 MET cc_start: 0.8309 (mmm) cc_final: 0.7989 (mmm) REVERT: E 13 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6631 (mmtt) REVERT: E 43 LYS cc_start: 0.8277 (mttt) cc_final: 0.8041 (mppt) outliers start: 15 outliers final: 11 residues processed: 98 average time/residue: 0.2385 time to fit residues: 32.1794 Evaluate side-chains 86 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS E 35 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9379 Z= 0.267 Angle : 0.575 6.316 12725 Z= 0.302 Chirality : 0.047 0.287 1454 Planarity : 0.004 0.041 1645 Dihedral : 6.984 78.119 1617 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.83 % Allowed : 7.84 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1170 helix: -0.26 (0.52), residues: 96 sheet: 0.71 (0.23), residues: 452 loop : 0.08 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 61 HIS 0.007 0.001 HIS B 63 PHE 0.013 0.002 PHE A 427 TYR 0.017 0.001 TYR E 100 ARG 0.006 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8045 (mtm) cc_final: 0.7841 (mtm) REVERT: B 135 MET cc_start: 0.8038 (mmm) cc_final: 0.7814 (mmm) REVERT: B 278 MET cc_start: 0.8634 (mtm) cc_final: 0.8391 (mtm) REVERT: B 394 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7191 (ttp) REVERT: E 43 LYS cc_start: 0.8263 (mttt) cc_final: 0.8052 (mppt) REVERT: E 80 TYR cc_start: 0.8143 (m-80) cc_final: 0.7925 (m-10) REVERT: E 100 TYR cc_start: 0.8855 (t80) cc_final: 0.8619 (t80) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.2256 time to fit residues: 29.2806 Evaluate side-chains 86 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.0000 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 0.0370 chunk 50 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN E 3 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9379 Z= 0.198 Angle : 0.516 6.411 12725 Z= 0.268 Chirality : 0.046 0.303 1454 Planarity : 0.004 0.039 1645 Dihedral : 6.395 70.351 1617 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.40 % Allowed : 9.02 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1170 helix: -0.06 (0.53), residues: 96 sheet: 0.68 (0.23), residues: 452 loop : 0.02 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 61 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE A 477 TYR 0.011 0.001 TYR A 112 ARG 0.007 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: B 278 MET cc_start: 0.8611 (mtm) cc_final: 0.8372 (mtm) REVERT: B 394 MET cc_start: 0.7636 (ttm) cc_final: 0.7294 (ttp) REVERT: E 100 TYR cc_start: 0.8734 (t80) cc_final: 0.8414 (t80) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 0.2361 time to fit residues: 28.8983 Evaluate side-chains 84 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 320 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9379 Z= 0.272 Angle : 0.541 7.230 12725 Z= 0.278 Chirality : 0.046 0.319 1454 Planarity : 0.004 0.039 1645 Dihedral : 6.149 64.141 1617 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.93 % Allowed : 8.81 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1170 helix: -0.20 (0.53), residues: 97 sheet: 0.56 (0.23), residues: 446 loop : -0.06 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 61 HIS 0.003 0.001 HIS B 161 PHE 0.017 0.002 PHE A 427 TYR 0.016 0.001 TYR F 55 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 278 MET cc_start: 0.8611 (mtm) cc_final: 0.8378 (mtm) REVERT: B 394 MET cc_start: 0.7625 (ttm) cc_final: 0.7287 (ttp) REVERT: E 100 TYR cc_start: 0.8859 (t80) cc_final: 0.8641 (t80) REVERT: F 4 MET cc_start: 0.8413 (mmm) cc_final: 0.8192 (mmm) REVERT: F 42 TYR cc_start: 0.9329 (m-80) cc_final: 0.8812 (m-10) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.2157 time to fit residues: 27.2731 Evaluate side-chains 87 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9379 Z= 0.423 Angle : 0.617 7.122 12725 Z= 0.316 Chirality : 0.049 0.331 1454 Planarity : 0.004 0.047 1645 Dihedral : 6.237 59.198 1617 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.26 % Allowed : 8.92 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1170 helix: -0.45 (0.53), residues: 97 sheet: 0.34 (0.23), residues: 445 loop : -0.29 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 230 HIS 0.005 0.001 HIS B 161 PHE 0.026 0.002 PHE A 427 TYR 0.021 0.002 TYR A 254 ARG 0.009 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: B 278 MET cc_start: 0.8653 (mtm) cc_final: 0.8445 (mtm) REVERT: B 394 MET cc_start: 0.7705 (ttm) cc_final: 0.7362 (ttp) REVERT: E 104 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8128 (p0) REVERT: E 108 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: F 42 TYR cc_start: 0.9352 (m-80) cc_final: 0.8866 (m-10) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.2344 time to fit residues: 30.8602 Evaluate side-chains 88 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN B 119 ASN B 280 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9379 Z= 0.214 Angle : 0.526 7.567 12725 Z= 0.269 Chirality : 0.046 0.303 1454 Planarity : 0.004 0.043 1645 Dihedral : 5.992 56.819 1617 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.50 % Allowed : 10.42 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1170 helix: -0.26 (0.53), residues: 97 sheet: 0.39 (0.23), residues: 445 loop : -0.24 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 427 TYR 0.012 0.001 TYR A 112 ARG 0.006 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.153 Fit side-chains REVERT: B 278 MET cc_start: 0.8584 (mtm) cc_final: 0.8364 (mtm) REVERT: B 394 MET cc_start: 0.7631 (ttm) cc_final: 0.7310 (ttp) REVERT: E 108 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: F 42 TYR cc_start: 0.9340 (m-80) cc_final: 0.8817 (m-10) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.2350 time to fit residues: 27.8163 Evaluate side-chains 85 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9379 Z= 0.357 Angle : 0.593 8.791 12725 Z= 0.301 Chirality : 0.048 0.307 1454 Planarity : 0.004 0.047 1645 Dihedral : 6.017 53.001 1617 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.83 % Allowed : 10.42 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1170 helix: -0.49 (0.53), residues: 97 sheet: 0.23 (0.23), residues: 448 loop : -0.31 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 230 HIS 0.004 0.001 HIS B 266 PHE 0.023 0.002 PHE A 427 TYR 0.019 0.002 TYR F 55 ARG 0.007 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: B 394 MET cc_start: 0.7704 (ttm) cc_final: 0.7365 (ttp) REVERT: E 104 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8191 (p0) REVERT: E 108 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: F 42 TYR cc_start: 0.9351 (m-80) cc_final: 0.8890 (m-10) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.2318 time to fit residues: 29.6790 Evaluate side-chains 89 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9379 Z= 0.206 Angle : 0.532 8.238 12725 Z= 0.272 Chirality : 0.046 0.286 1454 Planarity : 0.004 0.044 1645 Dihedral : 5.738 50.887 1617 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.72 % Allowed : 10.63 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1170 helix: -0.29 (0.53), residues: 97 sheet: 0.32 (0.24), residues: 448 loop : -0.27 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS B 161 PHE 0.012 0.001 PHE A 427 TYR 0.011 0.001 TYR A 112 ARG 0.008 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: B 94 MET cc_start: 0.7505 (tpt) cc_final: 0.6857 (tpt) REVERT: B 172 TYR cc_start: 0.8111 (m-80) cc_final: 0.7891 (m-10) REVERT: B 394 MET cc_start: 0.7660 (ttm) cc_final: 0.7351 (ttp) REVERT: E 108 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: F 4 MET cc_start: 0.8721 (tpt) cc_final: 0.8123 (tpt) REVERT: F 42 TYR cc_start: 0.9335 (m-80) cc_final: 0.8874 (m-10) outliers start: 16 outliers final: 13 residues processed: 94 average time/residue: 0.2265 time to fit residues: 29.9341 Evaluate side-chains 90 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9379 Z= 0.207 Angle : 0.530 8.096 12725 Z= 0.271 Chirality : 0.046 0.277 1454 Planarity : 0.004 0.041 1645 Dihedral : 5.687 48.370 1617 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.61 % Allowed : 10.96 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1170 helix: -0.26 (0.53), residues: 97 sheet: 0.33 (0.23), residues: 450 loop : -0.33 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.002 0.001 HIS B 161 PHE 0.013 0.001 PHE A 427 TYR 0.019 0.001 TYR E 100 ARG 0.007 0.000 ARG F 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: B 94 MET cc_start: 0.7493 (tpt) cc_final: 0.7140 (tpt) REVERT: B 394 MET cc_start: 0.7677 (ttm) cc_final: 0.7353 (ttp) REVERT: E 108 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: F 4 MET cc_start: 0.8718 (tpt) cc_final: 0.8115 (tpt) REVERT: F 42 TYR cc_start: 0.9328 (m-80) cc_final: 0.8868 (m-10) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.2296 time to fit residues: 29.4537 Evaluate side-chains 88 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.0770 chunk 13 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.085035 restraints weight = 15771.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.087184 restraints weight = 10265.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088627 restraints weight = 7749.368| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9379 Z= 0.146 Angle : 0.510 8.404 12725 Z= 0.262 Chirality : 0.045 0.260 1454 Planarity : 0.004 0.039 1645 Dihedral : 5.496 46.667 1617 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.29 % Allowed : 11.39 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1170 helix: -0.20 (0.53), residues: 97 sheet: 0.39 (0.23), residues: 452 loop : -0.30 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 61 HIS 0.003 0.001 HIS B 63 PHE 0.009 0.001 PHE B 413 TYR 0.010 0.001 TYR B 109 ARG 0.007 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.37 seconds wall clock time: 34 minutes 30.93 seconds (2070.93 seconds total)