Starting phenix.real_space_refine on Thu Mar 14 16:26:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujc_20796/03_2024/6ujc_20796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujc_20796/03_2024/6ujc_20796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujc_20796/03_2024/6ujc_20796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujc_20796/03_2024/6ujc_20796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujc_20796/03_2024/6ujc_20796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ujc_20796/03_2024/6ujc_20796.pdb" } resolution = 3.56 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= 0.002 sd= 0.048 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 5803 2.51 5 N 1553 2.21 5 O 1804 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 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 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "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 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 561": "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 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9209 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: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 4} 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: 11 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: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 112} 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: 5.28, per 1000 atoms: 0.57 Number of scatterers: 9209 At special positions: 0 Unit cell: (72.63, 100.875, 164.09, 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 1804 8.00 N 1553 7.00 C 5803 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=2.02 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.16 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.02 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.04 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 98 " distance=2.04 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: 3.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 13.3% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 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 126 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.810A pdb=" N HIS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (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: 4.032A 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 31 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 'F' and resid 89 through 93 removed outlier: 3.852A pdb=" N LEU F 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.034A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (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: 7.010A 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 98 through 101 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.537A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.513A 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: 6.498A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.572A 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: 5.665A pdb=" N ASP A 357 " --> pdb=" O LEU A 347 " (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 511 through 513 Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.746A pdb=" N LEU A 454 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.554A pdb=" N CYS A 461 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.654A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.326A 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: 5.330A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.202A 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: 6.453A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.760A 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 4 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.808A pdb=" N LEU F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR F 59 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP F 45 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 344 hydrogen bonds defined for protein. 873 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: 2.93 Time building geometry restraints manager: 3.65 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: 1936 1.32 - 1.45: 2441 1.45 - 1.58: 4947 1.58 - 1.71: 5 1.71 - 1.84: 66 Bond restraints: 9395 Sorted by residual: bond pdb=" NE ARG F 32 " pdb=" CZ ARG F 32 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.10e-02 8.26e+03 1.21e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.456 -0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+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 1.13e+01 ... (remaining 9390 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 249 105.94 - 112.96: 4843 112.96 - 119.99: 3290 119.99 - 127.01: 4292 127.01 - 134.03: 70 Bond angle restraints: 12744 Sorted by residual: angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 128.10 -8.54 1.02e+00 9.61e-01 7.02e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.02 -8.46 1.02e+00 9.61e-01 6.88e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.27e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.45 -7.89 1.02e+00 9.61e-01 5.98e+01 angle pdb=" C LEU A 463 " pdb=" N PRO A 464 " pdb=" CA PRO A 464 " ideal model delta sigma weight residual 119.78 127.54 -7.76 1.03e+00 9.43e-01 5.68e+01 ... (remaining 12739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 5669 21.51 - 43.01: 107 43.01 - 64.52: 30 64.52 - 86.02: 19 86.02 - 107.53: 7 Dihedral angle restraints: 5832 sinusoidal: 2437 harmonic: 3395 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 41.37 51.63 1 1.00e+01 1.00e-02 3.64e+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 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.19 34.81 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 5829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 998 0.074 - 0.148: 342 0.148 - 0.221: 74 0.221 - 0.295: 27 0.295 - 0.369: 15 Chirality restraints: 1456 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 2.28 0.12 2.00e-02 2.50e+03 3.90e+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 -2.28 -0.12 2.00e-02 2.50e+03 3.50e+01 chirality pdb=" C1 MAN C 6 " pdb=" O6 BMA C 3 " pdb=" C2 MAN C 6 " pdb=" O5 MAN C 6 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.33e+01 ... (remaining 1453 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.09e-02 1.19e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.027 2.00e-02 2.50e+03 2.82e-02 9.93e+00 pdb=" CG ASN A 44 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 103 " 0.030 2.00e-02 2.50e+03 1.54e-02 4.75e+00 pdb=" CG TYR B 103 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 103 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 103 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 103 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 103 " 0.018 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 30 2.41 - 3.04: 5613 3.04 - 3.66: 12870 3.66 - 4.28: 21662 4.28 - 4.90: 34679 Nonbonded interactions: 74854 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.792 2.170 nonbonded pdb=" OD1 ASP F 34 " pdb="MG MG B2002 " model vdw 1.885 2.170 nonbonded pdb=" OD2 ASP F 34 " pdb="MG MG B2002 " model vdw 1.901 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 2.003 2.170 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.081 2.510 ... (remaining 74849 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: 1.130 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: 5.710 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.380 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 0.080 9395 Z= 0.904 Angle : 1.396 8.544 12744 Z= 0.948 Chirality : 0.087 0.369 1456 Planarity : 0.006 0.028 1648 Dihedral : 11.400 107.525 3635 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % 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: 0.47 (0.23), residues: 1174 helix: -1.21 (0.44), residues: 95 sheet: 0.80 (0.23), residues: 457 loop : 0.32 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP B 308 HIS 0.005 0.001 HIS A 521 PHE 0.024 0.004 PHE A 276 TYR 0.030 0.005 TYR B 103 ARG 0.005 0.001 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.7852 (ptm) cc_final: 0.7498 (ptp) REVERT: E 52 ASN cc_start: 0.7606 (t0) cc_final: 0.6974 (p0) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2617 time to fit residues: 55.9674 Evaluate side-chains 70 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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: 0.7980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN B 118 HIS B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9395 Z= 0.242 Angle : 0.644 14.450 12744 Z= 0.333 Chirality : 0.048 0.176 1456 Planarity : 0.004 0.032 1648 Dihedral : 7.578 86.655 1620 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.72 % Allowed : 6.23 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1174 helix: 0.09 (0.54), residues: 90 sheet: 0.83 (0.22), residues: 467 loop : 0.13 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.002 0.001 HIS B 118 PHE 0.015 0.002 PHE A 276 TYR 0.015 0.002 TYR A 112 ARG 0.006 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.7704 (ptm) cc_final: 0.7348 (ptp) REVERT: B 117 MET cc_start: 0.8447 (mmm) cc_final: 0.8216 (tpp) REVERT: B 392 VAL cc_start: 0.8718 (t) cc_final: 0.8505 (p) REVERT: E 52 ASN cc_start: 0.7282 (t0) cc_final: 0.6946 (t0) outliers start: 16 outliers final: 11 residues processed: 90 average time/residue: 0.2360 time to fit residues: 29.5317 Evaluate side-chains 68 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9395 Z= 0.210 Angle : 0.580 13.206 12744 Z= 0.294 Chirality : 0.046 0.218 1456 Planarity : 0.004 0.026 1648 Dihedral : 6.200 66.621 1620 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.50 % Allowed : 7.09 % Favored : 91.41 % 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: 1174 helix: 0.41 (0.57), residues: 89 sheet: 0.74 (0.23), residues: 459 loop : 0.09 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS A 113 PHE 0.014 0.001 PHE A 477 TYR 0.013 0.001 TYR A 112 ARG 0.004 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.7792 (ptm) cc_final: 0.7437 (ptp) REVERT: B 392 VAL cc_start: 0.8711 (t) cc_final: 0.8477 (p) REVERT: E 52 ASN cc_start: 0.7349 (t0) cc_final: 0.7110 (t0) REVERT: F 21 MET cc_start: 0.7372 (ptp) cc_final: 0.7076 (ptp) outliers start: 14 outliers final: 7 residues processed: 75 average time/residue: 0.2058 time to fit residues: 22.6573 Evaluate side-chains 59 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9395 Z= 0.269 Angle : 0.591 12.756 12744 Z= 0.302 Chirality : 0.046 0.251 1456 Planarity : 0.004 0.033 1648 Dihedral : 5.820 56.707 1620 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.04 % Allowed : 7.63 % 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: 0.32 (0.24), residues: 1174 helix: 0.44 (0.58), residues: 90 sheet: 0.70 (0.24), residues: 448 loop : -0.10 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 47 HIS 0.003 0.001 HIS B 280 PHE 0.011 0.001 PHE A 276 TYR 0.017 0.001 TYR A 112 ARG 0.004 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7075 (mtp) REVERT: A 400 MET cc_start: 0.7950 (ptm) cc_final: 0.7651 (ptp) REVERT: B 94 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7410 (ppp) REVERT: B 110 LEU cc_start: 0.8917 (tp) cc_final: 0.8569 (tt) REVERT: F 87 SER cc_start: 0.6218 (m) cc_final: 0.5745 (t) outliers start: 19 outliers final: 11 residues processed: 73 average time/residue: 0.2207 time to fit residues: 23.3021 Evaluate side-chains 65 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 105 SER 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: 0.9980 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9395 Z= 0.270 Angle : 0.589 12.183 12744 Z= 0.298 Chirality : 0.046 0.261 1456 Planarity : 0.004 0.035 1648 Dihedral : 5.488 49.149 1620 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.36 % Allowed : 7.52 % Favored : 90.12 % 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: 1174 helix: 0.47 (0.58), residues: 90 sheet: 0.48 (0.24), residues: 453 loop : -0.29 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 47 HIS 0.003 0.001 HIS B 166 PHE 0.014 0.001 PHE A 477 TYR 0.018 0.001 TYR A 112 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7182 (mtp) REVERT: A 400 MET cc_start: 0.7891 (ptm) cc_final: 0.7627 (ptp) REVERT: B 94 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7325 (ppp) REVERT: B 110 LEU cc_start: 0.8904 (tp) cc_final: 0.8542 (tt) REVERT: F 87 SER cc_start: 0.6030 (m) cc_final: 0.5447 (t) outliers start: 22 outliers final: 13 residues processed: 71 average time/residue: 0.1988 time to fit residues: 21.0234 Evaluate side-chains 62 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 0.0170 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9395 Z= 0.319 Angle : 0.614 11.609 12744 Z= 0.314 Chirality : 0.047 0.248 1456 Planarity : 0.004 0.034 1648 Dihedral : 5.485 44.257 1620 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.69 % Allowed : 8.81 % Favored : 88.51 % 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: 1174 helix: 0.46 (0.58), residues: 90 sheet: 0.35 (0.24), residues: 443 loop : -0.44 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 47 HIS 0.004 0.001 HIS B 166 PHE 0.012 0.002 PHE A 94 TYR 0.018 0.002 TYR A 112 ARG 0.002 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 52 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7281 (mtp) REVERT: A 400 MET cc_start: 0.8014 (ptm) cc_final: 0.7789 (ptp) REVERT: B 94 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7319 (ppp) REVERT: B 110 LEU cc_start: 0.8908 (tp) cc_final: 0.8557 (tt) REVERT: B 394 MET cc_start: 0.4782 (ppp) cc_final: 0.4445 (ppp) REVERT: B 407 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8521 (tp) outliers start: 25 outliers final: 17 residues processed: 71 average time/residue: 0.1938 time to fit residues: 20.7819 Evaluate side-chains 65 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 62 SER 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: 1.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 0.0060 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9395 Z= 0.178 Angle : 0.533 11.880 12744 Z= 0.269 Chirality : 0.045 0.238 1456 Planarity : 0.003 0.031 1648 Dihedral : 5.059 42.282 1620 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.69 % Allowed : 9.02 % Favored : 88.29 % 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: -0.17 (0.24), residues: 1174 helix: 0.69 (0.60), residues: 90 sheet: 0.23 (0.24), residues: 457 loop : -0.42 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE A 477 TYR 0.013 0.001 TYR A 112 ARG 0.002 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7113 (mtp) REVERT: A 400 MET cc_start: 0.7942 (ptm) cc_final: 0.7740 (ptp) REVERT: B 94 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7251 (ppp) REVERT: B 394 MET cc_start: 0.4946 (ppp) cc_final: 0.4591 (ppp) REVERT: B 407 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8505 (tp) outliers start: 25 outliers final: 18 residues processed: 68 average time/residue: 0.2070 time to fit residues: 21.1248 Evaluate side-chains 66 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9395 Z= 0.193 Angle : 0.526 11.356 12744 Z= 0.266 Chirality : 0.045 0.215 1456 Planarity : 0.003 0.032 1648 Dihedral : 4.874 39.930 1620 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.36 % Allowed : 9.45 % Favored : 88.18 % 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: -0.15 (0.25), residues: 1174 helix: 0.82 (0.60), residues: 90 sheet: 0.25 (0.24), residues: 455 loop : -0.43 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.002 0.001 HIS A 113 PHE 0.017 0.001 PHE B 388 TYR 0.012 0.001 TYR A 112 ARG 0.003 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6955 (mtp) REVERT: B 94 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7220 (ppp) REVERT: B 143 ARG cc_start: 0.7545 (mtp85) cc_final: 0.6984 (mtp85) REVERT: B 407 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8536 (tp) outliers start: 22 outliers final: 17 residues processed: 69 average time/residue: 0.1994 time to fit residues: 20.3400 Evaluate side-chains 67 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR 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: 0.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 103 optimal weight: 0.5980 chunk 68 optimal weight: 0.0570 chunk 110 optimal weight: 0.0010 chunk 67 optimal weight: 0.7980 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 84 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9395 Z= 0.139 Angle : 0.511 11.380 12744 Z= 0.256 Chirality : 0.044 0.203 1456 Planarity : 0.003 0.033 1648 Dihedral : 4.611 38.400 1620 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.26 % Allowed : 9.56 % Favored : 88.18 % 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: -0.03 (0.24), residues: 1174 helix: 0.94 (0.61), residues: 90 sheet: 0.34 (0.24), residues: 455 loop : -0.36 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.003 0.000 HIS A 113 PHE 0.012 0.001 PHE A 477 TYR 0.019 0.001 TYR F 59 ARG 0.002 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7111 (mtp) REVERT: B 94 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7259 (ppp) REVERT: B 117 MET cc_start: 0.8811 (tpp) cc_final: 0.8505 (tpp) REVERT: B 407 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8531 (tp) REVERT: F 21 MET cc_start: 0.8301 (mtm) cc_final: 0.8086 (mtm) outliers start: 21 outliers final: 17 residues processed: 72 average time/residue: 0.2081 time to fit residues: 22.0990 Evaluate side-chains 68 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9395 Z= 0.222 Angle : 0.542 10.766 12744 Z= 0.275 Chirality : 0.045 0.193 1456 Planarity : 0.003 0.033 1648 Dihedral : 4.719 37.377 1620 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 9.99 % Favored : 87.86 % 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 (0.25), residues: 1174 helix: 0.94 (0.61), residues: 90 sheet: 0.31 (0.24), residues: 455 loop : -0.39 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS A 113 PHE 0.012 0.001 PHE A 477 TYR 0.013 0.001 TYR A 435 ARG 0.002 0.000 ARG E 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6964 (mtp) REVERT: B 94 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7332 (ppp) REVERT: B 143 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7010 (mtp85) REVERT: B 407 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8537 (tp) outliers start: 20 outliers final: 16 residues processed: 65 average time/residue: 0.2070 time to fit residues: 19.9100 Evaluate side-chains 65 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 0.0020 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.115823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.098351 restraints weight = 20789.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100850 restraints weight = 12189.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.102541 restraints weight = 8306.868| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9395 Z= 0.206 Angle : 0.536 11.741 12744 Z= 0.271 Chirality : 0.045 0.186 1456 Planarity : 0.003 0.033 1648 Dihedral : 4.693 36.353 1620 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.26 % Allowed : 9.99 % 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: -0.06 (0.25), residues: 1174 helix: 0.93 (0.61), residues: 90 sheet: 0.32 (0.24), residues: 454 loop : -0.39 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS A 113 PHE 0.011 0.001 PHE A 477 TYR 0.014 0.001 TYR F 59 ARG 0.002 0.000 ARG E 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.12 seconds wall clock time: 33 minutes 44.88 seconds (2024.88 seconds total)