Starting phenix.real_space_refine on Mon Oct 14 00:33:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsd_43494/10_2024/8vsd_43494.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsd_43494/10_2024/8vsd_43494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsd_43494/10_2024/8vsd_43494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsd_43494/10_2024/8vsd_43494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsd_43494/10_2024/8vsd_43494.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsd_43494/10_2024/8vsd_43494.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.059 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 83 5.16 5 C 10288 2.51 5 N 2813 2.21 5 O 3086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 16276 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3950 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 29, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 86 Chain: "A" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4242 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 200 Chain: "B" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2744 Classifications: {'peptide': 349} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "E" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2555 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 296} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2553 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 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: "J" 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: 11.38, per 1000 atoms: 0.70 Number of scatterers: 16276 At special positions: 0 Unit cell: (100.981, 118.594, 237.188, 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 83 16.00 Mg 1 11.99 O 3086 8.00 N 2813 7.00 C 10288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 35 " distance=2.03 Simple disulfide: pdb=" SG CYS I 211 " - pdb=" SG CYS F 4 " distance=2.03 Simple disulfide: pdb=" SG CYS I 350 " - pdb=" SG CYS E 4 " distance=2.03 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 436 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 194 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 264 " - pdb=" SG CYS E 327 " distance=2.03 Simple disulfide: pdb=" SG CYS E 293 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 360 " distance=2.03 Simple disulfide: pdb=" SG CYS E 326 " - pdb=" SG CYS F 326 " distance=2.03 Simple disulfide: pdb=" SG CYS F 264 " - pdb=" SG CYS F 327 " distance=2.03 Simple disulfide: pdb=" SG CYS F 293 " - pdb=" SG CYS F 358 " distance=2.02 Simple disulfide: pdb=" SG CYS F 297 " - pdb=" SG CYS F 360 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 260 " " NAG B 501 " - " ASN B 360 " " NAG B 502 " - " 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 J 1 " - " ASN B 414 " Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.6 seconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3928 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 31 sheets defined 16.2% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'I' and resid 65 through 71 removed outlier: 3.823A pdb=" N LEU I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE I 71 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 96 removed outlier: 4.050A pdb=" N ALA I 95 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 96 " --> pdb=" O PHE I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 96' Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'I' and resid 139 through 145 removed outlier: 3.825A pdb=" N ARG I 143 " --> pdb=" O GLY I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 338 removed outlier: 3.832A pdb=" N HIS I 337 " --> pdb=" O SER I 333 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 338 " --> pdb=" O PHE I 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 333 through 338' Processing helix chain 'I' and resid 509 through 513 Processing helix chain 'I' and resid 579 through 587 removed outlier: 3.554A pdb=" N HIS I 586 " --> pdb=" O ALA I 582 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 587 " --> pdb=" O ALA I 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.596A pdb=" N ASP A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) 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 'A' and resid 513 through 517 Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.325A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.727A pdb=" N SER B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.601A pdb=" N ARG B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 4.145A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 removed outlier: 4.004A pdb=" N ILE B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.636A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 253 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 277' Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.663A pdb=" N LEU B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.686A pdb=" N LEU E 28 " --> pdb=" O ILE E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.874A pdb=" N LYS E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.794A pdb=" N GLN E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 removed outlier: 4.173A pdb=" N LEU E 218 " --> pdb=" O ARG E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'E' and resid 235 through 239 removed outlier: 4.132A pdb=" N ALA E 239 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 315 removed outlier: 3.650A pdb=" N ASN E 315 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 323 removed outlier: 4.300A pdb=" N SER E 322 " --> pdb=" O ASN E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 108 through 115 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 171 through 182 Processing helix chain 'F' and resid 235 through 239 Processing helix chain 'F' and resid 310 through 318 removed outlier: 4.103A pdb=" N TYR F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'I' and resid 102 through 103 removed outlier: 6.962A pdb=" N LEU I 102 " --> pdb=" O ASP I 130 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU I 129 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'I' and resid 270 through 271 removed outlier: 7.157A pdb=" N LEU I 344 " --> pdb=" O ASP I 369 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU I 368 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER I 449 " --> pdb=" O LEU I 415 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU I 448 " --> pdb=" O ASP I 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 353 through 354 Processing sheet with id=AA6, first strand: chain 'I' and resid 540 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.279A 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: 11.026A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 431 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.783A pdb=" N CYS A 59 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.814A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.810A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.506A pdb=" N ALA A 107 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.676A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 225 through 229 removed outlier: 3.954A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AB6, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB7, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.453A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN A 377 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.821A pdb=" N PHE A 473 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 540 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 541 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 512 " --> pdb=" O TYR A 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AC2, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AC3, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.779A pdb=" N LEU B 387 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 371 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.347A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 407 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 183 through 189 removed outlier: 3.557A pdb=" N VAL B 185 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE B 146 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER B 187 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 144 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 189 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE B 142 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG B 236 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 298 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 238 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA B 300 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 240 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AC7, first strand: chain 'E' and resid 165 through 170 removed outlier: 5.335A pdb=" N VAL F 347 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N ARG E 81 " --> pdb=" O PRO F 345 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N VAL F 347 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N TYR F 340 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N GLN F 349 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL F 338 " --> pdb=" O GLN F 349 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N SER F 351 " --> pdb=" O PRO F 336 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET F 353 " --> pdb=" O PRO F 334 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL F 355 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU F 332 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER F 357 " --> pdb=" O GLN F 330 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU F 284 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR F 340 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE F 282 " --> pdb=" O TYR F 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 105 removed outlier: 6.775A pdb=" N GLN E 137 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU E 157 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 139 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN E 155 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU E 141 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 265 through 268 removed outlier: 3.643A pdb=" N PHE E 292 " --> pdb=" O ARG E 267 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 282 through 284 removed outlier: 7.374A pdb=" N ILE E 282 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR E 340 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 284 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER E 357 " --> pdb=" O GLN E 330 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU E 332 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL E 355 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET E 353 " --> pdb=" O PRO E 334 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N SER E 351 " --> pdb=" O PRO E 336 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N VAL E 338 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N GLN E 349 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N TYR E 340 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N VAL E 347 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N ARG F 81 " --> pdb=" O PRO E 345 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL E 347 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 77 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 125 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU F 165 " --> pdb=" O ARG F 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 101 through 107 removed outlier: 5.634A pdb=" N GLY F 187 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN F 143 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR F 152 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 265 through 267 removed outlier: 3.597A pdb=" N LEU F 294 " --> pdb=" O CYS F 265 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 270 through 272 390 hydrogen bonds defined for protein. 1005 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: 5.72 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4755 1.33 - 1.45: 2600 1.45 - 1.57: 9131 1.57 - 1.69: 1 1.69 - 1.82: 118 Bond restraints: 16605 Sorted by residual: bond pdb=" CA ILE I 330 " pdb=" C ILE I 330 " ideal model delta sigma weight residual 1.525 1.555 -0.030 8.80e-03 1.29e+04 1.13e+01 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" CZ ARG I 278 " pdb=" NH2 ARG I 278 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" CZ ARG I 348 " pdb=" NH2 ARG I 348 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.53e+00 bond pdb=" CZ ARG I 352 " pdb=" NH2 ARG I 352 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.08e+00 ... (remaining 16600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 21667 1.61 - 3.21: 751 3.21 - 4.82: 117 4.82 - 6.42: 20 6.42 - 8.03: 8 Bond angle restraints: 22563 Sorted by residual: angle pdb=" N ASP B 251 " pdb=" CA ASP B 251 " pdb=" C ASP B 251 " ideal model delta sigma weight residual 113.18 108.19 4.99 1.21e+00 6.83e-01 1.70e+01 angle pdb=" C ILE I 330 " pdb=" CA ILE I 330 " pdb=" CB ILE I 330 " ideal model delta sigma weight residual 110.85 115.50 -4.65 1.15e+00 7.56e-01 1.64e+01 angle pdb=" N ASN I 349 " pdb=" CA ASN I 349 " pdb=" C ASN I 349 " ideal model delta sigma weight residual 113.16 117.96 -4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" CA ASN I 325 " pdb=" CB ASN I 325 " pdb=" CG ASN I 325 " ideal model delta sigma weight residual 112.60 108.74 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CB HIS I 372 " pdb=" CG HIS I 372 " pdb=" CD2 HIS I 372 " ideal model delta sigma weight residual 131.20 126.28 4.92 1.30e+00 5.92e-01 1.43e+01 ... (remaining 22558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9595 21.13 - 42.27: 593 42.27 - 63.40: 57 63.40 - 84.54: 20 84.54 - 105.67: 10 Dihedral angle restraints: 10275 sinusoidal: 4184 harmonic: 6091 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 39.43 53.57 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS I 425 " pdb=" SG CYS I 425 " pdb=" SG CYS I 436 " pdb=" CB CYS I 436 " ideal model delta sinusoidal sigma weight residual 93.00 41.78 51.22 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA CYS B 224 " pdb=" CB CYS B 224 " pdb=" SG CYS B 224 " pdb=" SG CYS B 265 " ideal model delta sinusoidal sigma weight residual -73.00 2.43 -75.43 1 2.00e+01 2.50e-03 1.80e+01 ... (remaining 10272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2164 0.061 - 0.122: 391 0.122 - 0.183: 32 0.183 - 0.244: 5 0.244 - 0.305: 5 Chirality restraints: 2597 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 44 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ASN I 274 " pdb=" N ASN I 274 " pdb=" C ASN I 274 " pdb=" CB ASN I 274 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 2.75 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2594 not shown) Planarity restraints: 2938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 575 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 576 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 576 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 576 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 395 " 0.019 2.00e-02 2.50e+03 1.70e-02 7.21e+00 pdb=" CG TRP A 395 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 395 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 395 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 395 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 395 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 395 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 395 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 395 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 395 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 372 " -0.027 2.00e-02 2.50e+03 2.03e-02 6.17e+00 pdb=" CG HIS I 372 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS I 372 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS I 372 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS I 372 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS I 372 " -0.015 2.00e-02 2.50e+03 ... (remaining 2935 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 69 2.45 - 3.06: 10198 3.06 - 3.67: 22983 3.67 - 4.29: 34317 4.29 - 4.90: 59149 Nonbonded interactions: 126716 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B 504 " model vdw 1.833 2.170 nonbonded pdb=" OG SER B 116 " pdb="MG MG B 504 " model vdw 1.855 2.170 nonbonded pdb=" OD2 ASP B 151 " pdb="CA CA B 503 " model vdw 2.173 2.510 nonbonded pdb=" OD1 ASN E 107 " pdb=" OG SER E 109 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR E 99 " pdb=" OG1 THR E 202 " model vdw 2.212 3.040 ... (remaining 126711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'E' and (resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD )) or resid 6 or (resid 7 and (name N \ or name CA or name C or name O or name CB )) or resid 8 through 60 or resid 73 t \ hrough 210 or resid 224 through 361)) selection = (chain 'F' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 60 or resid 73 through 132 or resid 134 through 240 or resi \ d 262 through 301 or resid 310 through 361)) } 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 individual isotropic 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: 8.490 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.410 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16605 Z= 0.332 Angle : 0.718 8.027 22563 Z= 0.404 Chirality : 0.049 0.305 2597 Planarity : 0.004 0.077 2930 Dihedral : 13.626 105.671 6287 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.18), residues: 2079 helix: -0.47 (0.33), residues: 245 sheet: -1.40 (0.21), residues: 558 loop : -1.23 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 395 HIS 0.005 0.001 HIS E 222 PHE 0.015 0.001 PHE A 427 TYR 0.032 0.002 TYR A 275 ARG 0.011 0.001 ARG E 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3461 time to fit residues: 66.2042 Evaluate side-chains 102 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 121 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16605 Z= 0.208 Angle : 0.574 7.200 22563 Z= 0.295 Chirality : 0.044 0.215 2597 Planarity : 0.004 0.049 2930 Dihedral : 7.472 87.073 2619 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.54 % Allowed : 6.44 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2079 helix: -0.39 (0.33), residues: 252 sheet: -1.28 (0.21), residues: 593 loop : -1.02 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 395 HIS 0.005 0.001 HIS B 200 PHE 0.012 0.001 PHE A 427 TYR 0.018 0.001 TYR F 142 ARG 0.006 0.000 ARG I 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 2.498 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 119 average time/residue: 0.3404 time to fit residues: 61.3544 Evaluate side-chains 106 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 187 optimal weight: 0.0060 chunk 64 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16605 Z= 0.302 Angle : 0.591 7.765 22563 Z= 0.300 Chirality : 0.045 0.193 2597 Planarity : 0.004 0.044 2930 Dihedral : 6.925 71.657 2619 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.13 % Allowed : 9.18 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2079 helix: -0.45 (0.33), residues: 260 sheet: -1.26 (0.21), residues: 575 loop : -1.10 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 114 HIS 0.006 0.001 HIS B 280 PHE 0.018 0.002 PHE A 19 TYR 0.015 0.002 TYR A 275 ARG 0.004 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 2.210 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 0.3507 time to fit residues: 62.2905 Evaluate side-chains 111 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 201 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16605 Z= 0.155 Angle : 0.503 7.412 22563 Z= 0.257 Chirality : 0.042 0.204 2597 Planarity : 0.003 0.042 2930 Dihedral : 6.095 70.899 2619 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.77 % Allowed : 10.43 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2079 helix: -0.03 (0.35), residues: 247 sheet: -1.03 (0.21), residues: 576 loop : -0.97 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.004 0.001 HIS E 100 PHE 0.011 0.001 PHE A 427 TYR 0.014 0.001 TYR F 142 ARG 0.002 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 2.633 Fit side-chains REVERT: I 89 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6903 (mt0) REVERT: A 275 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: B 192 ILE cc_start: 0.7826 (mm) cc_final: 0.7618 (mm) outliers start: 13 outliers final: 5 residues processed: 117 average time/residue: 0.3284 time to fit residues: 58.4105 Evaluate side-chains 106 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 275 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16605 Z= 0.218 Angle : 0.526 7.551 22563 Z= 0.268 Chirality : 0.043 0.266 2597 Planarity : 0.003 0.041 2930 Dihedral : 5.853 68.091 2619 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.73 % Allowed : 10.19 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2079 helix: -0.03 (0.35), residues: 247 sheet: -1.04 (0.21), residues: 563 loop : -0.96 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.004 0.001 HIS I 181 PHE 0.014 0.001 PHE A 19 TYR 0.013 0.001 TYR F 142 ARG 0.002 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8770 (m-80) outliers start: 29 outliers final: 18 residues processed: 124 average time/residue: 0.2843 time to fit residues: 54.8365 Evaluate side-chains 120 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.7821 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16605 Z= 0.242 Angle : 0.537 7.856 22563 Z= 0.273 Chirality : 0.044 0.274 2597 Planarity : 0.003 0.040 2930 Dihedral : 5.615 65.024 2619 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.79 % Allowed : 10.79 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2079 helix: -0.04 (0.35), residues: 247 sheet: -1.03 (0.21), residues: 562 loop : -0.96 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.005 0.001 HIS E 100 PHE 0.015 0.001 PHE A 19 TYR 0.013 0.001 TYR F 142 ARG 0.002 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 2.760 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.9072 (tpp) cc_final: 0.8803 (tpp) REVERT: A 275 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8814 (m-80) outliers start: 30 outliers final: 24 residues processed: 127 average time/residue: 0.3307 time to fit residues: 65.1693 Evaluate side-chains 124 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16605 Z= 0.289 Angle : 0.569 7.461 22563 Z= 0.290 Chirality : 0.045 0.285 2597 Planarity : 0.004 0.040 2930 Dihedral : 5.600 61.635 2619 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.91 % Allowed : 11.14 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2079 helix: -0.25 (0.34), residues: 259 sheet: -1.10 (0.21), residues: 565 loop : -1.01 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 114 HIS 0.005 0.001 HIS B 180 PHE 0.017 0.001 PHE A 19 TYR 0.014 0.002 TYR A 224 ARG 0.004 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.9072 (tpp) cc_final: 0.8808 (tpp) REVERT: A 275 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: F 311 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8416 (mp) outliers start: 32 outliers final: 25 residues processed: 131 average time/residue: 0.2985 time to fit residues: 60.0542 Evaluate side-chains 130 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 136 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16605 Z= 0.200 Angle : 0.527 8.231 22563 Z= 0.268 Chirality : 0.043 0.271 2597 Planarity : 0.003 0.040 2930 Dihedral : 5.342 62.369 2619 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.61 % Allowed : 11.74 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2079 helix: -0.12 (0.34), residues: 253 sheet: -1.02 (0.21), residues: 564 loop : -0.95 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.005 0.001 HIS E 100 PHE 0.012 0.001 PHE A 19 TYR 0.013 0.001 TYR F 142 ARG 0.006 0.000 ARG I 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 2.214 Fit side-chains revert: symmetry clash REVERT: I 568 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7253 (mp) REVERT: A 261 MET cc_start: 0.9058 (tpp) cc_final: 0.8811 (tpp) REVERT: A 275 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (m-80) REVERT: A 395 TRP cc_start: 0.7249 (m100) cc_final: 0.6841 (m100) outliers start: 27 outliers final: 23 residues processed: 126 average time/residue: 0.3187 time to fit residues: 63.6882 Evaluate side-chains 125 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 chunk 146 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7790 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16605 Z= 0.164 Angle : 0.504 8.183 22563 Z= 0.256 Chirality : 0.042 0.226 2597 Planarity : 0.003 0.040 2930 Dihedral : 5.024 63.773 2619 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.37 % Allowed : 12.16 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2079 helix: 0.08 (0.35), residues: 246 sheet: -0.90 (0.21), residues: 567 loop : -0.91 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 114 HIS 0.003 0.001 HIS B 266 PHE 0.009 0.001 PHE A 340 TYR 0.012 0.001 TYR F 142 ARG 0.004 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 2.006 Fit side-chains revert: symmetry clash REVERT: I 568 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7244 (mp) REVERT: A 261 MET cc_start: 0.9058 (tpp) cc_final: 0.8847 (tpp) REVERT: F 311 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8410 (mp) outliers start: 23 outliers final: 20 residues processed: 126 average time/residue: 0.3044 time to fit residues: 59.6266 Evaluate side-chains 122 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 165 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 131 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16605 Z= 0.160 Angle : 0.501 8.336 22563 Z= 0.254 Chirality : 0.042 0.226 2597 Planarity : 0.003 0.041 2930 Dihedral : 4.871 64.615 2619 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.55 % Allowed : 12.22 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2079 helix: 0.13 (0.35), residues: 246 sheet: -0.85 (0.21), residues: 571 loop : -0.88 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.003 0.001 HIS B 280 PHE 0.009 0.001 PHE A 427 TYR 0.013 0.001 TYR A 275 ARG 0.003 0.000 ARG B 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: I 568 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7232 (mp) REVERT: A 261 MET cc_start: 0.9062 (tpp) cc_final: 0.8861 (tpp) REVERT: F 311 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (mp) outliers start: 26 outliers final: 21 residues processed: 134 average time/residue: 0.3312 time to fit residues: 68.7827 Evaluate side-chains 129 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 145 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106045 restraints weight = 29009.348| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.46 r_work: 0.3271 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16605 Z= 0.180 Angle : 0.514 8.968 22563 Z= 0.259 Chirality : 0.043 0.220 2597 Planarity : 0.003 0.041 2930 Dihedral : 4.848 64.612 2619 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.49 % Allowed : 12.46 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2079 helix: 0.14 (0.35), residues: 246 sheet: -0.83 (0.21), residues: 571 loop : -0.88 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 395 HIS 0.005 0.001 HIS E 100 PHE 0.011 0.001 PHE A 19 TYR 0.013 0.001 TYR F 142 ARG 0.002 0.000 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.34 seconds wall clock time: 69 minutes 56.61 seconds (4196.61 seconds total)