Starting phenix.real_space_refine on Thu Mar 14 08:11:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd5_14636/03_2024/7zd5_14636_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd5_14636/03_2024/7zd5_14636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd5_14636/03_2024/7zd5_14636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd5_14636/03_2024/7zd5_14636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd5_14636/03_2024/7zd5_14636_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd5_14636/03_2024/7zd5_14636_neut.pdb" } resolution = 3.17 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= 0.005 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5750 2.51 5 N 1575 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 13": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C ASP 391": "OD1" <-> "OD2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C ASP 499": "OD1" <-> "OD2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D ASP 346": "OD1" <-> "OD2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D ARG 447": "NH1" <-> "NH2" Residue "D ASP 476": "OD1" <-> "OD2" Residue "D ARG 485": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D GLU 511": "OE1" <-> "OE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D ARG 566": "NH1" <-> "NH2" Residue "D TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 584": "NH1" <-> "NH2" 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: 8967 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4383 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 551} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 4584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4584 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 27, 'TRANS': 559} Time building chain proxies: 5.27, per 1000 atoms: 0.59 Number of scatterers: 8967 At special positions: 0 Unit cell: (115.506, 95.418, 112.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1613 8.00 N 1575 7.00 C 5750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 67.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.854A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 14 through 50 removed outlier: 3.657A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 61 through 103 removed outlier: 3.759A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.979A pdb=" N GLN C 116 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'C' and resid 131 through 137 removed outlier: 4.518A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 157 removed outlier: 3.854A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 176 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 185 through 208 removed outlier: 3.600A pdb=" N GLY C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 220 through 267 removed outlier: 3.664A pdb=" N THR C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.548A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 296 through 318 removed outlier: 3.754A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 408 through 415 removed outlier: 3.903A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 476 through 492 Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.959A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 555 through 562 removed outlier: 3.645A pdb=" N ARG C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.640A pdb=" N GLN C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 21 through 54 removed outlier: 3.613A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 109 removed outlier: 3.589A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.588A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 162 removed outlier: 3.667A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 164 through 183 removed outlier: 3.627A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.618A pdb=" N ASN D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.564A pdb=" N PHE D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 273 removed outlier: 4.069A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 310 Proline residue: D 298 - end of helix removed outlier: 3.921A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.822A pdb=" N THR D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 398 removed outlier: 3.955A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.519A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.823A pdb=" N ASP D 476 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 500 removed outlier: 3.731A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 535 removed outlier: 3.870A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 533 " --> pdb=" O ASN D 529 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 removed outlier: 4.168A pdb=" N ASP D 549 " --> pdb=" O ASP D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.989A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 removed outlier: 3.541A pdb=" N GLU D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 339 through 342 Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.462A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR C 530 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE C 371 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 428 through 429 Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.462A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 429 removed outlier: 6.932A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D 539 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY D 383 " --> pdb=" O THR D 541 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1521 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: 2.94 Time building geometry restraints manager: 3.83 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: 1866 1.33 - 1.45: 2024 1.45 - 1.57: 5198 1.57 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 9143 Sorted by residual: bond pdb=" N ASN D 431 " pdb=" CA ASN D 431 " ideal model delta sigma weight residual 1.457 1.488 -0.032 9.10e-03 1.21e+04 1.22e+01 bond pdb=" N LEU C 533 " pdb=" CA LEU C 533 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.08e-02 8.57e+03 9.17e+00 bond pdb=" N GLN D 430 " pdb=" CA GLN D 430 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.34e-02 5.57e+03 7.91e+00 bond pdb=" N GLN D 302 " pdb=" CA GLN D 302 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.04e-02 9.25e+03 7.39e+00 bond pdb=" C ALA D 90 " pdb=" O ALA D 90 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.16e-02 7.43e+03 7.21e+00 ... (remaining 9138 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.56: 181 105.56 - 112.70: 4913 112.70 - 119.83: 3009 119.83 - 126.97: 4199 126.97 - 134.11: 119 Bond angle restraints: 12421 Sorted by residual: angle pdb=" C GLU C 118 " pdb=" N LEU C 119 " pdb=" CA LEU C 119 " ideal model delta sigma weight residual 120.44 129.95 -9.51 1.36e+00 5.41e-01 4.89e+01 angle pdb=" N GLU C 118 " pdb=" CA GLU C 118 " pdb=" C GLU C 118 " ideal model delta sigma weight residual 113.17 104.45 8.72 1.26e+00 6.30e-01 4.79e+01 angle pdb=" N ILE D 19 " pdb=" CA ILE D 19 " pdb=" C ILE D 19 " ideal model delta sigma weight residual 109.30 102.95 6.35 1.25e+00 6.40e-01 2.58e+01 angle pdb=" CA GLU C 118 " pdb=" C GLU C 118 " pdb=" N LEU C 119 " ideal model delta sigma weight residual 118.27 112.69 5.58 1.31e+00 5.83e-01 1.82e+01 angle pdb=" C ASN D 431 " pdb=" CA ASN D 431 " pdb=" CB ASN D 431 " ideal model delta sigma weight residual 110.71 114.59 -3.88 9.40e-01 1.13e+00 1.71e+01 ... (remaining 12416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 4853 16.91 - 33.82: 484 33.82 - 50.73: 106 50.73 - 67.64: 10 67.64 - 84.55: 6 Dihedral angle restraints: 5459 sinusoidal: 2142 harmonic: 3317 Sorted by residual: dihedral pdb=" CA THR D 541 " pdb=" C THR D 541 " pdb=" N HIS D 542 " pdb=" CA HIS D 542 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO C 296 " pdb=" C PRO C 296 " pdb=" N VAL C 297 " pdb=" CA VAL C 297 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" C HIS D 93 " pdb=" N HIS D 93 " pdb=" CA HIS D 93 " pdb=" CB HIS D 93 " ideal model delta harmonic sigma weight residual -122.60 -131.27 8.67 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1216 0.058 - 0.116: 203 0.116 - 0.174: 22 0.174 - 0.232: 6 0.232 - 0.289: 2 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CA ILE D 19 " pdb=" N ILE D 19 " pdb=" C ILE D 19 " pdb=" CB ILE D 19 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA HIS D 93 " pdb=" N HIS D 93 " pdb=" C HIS D 93 " pdb=" CB HIS D 93 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ARG C 2 " pdb=" N ARG C 2 " pdb=" C ARG C 2 " pdb=" CB ARG C 2 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1446 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 90 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C ALA D 90 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA D 90 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY D 91 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 557 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C GLN D 557 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN D 557 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP D 558 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 89 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C HIS D 89 " -0.036 2.00e-02 2.50e+03 pdb=" O HIS D 89 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 90 " 0.012 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1421 2.76 - 3.29: 8859 3.29 - 3.83: 14276 3.83 - 4.36: 17801 4.36 - 4.90: 30676 Nonbonded interactions: 73033 Sorted by model distance: nonbonded pdb=" NH2 ARG D 105 " pdb=" O THR D 330 " model vdw 2.219 2.520 nonbonded pdb=" ND2 ASN D 162 " pdb=" OH TYR D 267 " model vdw 2.229 2.520 nonbonded pdb=" NE2 GLN C 421 " pdb=" OE1 GLU C 500 " model vdw 2.230 2.520 nonbonded pdb=" O ALA C 365 " pdb=" OG1 THR C 525 " model vdw 2.249 2.440 nonbonded pdb=" O SER C 315 " pdb=" CB ASP C 319 " model vdw 2.262 3.440 ... (remaining 73028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.080 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: 5.240 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.680 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.006 0.055 9143 Z= 0.371 Angle : 0.725 9.515 12421 Z= 0.449 Chirality : 0.047 0.289 1449 Planarity : 0.004 0.041 1590 Dihedral : 13.880 84.554 3319 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.11 % Allowed : 1.60 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.23), residues: 1151 helix: -1.55 (0.18), residues: 683 sheet: -0.66 (0.75), residues: 49 loop : -0.40 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 427 HIS 0.004 0.001 HIS D 93 PHE 0.012 0.001 PHE C 216 TYR 0.011 0.001 TYR D 88 ARG 0.006 0.001 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8534 (tttt) cc_final: 0.8149 (mmtm) REVERT: C 262 MET cc_start: 0.8726 (mmp) cc_final: 0.8499 (mmp) REVERT: C 520 MET cc_start: 0.7007 (mtm) cc_final: 0.6756 (mtm) REVERT: D 19 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7694 (tp) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.2871 time to fit residues: 33.6155 Evaluate side-chains 72 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN C 571 GLN D 41 GLN D 92 GLN D 93 HIS D 129 GLN D 377 GLN D 431 ASN D 490 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9143 Z= 0.243 Angle : 0.597 5.929 12421 Z= 0.306 Chirality : 0.041 0.145 1449 Planarity : 0.004 0.037 1590 Dihedral : 4.354 17.398 1259 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.86 % Allowed : 7.49 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1151 helix: 0.14 (0.19), residues: 691 sheet: -0.21 (0.79), residues: 49 loop : -0.52 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 427 HIS 0.004 0.001 HIS C 85 PHE 0.013 0.001 PHE C 346 TYR 0.019 0.001 TYR D 88 ARG 0.003 0.000 ARG C 522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.059 Fit side-chains REVERT: C 12 LYS cc_start: 0.8497 (tttt) cc_final: 0.8143 (mmtm) REVERT: C 515 GLU cc_start: 0.7786 (mp0) cc_final: 0.7531 (mp0) REVERT: D 71 LEU cc_start: 0.8716 (tp) cc_final: 0.8434 (mt) REVERT: D 94 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8892 (mp) REVERT: D 154 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8159 (mp) REVERT: D 441 ASP cc_start: 0.7916 (t0) cc_final: 0.7705 (t0) outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 0.2487 time to fit residues: 33.1793 Evaluate side-chains 84 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9143 Z= 0.324 Angle : 0.589 6.076 12421 Z= 0.297 Chirality : 0.042 0.135 1449 Planarity : 0.004 0.038 1590 Dihedral : 4.260 17.347 1257 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.39 % Allowed : 11.44 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1151 helix: 0.83 (0.20), residues: 694 sheet: -0.14 (0.78), residues: 49 loop : -0.49 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 427 HIS 0.004 0.001 HIS C 85 PHE 0.016 0.002 PHE C 216 TYR 0.019 0.002 TYR D 88 ARG 0.003 0.000 ARG D 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.013 Fit side-chains REVERT: C 12 LYS cc_start: 0.8528 (tttt) cc_final: 0.8149 (mmtm) REVERT: C 183 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7633 (mtm110) REVERT: D 71 LEU cc_start: 0.8663 (tp) cc_final: 0.8415 (mt) REVERT: D 154 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8268 (mp) REVERT: D 441 ASP cc_start: 0.7901 (t0) cc_final: 0.7675 (t0) REVERT: D 525 MET cc_start: 0.8309 (mmt) cc_final: 0.7812 (mmt) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 0.2507 time to fit residues: 32.2706 Evaluate side-chains 88 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 580 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9143 Z= 0.204 Angle : 0.524 6.323 12421 Z= 0.265 Chirality : 0.039 0.141 1449 Planarity : 0.003 0.038 1590 Dihedral : 4.030 16.912 1257 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.28 % Allowed : 13.90 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1151 helix: 1.32 (0.20), residues: 695 sheet: -0.22 (0.72), residues: 54 loop : -0.43 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.010 0.001 PHE C 216 TYR 0.019 0.001 TYR D 88 ARG 0.002 0.000 ARG C 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.997 Fit side-chains REVERT: C 12 LYS cc_start: 0.8476 (tttt) cc_final: 0.8186 (mmtm) REVERT: C 183 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7607 (mtm110) REVERT: D 71 LEU cc_start: 0.8624 (tp) cc_final: 0.8417 (mt) REVERT: D 154 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 427 TRP cc_start: 0.6201 (p-90) cc_final: 0.5861 (p-90) REVERT: D 441 ASP cc_start: 0.7855 (t0) cc_final: 0.7582 (t0) REVERT: D 525 MET cc_start: 0.8306 (mmt) cc_final: 0.7781 (mmt) REVERT: D 570 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7728 (tt) outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.2571 time to fit residues: 33.6751 Evaluate side-chains 89 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9143 Z= 0.197 Angle : 0.534 13.336 12421 Z= 0.263 Chirality : 0.039 0.131 1449 Planarity : 0.003 0.037 1590 Dihedral : 3.930 17.521 1257 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.50 % Allowed : 14.55 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1151 helix: 1.59 (0.20), residues: 695 sheet: -0.14 (0.73), residues: 54 loop : -0.36 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.010 0.001 PHE C 216 TYR 0.018 0.001 TYR D 88 ARG 0.006 0.000 ARG C 522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.035 Fit side-chains REVERT: C 12 LYS cc_start: 0.8442 (tttt) cc_final: 0.8166 (mmtm) REVERT: C 183 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7618 (mtm110) REVERT: D 154 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8288 (mp) REVERT: D 441 ASP cc_start: 0.7878 (t0) cc_final: 0.7586 (t0) REVERT: D 525 MET cc_start: 0.8318 (mmt) cc_final: 0.7752 (mmt) REVERT: D 570 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7719 (tt) outliers start: 14 outliers final: 9 residues processed: 103 average time/residue: 0.2315 time to fit residues: 32.6706 Evaluate side-chains 93 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9143 Z= 0.184 Angle : 0.524 12.247 12421 Z= 0.259 Chirality : 0.039 0.133 1449 Planarity : 0.003 0.037 1590 Dihedral : 3.853 17.293 1257 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.82 % Allowed : 15.61 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1151 helix: 1.70 (0.20), residues: 702 sheet: 0.20 (0.75), residues: 55 loop : -0.29 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.010 0.001 PHE C 216 TYR 0.018 0.001 TYR D 88 ARG 0.003 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.976 Fit side-chains REVERT: C 12 LYS cc_start: 0.8427 (tttt) cc_final: 0.8158 (mmtm) REVERT: C 183 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7598 (mtm110) REVERT: D 154 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8273 (mp) REVERT: D 441 ASP cc_start: 0.7879 (t0) cc_final: 0.7601 (t0) REVERT: D 525 MET cc_start: 0.8279 (mmt) cc_final: 0.7782 (mmt) REVERT: D 570 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7698 (tt) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 0.2611 time to fit residues: 36.7988 Evaluate side-chains 95 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 110 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN D 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9143 Z= 0.181 Angle : 0.522 11.262 12421 Z= 0.259 Chirality : 0.039 0.131 1449 Planarity : 0.003 0.037 1590 Dihedral : 3.800 17.222 1257 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.14 % Allowed : 15.51 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1151 helix: 1.82 (0.20), residues: 703 sheet: 0.04 (0.79), residues: 49 loop : -0.25 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.009 0.001 PHE C 216 TYR 0.017 0.001 TYR D 88 ARG 0.004 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.991 Fit side-chains REVERT: C 12 LYS cc_start: 0.8415 (tttt) cc_final: 0.8153 (mmtm) REVERT: C 183 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7609 (mtm110) REVERT: D 154 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8278 (mp) REVERT: D 201 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8507 (mp) REVERT: D 416 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7829 (mt) REVERT: D 441 ASP cc_start: 0.7945 (t70) cc_final: 0.7628 (t0) REVERT: D 525 MET cc_start: 0.8190 (mmt) cc_final: 0.7651 (mmt) REVERT: D 570 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7651 (tt) outliers start: 20 outliers final: 10 residues processed: 105 average time/residue: 0.2351 time to fit residues: 33.8406 Evaluate side-chains 99 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9143 Z= 0.215 Angle : 0.543 10.878 12421 Z= 0.267 Chirality : 0.040 0.133 1449 Planarity : 0.003 0.037 1590 Dihedral : 3.818 17.308 1257 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.03 % Allowed : 16.26 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1151 helix: 1.85 (0.20), residues: 703 sheet: 0.06 (0.79), residues: 49 loop : -0.25 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE C 216 TYR 0.017 0.001 TYR D 88 ARG 0.004 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.006 Fit side-chains REVERT: C 12 LYS cc_start: 0.8431 (tttt) cc_final: 0.8163 (mmtm) REVERT: C 183 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7612 (mtm110) REVERT: C 565 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7272 (tpt-90) REVERT: D 154 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8276 (mp) REVERT: D 201 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8514 (mp) REVERT: D 416 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7854 (mt) REVERT: D 441 ASP cc_start: 0.7948 (t70) cc_final: 0.7622 (t0) REVERT: D 525 MET cc_start: 0.8182 (mmt) cc_final: 0.7711 (mmt) REVERT: D 570 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7595 (tt) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.2408 time to fit residues: 33.6878 Evaluate side-chains 101 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 588 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.0980 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8413 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9143 Z= 0.175 Angle : 0.534 10.345 12421 Z= 0.263 Chirality : 0.039 0.182 1449 Planarity : 0.003 0.037 1590 Dihedral : 3.749 17.047 1257 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.03 % Allowed : 16.04 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1151 helix: 1.97 (0.20), residues: 705 sheet: 0.13 (0.80), residues: 49 loop : -0.21 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 427 HIS 0.003 0.000 HIS D 204 PHE 0.008 0.001 PHE C 291 TYR 0.017 0.001 TYR D 88 ARG 0.004 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.910 Fit side-chains REVERT: C 12 LYS cc_start: 0.8409 (tttt) cc_final: 0.8155 (mmtm) REVERT: C 183 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7616 (mtm110) REVERT: D 154 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8283 (mp) REVERT: D 201 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8501 (mp) REVERT: D 416 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7842 (mt) REVERT: D 441 ASP cc_start: 0.7934 (t70) cc_final: 0.7606 (t0) REVERT: D 525 MET cc_start: 0.8176 (mmt) cc_final: 0.7707 (mmt) REVERT: D 570 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (tt) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.2371 time to fit residues: 33.7614 Evaluate side-chains 101 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9143 Z= 0.214 Angle : 0.555 10.418 12421 Z= 0.272 Chirality : 0.040 0.168 1449 Planarity : 0.003 0.038 1590 Dihedral : 3.789 17.044 1257 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 16.79 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1151 helix: 1.92 (0.20), residues: 705 sheet: 0.10 (0.79), residues: 49 loop : -0.19 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.010 0.001 PHE C 181 TYR 0.017 0.001 TYR D 88 ARG 0.004 0.000 ARG D 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.911 Fit side-chains REVERT: C 12 LYS cc_start: 0.8422 (tttt) cc_final: 0.8165 (mmtm) REVERT: C 183 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7608 (mtm110) REVERT: C 565 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7242 (tpt-90) REVERT: D 154 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8273 (mp) REVERT: D 416 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7853 (mt) REVERT: D 441 ASP cc_start: 0.7943 (t70) cc_final: 0.7607 (t0) REVERT: D 525 MET cc_start: 0.8181 (mmt) cc_final: 0.7681 (mmt) REVERT: D 570 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7606 (tt) outliers start: 16 outliers final: 11 residues processed: 101 average time/residue: 0.2472 time to fit residues: 33.6425 Evaluate side-chains 100 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.091761 restraints weight = 11171.032| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.77 r_work: 0.2863 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9143 Z= 0.234 Angle : 0.567 10.284 12421 Z= 0.278 Chirality : 0.040 0.174 1449 Planarity : 0.004 0.041 1590 Dihedral : 3.823 17.029 1257 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 16.58 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1151 helix: 1.87 (0.20), residues: 706 sheet: 0.21 (0.77), residues: 55 loop : -0.18 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE C 216 TYR 0.017 0.001 TYR D 88 ARG 0.009 0.000 ARG C 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.15 seconds wall clock time: 342 minutes 0.27 seconds (20520.27 seconds total)