Starting phenix.real_space_refine on Tue Feb 13 12:31:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzv_8940/02_2024/6dzv_8940.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzv_8940/02_2024/6dzv_8940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzv_8940/02_2024/6dzv_8940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzv_8940/02_2024/6dzv_8940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzv_8940/02_2024/6dzv_8940.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzv_8940/02_2024/6dzv_8940.pdb" } resolution = 4.2 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= 0.003 sd= 0.522 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 34 5.16 5 C 4039 2.51 5 N 962 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6121 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} 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: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'HJM': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.10, per 1000 atoms: 0.67 Number of scatterers: 6121 At special positions: 0 Unit cell: (83.123, 76.539, 117.689, 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 34 16.00 O 1086 8.00 N 962 7.00 C 4039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 56.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.601A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.724A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.810A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.826A pdb=" N LEU A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 128 through 144 removed outlier: 4.360A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.103A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 removed outlier: 3.550A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 160 through 190 removed outlier: 3.720A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 252 through 273 removed outlier: 3.667A pdb=" N ALA A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 3.588A pdb=" N VAL A 280 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 4.574A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.846A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 310 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 4.169A pdb=" N LYS A 319 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.785A pdb=" N ALA A 330 " --> pdb=" O TRP A 326 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 356 through 391 removed outlier: 3.525A pdb=" N ASP A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 373 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 4.074A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 414 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 454 removed outlier: 3.661A pdb=" N ILE A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 removed outlier: 4.254A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.717A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 4.569A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.507A pdb=" N ALA A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.809A pdb=" N ARG A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 4.132A pdb=" N CYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 541' Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.806A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.575A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 577 " --> pdb=" O TRP A 573 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.717A pdb=" N ILE A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 595 " --> pdb=" O THR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.702A pdb=" N THR C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.882A pdb=" N GLU B 29 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 113 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 114 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 56 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP B 55 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 68 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 39 removed outlier: 3.662A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 102 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 97 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 92 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AA4, first strand: chain 'C' and resid 30 through 32 removed outlier: 5.852A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.314A pdb=" N ASN C 51 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 7.290A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN C 58 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 90 removed outlier: 3.661A pdb=" N SER C 89 " --> pdb=" O SER C 96 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 618 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: 1.51 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 1 1.16 - 1.33: 955 1.33 - 1.49: 2754 1.49 - 1.65: 2541 1.65 - 1.81: 56 Bond restraints: 6307 Sorted by residual: bond pdb=" CBD Y01 A 704 " pdb=" CBG Y01 A 704 " ideal model delta sigma weight residual 1.520 1.001 0.519 2.00e-02 2.50e+03 6.73e+02 bond pdb=" CAS Y01 A 704 " pdb=" CAU Y01 A 704 " ideal model delta sigma weight residual 1.530 1.191 0.339 2.00e-02 2.50e+03 2.88e+02 bond pdb=" CAU Y01 A 704 " pdb=" CBI Y01 A 704 " ideal model delta sigma weight residual 1.530 1.254 0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" CAP Y01 A 704 " pdb=" CAQ Y01 A 704 " ideal model delta sigma weight residual 1.541 1.803 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" CAK Y01 A 704 " pdb=" CBD Y01 A 704 " ideal model delta sigma weight residual 1.525 1.264 0.261 2.00e-02 2.50e+03 1.70e+02 ... (remaining 6302 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.53: 127 105.53 - 112.65: 3179 112.65 - 119.76: 2111 119.76 - 126.88: 3060 126.88 - 133.99: 119 Bond angle restraints: 8596 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 133.45 -11.75 1.80e+00 3.09e-01 4.26e+01 angle pdb=" CAK Y01 A 704 " pdb=" CAI Y01 A 704 " pdb=" CAZ Y01 A 704 " ideal model delta sigma weight residual 124.96 113.98 10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.51 119.43 -3.92 1.27e+00 6.20e-01 9.51e+00 angle pdb=" CAM Y01 A 704 " pdb=" CAY Y01 A 704 " pdb=" OAW Y01 A 704 " ideal model delta sigma weight residual 111.19 120.17 -8.98 3.00e+00 1.11e-01 8.96e+00 angle pdb=" CAQ Y01 A 704 " pdb=" CBG Y01 A 704 " pdb=" CBD Y01 A 704 " ideal model delta sigma weight residual 118.56 127.14 -8.58 3.00e+00 1.11e-01 8.18e+00 ... (remaining 8591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 3594 22.71 - 45.42: 73 45.42 - 68.13: 12 68.13 - 90.84: 12 90.84 - 113.55: 6 Dihedral angle restraints: 3697 sinusoidal: 1497 harmonic: 2200 Sorted by residual: dihedral pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta harmonic sigma weight residual 0.00 27.72 -27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual -175.09 -61.54 -113.55 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" N2 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual 62.25 174.86 -112.61 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 3694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 949 0.317 - 0.633: 1 0.633 - 0.950: 2 0.950 - 1.267: 0 1.267 - 1.584: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" CBD Y01 A 704 " pdb=" CAK Y01 A 704 " pdb=" CBF Y01 A 704 " pdb=" CBG Y01 A 704 " both_signs ideal model delta sigma weight residual False 2.70 1.11 1.58 2.00e-01 2.50e+01 6.27e+01 chirality pdb=" CBG Y01 A 704 " pdb=" CAQ Y01 A 704 " pdb=" CBD Y01 A 704 " pdb=" CBI Y01 A 704 " both_signs ideal model delta sigma weight residual False -2.33 -1.63 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CBI Y01 A 704 " pdb=" CAU Y01 A 704 " pdb=" CBE Y01 A 704 " pdb=" CBG Y01 A 704 " both_signs ideal model delta sigma weight residual False 2.94 2.27 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 950 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O HJM A 703 " -0.163 2.00e-02 2.50e+03 1.03e-01 3.16e+02 pdb=" C11 HJM A 703 " 0.031 2.00e-02 2.50e+03 pdb=" C12 HJM A 703 " 0.149 2.00e-02 2.50e+03 pdb=" C13 HJM A 703 " 0.070 2.00e-02 2.50e+03 pdb=" C15 HJM A 703 " 0.075 2.00e-02 2.50e+03 pdb=" C16 HJM A 703 " -0.004 2.00e-02 2.50e+03 pdb=" C17 HJM A 703 " 0.065 2.00e-02 2.50e+03 pdb=" C18 HJM A 703 " -0.011 2.00e-02 2.50e+03 pdb=" C19 HJM A 703 " -0.004 2.00e-02 2.50e+03 pdb=" C2 HJM A 703 " -0.229 2.00e-02 2.50e+03 pdb=" C8 HJM A 703 " -0.057 2.00e-02 2.50e+03 pdb=" N2 HJM A 703 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 417 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 418 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 155 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 156 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.019 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 66 2.65 - 3.21: 5806 3.21 - 3.78: 8553 3.78 - 4.34: 12529 4.34 - 4.90: 19883 Nonbonded interactions: 46837 Sorted by model distance: nonbonded pdb=" O ASN A 145 " pdb=" OG SER A 149 " model vdw 2.088 2.440 nonbonded pdb=" O MET A 260 " pdb=" OG1 THR A 264 " model vdw 2.090 2.440 nonbonded pdb=" O SER B 49 " pdb=" OH TYR B 71 " model vdw 2.119 2.440 nonbonded pdb=" OG1 THR A 221 " pdb=" OG SER A 224 " model vdw 2.121 2.440 nonbonded pdb=" O LEU A 478 " pdb=" OG1 THR A 482 " model vdw 2.140 2.440 ... (remaining 46832 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 10.020 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 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 : 0.013 0.519 6307 Z= 0.844 Angle : 0.705 11.748 8596 Z= 0.334 Chirality : 0.075 1.584 953 Planarity : 0.005 0.103 1050 Dihedral : 12.108 113.546 2292 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -4.08 (0.25), residues: 759 helix: -3.53 (0.16), residues: 283 sheet: -3.51 (0.51), residues: 73 loop : -1.83 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 537 HIS 0.002 0.001 HIS A 456 PHE 0.009 0.001 PHE A 474 TYR 0.007 0.001 TYR A 134 ARG 0.003 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8800 (t80) cc_final: 0.8580 (t80) REVERT: A 157 ILE cc_start: 0.8426 (tt) cc_final: 0.8217 (mt) REVERT: A 186 TYR cc_start: 0.6988 (m-10) cc_final: 0.6758 (m-10) REVERT: A 253 TRP cc_start: 0.8190 (p-90) cc_final: 0.6784 (m100) REVERT: A 260 MET cc_start: 0.7397 (mmp) cc_final: 0.6648 (ttt) REVERT: A 332 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 414 ILE cc_start: 0.6103 (mm) cc_final: 0.5796 (mt) REVERT: A 495 TYR cc_start: 0.6069 (m-80) cc_final: 0.5795 (m-80) REVERT: A 558 MET cc_start: 0.8408 (mtm) cc_final: 0.8103 (tpt) REVERT: A 595 TYR cc_start: 0.7234 (m-10) cc_final: 0.6887 (m-80) REVERT: A 605 LYS cc_start: 0.8264 (tttt) cc_final: 0.7654 (pttt) REVERT: B 42 LYS cc_start: 0.8890 (tptt) cc_final: 0.8023 (tppt) REVERT: B 47 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7840 (ttp-110) REVERT: B 83 PHE cc_start: 0.7751 (m-80) cc_final: 0.7186 (m-10) REVERT: B 101 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8038 (tp40) REVERT: B 120 TYR cc_start: 0.5376 (m-80) cc_final: 0.4344 (m-80) REVERT: C 71 LEU cc_start: 0.8342 (mt) cc_final: 0.8064 (mm) REVERT: C 78 GLN cc_start: 0.7165 (mt0) cc_final: 0.6911 (mm-40) REVERT: C 118 VAL cc_start: 0.8148 (t) cc_final: 0.7820 (p) REVERT: C 130 ILE cc_start: 0.8802 (mt) cc_final: 0.8398 (mt) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2050 time to fit residues: 74.6163 Evaluate side-chains 150 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 520 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6307 Z= 0.275 Angle : 0.692 9.625 8596 Z= 0.354 Chirality : 0.045 0.228 953 Planarity : 0.005 0.034 1050 Dihedral : 11.667 87.610 982 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.31 % Allowed : 1.40 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.29), residues: 759 helix: -1.34 (0.26), residues: 321 sheet: -2.61 (0.48), residues: 78 loop : -1.76 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 151 HIS 0.003 0.001 HIS A 143 PHE 0.034 0.002 PHE A 287 TYR 0.016 0.002 TYR C 73 ARG 0.005 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.8620 (m-40) cc_final: 0.8345 (m110) REVERT: A 142 TYR cc_start: 0.7881 (t80) cc_final: 0.7579 (t80) REVERT: A 158 PHE cc_start: 0.8690 (m-80) cc_final: 0.8063 (m-80) REVERT: A 260 MET cc_start: 0.7414 (mmp) cc_final: 0.6629 (ttt) REVERT: A 262 ILE cc_start: 0.8427 (mm) cc_final: 0.8150 (mm) REVERT: A 332 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 414 ILE cc_start: 0.6786 (mm) cc_final: 0.6333 (mm) REVERT: A 431 LEU cc_start: 0.9087 (mp) cc_final: 0.8863 (mp) REVERT: A 454 PHE cc_start: 0.8686 (m-10) cc_final: 0.8406 (m-10) REVERT: A 461 ARG cc_start: 0.8816 (mtt90) cc_final: 0.8262 (mtt180) REVERT: A 471 ILE cc_start: 0.8708 (mt) cc_final: 0.8497 (mt) REVERT: A 529 LEU cc_start: 0.6966 (mt) cc_final: 0.6749 (tp) REVERT: A 547 LEU cc_start: 0.8751 (tp) cc_final: 0.8513 (tp) REVERT: A 558 MET cc_start: 0.8535 (mtm) cc_final: 0.8335 (tpt) REVERT: A 595 TYR cc_start: 0.7416 (m-10) cc_final: 0.6957 (m-80) REVERT: A 605 LYS cc_start: 0.8600 (tttt) cc_final: 0.8339 (tttm) REVERT: A 606 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8987 (mm-30) REVERT: B 42 LYS cc_start: 0.8893 (tptt) cc_final: 0.8378 (tppt) REVERT: B 50 TYR cc_start: 0.5756 (m-80) cc_final: 0.5458 (m-80) REVERT: B 59 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7242 (ttt180) REVERT: B 83 PHE cc_start: 0.7780 (m-80) cc_final: 0.7512 (m-10) REVERT: B 88 THR cc_start: 0.8198 (p) cc_final: 0.7904 (p) REVERT: B 114 PHE cc_start: 0.7985 (m-80) cc_final: 0.7552 (m-80) REVERT: B 127 MET cc_start: 0.8708 (mmm) cc_final: 0.8254 (mmm) REVERT: B 130 TRP cc_start: 0.8468 (m100) cc_final: 0.7896 (m100) REVERT: C 105 ASP cc_start: 0.8525 (m-30) cc_final: 0.8247 (m-30) REVERT: C 127 LYS cc_start: 0.8415 (mppt) cc_final: 0.7915 (mmtm) REVERT: C 130 ILE cc_start: 0.8979 (mt) cc_final: 0.8462 (mt) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.1874 time to fit residues: 48.6905 Evaluate side-chains 149 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 359 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6307 Z= 0.179 Angle : 0.590 9.592 8596 Z= 0.296 Chirality : 0.043 0.213 953 Planarity : 0.004 0.037 1050 Dihedral : 9.610 71.916 982 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.16 % Allowed : 2.18 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.97 (0.29), residues: 759 helix: -0.50 (0.27), residues: 329 sheet: -2.20 (0.54), residues: 74 loop : -1.84 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 120 HIS 0.001 0.000 HIS C 100 PHE 0.031 0.002 PHE A 287 TYR 0.012 0.001 TYR A 410 ARG 0.005 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8984 (m-30) cc_final: 0.8520 (m-30) REVERT: A 112 ASN cc_start: 0.8770 (m-40) cc_final: 0.8462 (m110) REVERT: A 158 PHE cc_start: 0.8723 (m-80) cc_final: 0.8138 (m-80) REVERT: A 253 TRP cc_start: 0.8264 (p-90) cc_final: 0.8042 (p-90) REVERT: A 260 MET cc_start: 0.7211 (mmp) cc_final: 0.6427 (ttt) REVERT: A 290 ILE cc_start: 0.8346 (mm) cc_final: 0.8043 (mt) REVERT: A 332 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 461 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8280 (mtt180) REVERT: A 544 ILE cc_start: 0.8293 (mm) cc_final: 0.7101 (mm) REVERT: A 547 LEU cc_start: 0.8682 (tp) cc_final: 0.8456 (tp) REVERT: A 595 TYR cc_start: 0.7185 (m-10) cc_final: 0.6709 (m-80) REVERT: A 605 LYS cc_start: 0.8591 (tttt) cc_final: 0.8318 (tttm) REVERT: A 606 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8949 (mm-30) REVERT: B 42 LYS cc_start: 0.8891 (tptt) cc_final: 0.8371 (tppt) REVERT: B 50 TYR cc_start: 0.5770 (m-80) cc_final: 0.5548 (m-80) REVERT: B 59 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7662 (ttt180) REVERT: B 83 PHE cc_start: 0.7878 (m-80) cc_final: 0.7616 (m-10) REVERT: B 88 THR cc_start: 0.8153 (p) cc_final: 0.7392 (p) REVERT: B 114 PHE cc_start: 0.7980 (m-80) cc_final: 0.7588 (m-80) REVERT: B 120 TYR cc_start: 0.5957 (m-80) cc_final: 0.5520 (m-10) REVERT: B 129 TYR cc_start: 0.7621 (m-10) cc_final: 0.7421 (m-10) REVERT: B 130 TRP cc_start: 0.8391 (m100) cc_final: 0.7931 (m100) REVERT: C 54 ILE cc_start: 0.8584 (mm) cc_final: 0.8303 (tp) REVERT: C 105 ASP cc_start: 0.8480 (m-30) cc_final: 0.8179 (m-30) REVERT: C 127 LYS cc_start: 0.8072 (mppt) cc_final: 0.7617 (mppt) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2005 time to fit residues: 50.2177 Evaluate side-chains 153 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6307 Z= 0.214 Angle : 0.617 12.801 8596 Z= 0.303 Chirality : 0.042 0.206 953 Planarity : 0.005 0.056 1050 Dihedral : 9.089 70.759 982 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.16 % Allowed : 1.71 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.42 (0.30), residues: 759 helix: -0.01 (0.28), residues: 322 sheet: -1.82 (0.55), residues: 75 loop : -1.58 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 120 HIS 0.002 0.001 HIS A 223 PHE 0.023 0.002 PHE A 423 TYR 0.018 0.001 TYR A 410 ARG 0.004 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.8817 (m-80) cc_final: 0.8216 (m-80) REVERT: A 253 TRP cc_start: 0.8242 (p-90) cc_final: 0.7944 (p-90) REVERT: A 260 MET cc_start: 0.7284 (mmp) cc_final: 0.6472 (ttp) REVERT: A 290 ILE cc_start: 0.8454 (mm) cc_final: 0.8179 (mt) REVERT: A 332 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7084 (tm-30) REVERT: A 461 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8285 (mtt180) REVERT: A 508 GLU cc_start: 0.8703 (pt0) cc_final: 0.8416 (pt0) REVERT: A 528 MET cc_start: 0.8423 (mpp) cc_final: 0.8197 (mpp) REVERT: A 529 LEU cc_start: 0.6952 (mt) cc_final: 0.6738 (tp) REVERT: A 547 LEU cc_start: 0.8678 (tp) cc_final: 0.8464 (tp) REVERT: A 595 TYR cc_start: 0.7285 (m-10) cc_final: 0.6779 (m-80) REVERT: A 605 LYS cc_start: 0.8571 (tttt) cc_final: 0.8293 (tttm) REVERT: A 606 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8979 (mm-30) REVERT: B 42 LYS cc_start: 0.8903 (tptt) cc_final: 0.8410 (tppt) REVERT: B 59 ARG cc_start: 0.8328 (ttt180) cc_final: 0.7888 (ttt180) REVERT: B 65 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 83 PHE cc_start: 0.8082 (m-80) cc_final: 0.7460 (m-10) REVERT: B 88 THR cc_start: 0.8354 (p) cc_final: 0.7714 (p) REVERT: B 120 TYR cc_start: 0.6150 (m-80) cc_final: 0.5701 (m-10) REVERT: C 54 ILE cc_start: 0.8536 (mm) cc_final: 0.8237 (tp) REVERT: C 105 ASP cc_start: 0.8558 (m-30) cc_final: 0.7974 (m-30) REVERT: C 127 LYS cc_start: 0.8191 (mppt) cc_final: 0.7738 (mppt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2082 time to fit residues: 51.0099 Evaluate side-chains 148 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 359 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6307 Z= 0.189 Angle : 0.594 9.569 8596 Z= 0.300 Chirality : 0.043 0.207 953 Planarity : 0.005 0.051 1050 Dihedral : 9.046 70.982 982 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.16 % Allowed : 1.71 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 (0.31), residues: 759 helix: 0.26 (0.28), residues: 326 sheet: -1.69 (0.59), residues: 75 loop : -1.50 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 55 HIS 0.002 0.001 HIS A 223 PHE 0.019 0.002 PHE A 380 TYR 0.015 0.001 TYR A 410 ARG 0.003 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.8996 (m110) cc_final: 0.8665 (m110) REVERT: A 158 PHE cc_start: 0.8857 (m-80) cc_final: 0.8286 (m-10) REVERT: A 260 MET cc_start: 0.7319 (mmp) cc_final: 0.6522 (ttp) REVERT: A 290 ILE cc_start: 0.8492 (mm) cc_final: 0.8266 (mt) REVERT: A 332 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 389 MET cc_start: 0.6998 (ttp) cc_final: 0.6797 (ttt) REVERT: A 461 ARG cc_start: 0.8795 (mtt90) cc_final: 0.8257 (mtt180) REVERT: A 508 GLU cc_start: 0.8692 (pt0) cc_final: 0.8440 (pt0) REVERT: A 528 MET cc_start: 0.8205 (mpp) cc_final: 0.8005 (mpp) REVERT: A 547 LEU cc_start: 0.8688 (tp) cc_final: 0.8486 (tp) REVERT: A 595 TYR cc_start: 0.7331 (m-10) cc_final: 0.6792 (m-80) REVERT: A 605 LYS cc_start: 0.8597 (tttt) cc_final: 0.8367 (tttm) REVERT: A 606 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8990 (mm-30) REVERT: B 42 LYS cc_start: 0.8898 (tptt) cc_final: 0.8426 (tppt) REVERT: B 53 MET cc_start: 0.7841 (tpp) cc_final: 0.7265 (tmm) REVERT: B 84 LYS cc_start: 0.8659 (mppt) cc_final: 0.8327 (mmtm) REVERT: B 88 THR cc_start: 0.8060 (p) cc_final: 0.7675 (p) REVERT: B 120 TYR cc_start: 0.6334 (m-80) cc_final: 0.5852 (m-80) REVERT: C 54 ILE cc_start: 0.8541 (mm) cc_final: 0.8256 (tp) REVERT: C 105 ASP cc_start: 0.8261 (m-30) cc_final: 0.8024 (m-30) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.1854 time to fit residues: 43.9891 Evaluate side-chains 145 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6307 Z= 0.227 Angle : 0.642 9.632 8596 Z= 0.320 Chirality : 0.043 0.222 953 Planarity : 0.005 0.048 1050 Dihedral : 8.777 71.468 982 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.31), residues: 759 helix: 0.33 (0.28), residues: 336 sheet: -1.56 (0.54), residues: 84 loop : -1.62 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 55 HIS 0.002 0.001 HIS C 100 PHE 0.013 0.002 PHE A 586 TYR 0.018 0.002 TYR C 73 ARG 0.005 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.9082 (m110) cc_final: 0.8786 (m110) REVERT: A 158 PHE cc_start: 0.8898 (m-80) cc_final: 0.8378 (m-10) REVERT: A 237 LEU cc_start: 0.8533 (tp) cc_final: 0.8328 (tp) REVERT: A 260 MET cc_start: 0.7344 (mmp) cc_final: 0.6558 (ttp) REVERT: A 332 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 392 GLU cc_start: 0.8633 (tp30) cc_final: 0.7971 (tp30) REVERT: A 396 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7803 (mp0) REVERT: A 461 ARG cc_start: 0.8877 (mtt90) cc_final: 0.8329 (mtt180) REVERT: A 495 TYR cc_start: 0.6924 (m-80) cc_final: 0.6508 (m-80) REVERT: A 508 GLU cc_start: 0.8717 (pt0) cc_final: 0.8412 (pt0) REVERT: A 595 TYR cc_start: 0.7371 (m-10) cc_final: 0.6818 (m-80) REVERT: A 606 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9075 (mm-30) REVERT: A 607 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7897 (mtt90) REVERT: B 50 TYR cc_start: 0.6300 (m-80) cc_final: 0.6092 (m-80) REVERT: B 59 ARG cc_start: 0.8460 (ttt180) cc_final: 0.7925 (ttm170) REVERT: B 65 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 114 PHE cc_start: 0.7407 (m-80) cc_final: 0.6791 (m-80) REVERT: B 120 TYR cc_start: 0.6433 (m-80) cc_final: 0.5888 (m-80) REVERT: B 127 MET cc_start: 0.9079 (mmp) cc_final: 0.8670 (mmp) REVERT: B 130 TRP cc_start: 0.8807 (m100) cc_final: 0.7999 (m100) REVERT: C 54 ILE cc_start: 0.8594 (mm) cc_final: 0.8363 (tp) REVERT: C 105 ASP cc_start: 0.8240 (m-30) cc_final: 0.8040 (m-30) REVERT: C 127 LYS cc_start: 0.8221 (mppt) cc_final: 0.7972 (mmtm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1990 time to fit residues: 47.5873 Evaluate side-chains 142 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 0.0670 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6307 Z= 0.165 Angle : 0.598 9.750 8596 Z= 0.297 Chirality : 0.042 0.204 953 Planarity : 0.005 0.039 1050 Dihedral : 8.452 70.252 982 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.99 (0.30), residues: 759 helix: 0.35 (0.28), residues: 337 sheet: -1.14 (0.56), residues: 84 loop : -1.53 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.002 0.001 HIS A 235 PHE 0.019 0.001 PHE A 380 TYR 0.012 0.001 TYR A 410 ARG 0.006 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9208 (t80) cc_final: 0.8774 (t80) REVERT: A 158 PHE cc_start: 0.8884 (m-80) cc_final: 0.8428 (m-10) REVERT: A 195 LEU cc_start: 0.8338 (pt) cc_final: 0.8111 (pp) REVERT: A 237 LEU cc_start: 0.8522 (tp) cc_final: 0.8302 (tp) REVERT: A 260 MET cc_start: 0.7334 (mmp) cc_final: 0.6595 (ttp) REVERT: A 332 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 392 GLU cc_start: 0.8629 (tp30) cc_final: 0.8037 (tp30) REVERT: A 396 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7778 (mp0) REVERT: A 461 ARG cc_start: 0.8811 (mtt90) cc_final: 0.8254 (mtt180) REVERT: A 548 PHE cc_start: 0.7281 (m-10) cc_final: 0.7071 (m-10) REVERT: A 595 TYR cc_start: 0.7224 (m-10) cc_final: 0.6692 (m-80) REVERT: A 606 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9025 (mm-30) REVERT: B 42 LYS cc_start: 0.8799 (tptt) cc_final: 0.8387 (tppt) REVERT: B 53 MET cc_start: 0.7747 (tpp) cc_final: 0.7059 (tmm) REVERT: B 59 ARG cc_start: 0.8404 (ttt180) cc_final: 0.8198 (ttt180) REVERT: B 65 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 83 PHE cc_start: 0.8143 (m-80) cc_final: 0.7452 (m-10) REVERT: B 120 TYR cc_start: 0.6528 (m-80) cc_final: 0.6015 (m-80) REVERT: B 127 MET cc_start: 0.9117 (mmp) cc_final: 0.8726 (mmp) REVERT: C 54 ILE cc_start: 0.8560 (mm) cc_final: 0.8332 (tp) REVERT: C 127 LYS cc_start: 0.8118 (mppt) cc_final: 0.7879 (mmtm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2021 time to fit residues: 47.1093 Evaluate side-chains 146 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 67 optimal weight: 0.0980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6307 Z= 0.185 Angle : 0.620 9.619 8596 Z= 0.307 Chirality : 0.043 0.205 953 Planarity : 0.006 0.113 1050 Dihedral : 8.424 69.949 982 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.90 (0.31), residues: 759 helix: 0.38 (0.28), residues: 337 sheet: -0.91 (0.58), residues: 84 loop : -1.49 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 537 HIS 0.002 0.001 HIS A 235 PHE 0.013 0.002 PHE A 347 TYR 0.019 0.001 TYR A 312 ARG 0.009 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9312 (t80) cc_final: 0.8850 (t80) REVERT: A 158 PHE cc_start: 0.8883 (m-80) cc_final: 0.8462 (m-10) REVERT: A 195 LEU cc_start: 0.8218 (pt) cc_final: 0.7970 (pp) REVERT: A 237 LEU cc_start: 0.8500 (tp) cc_final: 0.8271 (tp) REVERT: A 260 MET cc_start: 0.7316 (mmp) cc_final: 0.6452 (ttp) REVERT: A 430 MET cc_start: 0.8232 (mtp) cc_final: 0.7968 (mtp) REVERT: A 461 ARG cc_start: 0.8783 (mtt90) cc_final: 0.8192 (mtt180) REVERT: A 528 MET cc_start: 0.8247 (mpp) cc_final: 0.8024 (mpp) REVERT: A 548 PHE cc_start: 0.7322 (m-10) cc_final: 0.7090 (m-10) REVERT: A 595 TYR cc_start: 0.7225 (m-10) cc_final: 0.6640 (m-80) REVERT: A 606 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9066 (mm-30) REVERT: A 607 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7804 (mtt90) REVERT: B 42 LYS cc_start: 0.8812 (tptt) cc_final: 0.8305 (tppt) REVERT: B 53 MET cc_start: 0.7802 (tpp) cc_final: 0.7138 (tmm) REVERT: B 65 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7854 (tm-30) REVERT: B 83 PHE cc_start: 0.8164 (m-80) cc_final: 0.7580 (m-10) REVERT: B 84 LYS cc_start: 0.8649 (mppt) cc_final: 0.8380 (mmtm) REVERT: B 120 TYR cc_start: 0.6579 (m-80) cc_final: 0.6055 (m-80) REVERT: B 127 MET cc_start: 0.9110 (mmp) cc_final: 0.8784 (mmp) REVERT: B 130 TRP cc_start: 0.8733 (m100) cc_final: 0.8200 (m100) REVERT: C 54 ILE cc_start: 0.8561 (mm) cc_final: 0.8309 (tp) REVERT: C 60 PHE cc_start: 0.8519 (m-80) cc_final: 0.8255 (m-80) REVERT: C 107 THR cc_start: 0.8475 (p) cc_final: 0.8150 (t) REVERT: C 127 LYS cc_start: 0.8103 (mppt) cc_final: 0.7864 (mmtm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1854 time to fit residues: 42.0857 Evaluate side-chains 148 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6307 Z= 0.215 Angle : 0.642 9.449 8596 Z= 0.320 Chirality : 0.043 0.206 953 Planarity : 0.005 0.047 1050 Dihedral : 8.421 69.712 982 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.83 (0.31), residues: 759 helix: 0.45 (0.28), residues: 339 sheet: -0.84 (0.58), residues: 84 loop : -1.49 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 537 HIS 0.002 0.001 HIS A 235 PHE 0.023 0.002 PHE A 263 TYR 0.020 0.002 TYR A 176 ARG 0.008 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9328 (t80) cc_final: 0.8859 (t80) REVERT: A 135 MET cc_start: 0.9578 (ttp) cc_final: 0.9373 (ttp) REVERT: A 158 PHE cc_start: 0.8878 (m-80) cc_final: 0.8560 (m-10) REVERT: A 195 LEU cc_start: 0.8261 (pt) cc_final: 0.8013 (pp) REVERT: A 237 LEU cc_start: 0.8581 (tp) cc_final: 0.8346 (tp) REVERT: A 260 MET cc_start: 0.7168 (mmp) cc_final: 0.6400 (ttp) REVERT: A 430 MET cc_start: 0.8231 (mtp) cc_final: 0.7972 (mtp) REVERT: A 461 ARG cc_start: 0.8793 (mtt90) cc_final: 0.8228 (mtt180) REVERT: A 528 MET cc_start: 0.8310 (mpp) cc_final: 0.8090 (mpp) REVERT: A 548 PHE cc_start: 0.7452 (m-10) cc_final: 0.7229 (m-10) REVERT: A 595 TYR cc_start: 0.7293 (m-10) cc_final: 0.6708 (m-80) REVERT: A 606 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9099 (mm-30) REVERT: B 42 LYS cc_start: 0.8821 (tptt) cc_final: 0.8484 (tppt) REVERT: B 65 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 83 PHE cc_start: 0.8258 (m-80) cc_final: 0.7646 (m-10) REVERT: B 120 TYR cc_start: 0.6487 (m-80) cc_final: 0.5928 (m-80) REVERT: B 127 MET cc_start: 0.9143 (mmp) cc_final: 0.8934 (mmp) REVERT: B 130 TRP cc_start: 0.8840 (m100) cc_final: 0.8175 (m100) REVERT: C 54 ILE cc_start: 0.8525 (mm) cc_final: 0.8256 (tp) REVERT: C 60 PHE cc_start: 0.8583 (m-80) cc_final: 0.8301 (m-80) REVERT: C 107 THR cc_start: 0.8529 (p) cc_final: 0.8217 (t) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1880 time to fit residues: 43.1006 Evaluate side-chains 139 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 0.0170 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 520 GLN B 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.7731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6307 Z= 0.167 Angle : 0.610 9.698 8596 Z= 0.299 Chirality : 0.043 0.204 953 Planarity : 0.005 0.042 1050 Dihedral : 8.200 67.489 982 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.76 (0.30), residues: 759 helix: 0.54 (0.28), residues: 337 sheet: -0.68 (0.59), residues: 74 loop : -1.50 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 537 HIS 0.003 0.001 HIS A 235 PHE 0.016 0.001 PHE A 380 TYR 0.012 0.001 TYR A 410 ARG 0.005 0.001 ARG C 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9330 (t80) cc_final: 0.8955 (t80) REVERT: A 158 PHE cc_start: 0.8856 (m-80) cc_final: 0.8541 (m-10) REVERT: A 195 LEU cc_start: 0.8161 (pt) cc_final: 0.7926 (pp) REVERT: A 237 LEU cc_start: 0.8579 (tp) cc_final: 0.8341 (tp) REVERT: A 260 MET cc_start: 0.7195 (mmp) cc_final: 0.6358 (ttp) REVERT: A 430 MET cc_start: 0.8229 (mtp) cc_final: 0.7959 (mtp) REVERT: A 461 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8366 (mmm-85) REVERT: A 528 MET cc_start: 0.8205 (mpp) cc_final: 0.7946 (mpp) REVERT: A 595 TYR cc_start: 0.7174 (m-10) cc_final: 0.6596 (m-80) REVERT: A 606 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9058 (mm-30) REVERT: A 607 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7802 (mtt90) REVERT: B 42 LYS cc_start: 0.8811 (tptt) cc_final: 0.8281 (tppt) REVERT: B 53 MET cc_start: 0.7858 (tpp) cc_final: 0.7403 (mmm) REVERT: B 65 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 83 PHE cc_start: 0.8168 (m-80) cc_final: 0.7590 (m-10) REVERT: B 120 TYR cc_start: 0.6625 (m-80) cc_final: 0.6127 (m-80) REVERT: B 127 MET cc_start: 0.9086 (mmp) cc_final: 0.8815 (mmp) REVERT: B 130 TRP cc_start: 0.8755 (m100) cc_final: 0.8182 (m100) REVERT: C 54 ILE cc_start: 0.8491 (mm) cc_final: 0.8240 (tp) REVERT: C 60 PHE cc_start: 0.8467 (m-80) cc_final: 0.8233 (m-80) REVERT: C 107 THR cc_start: 0.8480 (p) cc_final: 0.8119 (t) REVERT: C 127 LYS cc_start: 0.7988 (mppt) cc_final: 0.7765 (mmtm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1811 time to fit residues: 40.4111 Evaluate side-chains 142 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 7.9990 chunk 8 optimal weight: 0.0470 chunk 16 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.116086 restraints weight = 20495.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.119482 restraints weight = 13131.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.121883 restraints weight = 9249.357| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6307 Z= 0.152 Angle : 0.605 9.512 8596 Z= 0.295 Chirality : 0.042 0.205 953 Planarity : 0.005 0.047 1050 Dihedral : 8.057 64.715 982 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.66 (0.30), residues: 759 helix: 0.65 (0.28), residues: 336 sheet: -0.64 (0.59), residues: 75 loop : -1.48 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 537 HIS 0.003 0.001 HIS A 235 PHE 0.013 0.001 PHE A 263 TYR 0.012 0.001 TYR A 410 ARG 0.008 0.001 ARG A 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.77 seconds wall clock time: 33 minutes 10.09 seconds (1990.09 seconds total)