Starting phenix.real_space_refine on Tue Feb 13 13:56:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/02_2024/7vx4_32168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/02_2024/7vx4_32168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/02_2024/7vx4_32168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/02_2024/7vx4_32168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/02_2024/7vx4_32168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/02_2024/7vx4_32168.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.062 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4152 2.51 5 N 1070 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" 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: 6493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1576 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.95, per 1000 atoms: 1.07 Number of scatterers: 6493 At special positions: 0 Unit cell: (77.603, 101.649, 118.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1233 8.00 N 1070 7.00 C 4152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG E1301 " - " ASN E 343 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 58.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.660A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.954A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.742A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.511A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.826A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.560A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.615A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.750A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.677A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.598A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.599A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.780A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.824A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.098A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.579A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 removed outlier: 4.396A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.599A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.407A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.750A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.990A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.773A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.729A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.648A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.948A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.585A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.102A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.140A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.923A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 273 hydrogen bonds defined for protein. 769 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: 1.74 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2081 1.34 - 1.46: 1727 1.46 - 1.58: 2810 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6676 Sorted by residual: bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 6671 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.54: 212 106.54 - 113.40: 3494 113.40 - 120.26: 2532 120.26 - 127.12: 2742 127.12 - 133.98: 98 Bond angle restraints: 9078 Sorted by residual: angle pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta sigma weight residual 121.98 131.85 -9.87 3.11e+00 1.03e-01 1.01e+01 angle pdb=" N TYR E 505 " pdb=" CA TYR E 505 " pdb=" C TYR E 505 " ideal model delta sigma weight residual 111.36 114.77 -3.41 1.09e+00 8.42e-01 9.78e+00 angle pdb=" N ASP A 136 " pdb=" CA ASP A 136 " pdb=" C ASP A 136 " ideal model delta sigma weight residual 111.07 114.15 -3.08 1.07e+00 8.73e-01 8.31e+00 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" C VAL A 293 " ideal model delta sigma weight residual 112.83 110.26 2.57 9.90e-01 1.02e+00 6.75e+00 angle pdb=" C LYS A 363 " pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 122.43 119.17 3.26 1.26e+00 6.30e-01 6.71e+00 ... (remaining 9073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3883 16.02 - 32.05: 77 32.05 - 48.07: 33 48.07 - 64.09: 8 64.09 - 80.12: 3 Dihedral angle restraints: 4004 sinusoidal: 1675 harmonic: 2329 Sorted by residual: dihedral pdb=" CA PHE E 497 " pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA E 352 " pdb=" C ALA E 352 " pdb=" N TRP E 353 " pdb=" CA TRP E 353 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 584 0.030 - 0.061: 242 0.061 - 0.091: 91 0.091 - 0.121: 42 0.121 - 0.151: 4 Chirality restraints: 963 Sorted by residual: chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA TYR E 505 " pdb=" N TYR E 505 " pdb=" C TYR E 505 " pdb=" CB TYR E 505 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 960 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 504 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C GLY E 504 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY E 504 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR E 505 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 611 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 612 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.012 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR E 495 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.001 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 87 2.65 - 3.21: 6043 3.21 - 3.77: 9658 3.77 - 4.34: 13646 4.34 - 4.90: 22092 Nonbonded interactions: 51526 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.082 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.189 2.230 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.225 2.440 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.234 2.440 ... (remaining 51521 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=0.50 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: 11.260 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: 0.000 Extract box with map and model: 11.890 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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 : 0.003 0.028 6676 Z= 0.182 Angle : 0.627 9.874 9078 Z= 0.393 Chirality : 0.042 0.151 963 Planarity : 0.004 0.038 1172 Dihedral : 8.878 80.115 2491 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.89 % Favored : 98.98 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.27 (0.26), residues: 789 helix: -2.59 (0.20), residues: 372 sheet: -0.28 (0.66), residues: 50 loop : -0.21 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 302 HIS 0.003 0.001 HIS A 34 PHE 0.020 0.002 PHE E 497 TYR 0.025 0.001 TYR E 495 ARG 0.006 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.8877 (m) cc_final: 0.8445 (p) REVERT: A 102 GLN cc_start: 0.7965 (pt0) cc_final: 0.7400 (pp30) REVERT: A 198 ASP cc_start: 0.8375 (p0) cc_final: 0.8070 (p0) REVERT: A 243 TYR cc_start: 0.8400 (t80) cc_final: 0.8043 (t80) REVERT: A 295 ASP cc_start: 0.7665 (m-30) cc_final: 0.7324 (t70) REVERT: A 442 GLN cc_start: 0.8439 (mm110) cc_final: 0.8125 (mt0) REVERT: A 484 ILE cc_start: 0.8329 (mt) cc_final: 0.8079 (mt) REVERT: A 559 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8191 (ttp-110) REVERT: A 584 LEU cc_start: 0.7155 (tp) cc_final: 0.6871 (tt) REVERT: E 334 ASN cc_start: 0.7192 (t0) cc_final: 0.6826 (m-40) REVERT: E 335 LEU cc_start: 0.7554 (mt) cc_final: 0.7284 (mt) REVERT: E 356 LYS cc_start: 0.8642 (tttp) cc_final: 0.8400 (ttpp) REVERT: E 422 ASN cc_start: 0.7524 (m-40) cc_final: 0.7095 (m110) REVERT: E 519 HIS cc_start: 0.6695 (m-70) cc_final: 0.6467 (t-170) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2074 time to fit residues: 61.7856 Evaluate side-chains 127 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 61 ASN A 524 GLN A 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6676 Z= 0.189 Angle : 0.627 8.536 9078 Z= 0.326 Chirality : 0.045 0.164 963 Planarity : 0.005 0.031 1172 Dihedral : 5.681 42.692 969 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.45 % Allowed : 10.63 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.51 (0.28), residues: 789 helix: -0.55 (0.24), residues: 380 sheet: -0.17 (0.63), residues: 44 loop : 0.12 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 PHE 0.025 0.002 PHE A 308 TYR 0.024 0.002 TYR E 495 ARG 0.007 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8379 (mttt) cc_final: 0.8114 (mtpt) REVERT: A 216 ASP cc_start: 0.8762 (p0) cc_final: 0.8541 (p0) REVERT: A 222 LEU cc_start: 0.8100 (tp) cc_final: 0.7625 (tp) REVERT: A 295 ASP cc_start: 0.7749 (m-30) cc_final: 0.7270 (t70) REVERT: A 299 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7561 (t0) REVERT: A 531 GLN cc_start: 0.7527 (tt0) cc_final: 0.7239 (tm-30) REVERT: E 335 LEU cc_start: 0.7617 (mt) cc_final: 0.7368 (mt) REVERT: E 355 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8094 (ttt90) REVERT: E 422 ASN cc_start: 0.7998 (m-40) cc_final: 0.7760 (m110) REVERT: E 519 HIS cc_start: 0.6771 (m-70) cc_final: 0.6487 (t-170) outliers start: 22 outliers final: 12 residues processed: 150 average time/residue: 0.1738 time to fit residues: 35.1314 Evaluate side-chains 117 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6676 Z= 0.169 Angle : 0.567 7.557 9078 Z= 0.291 Chirality : 0.042 0.168 963 Planarity : 0.004 0.033 1172 Dihedral : 4.982 41.566 969 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 2.73 % Allowed : 11.93 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.29), residues: 789 helix: 0.05 (0.25), residues: 399 sheet: 0.05 (0.67), residues: 49 loop : 0.21 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 PHE 0.019 0.002 PHE E 497 TYR 0.020 0.001 TYR E 495 ARG 0.005 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8478 (mttt) cc_final: 0.8167 (mtpt) REVERT: A 222 LEU cc_start: 0.8013 (tp) cc_final: 0.7586 (tp) REVERT: A 295 ASP cc_start: 0.7701 (m-30) cc_final: 0.7279 (t70) REVERT: A 323 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7446 (mmm) REVERT: A 531 GLN cc_start: 0.7529 (tt0) cc_final: 0.7152 (mt0) REVERT: A 598 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7184 (mp-120) REVERT: E 334 ASN cc_start: 0.7185 (t0) cc_final: 0.6914 (p0) REVERT: E 335 LEU cc_start: 0.7606 (mt) cc_final: 0.7280 (mt) REVERT: E 355 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.7874 (ttt90) REVERT: E 519 HIS cc_start: 0.6748 (m-70) cc_final: 0.6356 (t-170) outliers start: 17 outliers final: 10 residues processed: 133 average time/residue: 0.2583 time to fit residues: 46.4918 Evaluate side-chains 114 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.0770 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 373 HIS A 442 GLN A 598 GLN A 599 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6676 Z= 0.199 Angle : 0.575 7.166 9078 Z= 0.295 Chirality : 0.043 0.184 963 Planarity : 0.004 0.046 1172 Dihedral : 4.736 34.668 969 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.87 % Allowed : 14.08 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.24 (0.29), residues: 789 helix: 0.36 (0.26), residues: 401 sheet: 0.14 (0.69), residues: 49 loop : 0.12 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 594 HIS 0.004 0.001 HIS A 34 PHE 0.019 0.002 PHE E 497 TYR 0.019 0.001 TYR E 495 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8469 (mttt) cc_final: 0.8203 (mtpt) REVERT: A 62 MET cc_start: 0.8478 (tmm) cc_final: 0.8207 (tpp) REVERT: A 222 LEU cc_start: 0.8077 (tp) cc_final: 0.7092 (tt) REVERT: A 295 ASP cc_start: 0.7818 (m-30) cc_final: 0.7313 (t0) REVERT: A 305 GLN cc_start: 0.7778 (tp40) cc_final: 0.7432 (tp40) REVERT: A 323 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7570 (mmm) REVERT: A 531 GLN cc_start: 0.7624 (tt0) cc_final: 0.7243 (mt0) REVERT: E 334 ASN cc_start: 0.7297 (t0) cc_final: 0.6909 (p0) REVERT: E 335 LEU cc_start: 0.7658 (mt) cc_final: 0.7236 (mt) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.1459 time to fit residues: 24.0616 Evaluate side-chains 110 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6676 Z= 0.221 Angle : 0.586 7.530 9078 Z= 0.301 Chirality : 0.044 0.195 963 Planarity : 0.004 0.037 1172 Dihedral : 4.636 30.736 969 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.88 % Allowed : 13.51 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.23 (0.29), residues: 789 helix: 0.36 (0.26), residues: 403 sheet: -0.03 (0.68), residues: 49 loop : 0.14 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 302 HIS 0.003 0.001 HIS A 535 PHE 0.020 0.002 PHE E 497 TYR 0.019 0.002 TYR E 495 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.721 Fit side-chains REVERT: A 26 LYS cc_start: 0.8467 (mttt) cc_final: 0.8221 (mtpt) REVERT: A 62 MET cc_start: 0.8513 (tmm) cc_final: 0.8022 (tpt) REVERT: A 100 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 215 TYR cc_start: 0.8050 (m-80) cc_final: 0.7711 (m-10) REVERT: A 222 LEU cc_start: 0.8092 (tp) cc_final: 0.7381 (tt) REVERT: A 291 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6106 (tp) REVERT: A 295 ASP cc_start: 0.7818 (m-30) cc_final: 0.7456 (t0) REVERT: A 323 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7466 (mmm) REVERT: A 531 GLN cc_start: 0.7646 (tt0) cc_final: 0.7299 (mt0) REVERT: E 334 ASN cc_start: 0.7489 (t0) cc_final: 0.6884 (p0) REVERT: E 335 LEU cc_start: 0.7866 (mt) cc_final: 0.7405 (mt) outliers start: 25 outliers final: 15 residues processed: 113 average time/residue: 0.1520 time to fit residues: 24.3474 Evaluate side-chains 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.0470 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6676 Z= 0.211 Angle : 0.574 7.614 9078 Z= 0.294 Chirality : 0.044 0.203 963 Planarity : 0.004 0.037 1172 Dihedral : 4.592 30.489 969 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.45 % Allowed : 14.37 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.29), residues: 789 helix: 0.50 (0.26), residues: 402 sheet: -0.16 (0.69), residues: 49 loop : 0.12 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 302 HIS 0.003 0.001 HIS A 535 PHE 0.018 0.002 PHE E 497 TYR 0.017 0.001 TYR E 495 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.870 Fit side-chains REVERT: A 26 LYS cc_start: 0.8476 (mttt) cc_final: 0.8228 (mtpt) REVERT: A 62 MET cc_start: 0.8556 (tmm) cc_final: 0.8027 (tpt) REVERT: A 100 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (tt) REVERT: A 222 LEU cc_start: 0.8084 (tp) cc_final: 0.7823 (tp) REVERT: A 295 ASP cc_start: 0.8083 (m-30) cc_final: 0.7811 (t0) REVERT: A 531 GLN cc_start: 0.7625 (tt0) cc_final: 0.7352 (mt0) REVERT: A 556 ASN cc_start: 0.8642 (m-40) cc_final: 0.8424 (m110) REVERT: A 564 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8368 (tp30) REVERT: E 334 ASN cc_start: 0.7526 (t0) cc_final: 0.6782 (p0) REVERT: E 335 LEU cc_start: 0.7908 (mt) cc_final: 0.7431 (mt) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.1625 time to fit residues: 26.6353 Evaluate side-chains 110 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 417 HIS A 442 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6676 Z= 0.194 Angle : 0.591 7.933 9078 Z= 0.303 Chirality : 0.044 0.257 963 Planarity : 0.004 0.035 1172 Dihedral : 5.044 42.392 969 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.45 % Allowed : 14.37 % Favored : 82.18 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.70 % 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: 0.40 (0.30), residues: 789 helix: 0.60 (0.27), residues: 406 sheet: -0.29 (0.70), residues: 49 loop : 0.12 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 302 HIS 0.003 0.001 HIS A 535 PHE 0.016 0.002 PHE A 308 TYR 0.014 0.001 TYR E 508 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.715 Fit side-chains REVERT: A 26 LYS cc_start: 0.8470 (mttt) cc_final: 0.8220 (mtpt) REVERT: A 62 MET cc_start: 0.8532 (tmm) cc_final: 0.8020 (tpt) REVERT: A 100 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7759 (tt) REVERT: A 222 LEU cc_start: 0.8053 (tp) cc_final: 0.7806 (tp) REVERT: A 295 ASP cc_start: 0.8031 (m-30) cc_final: 0.7768 (t0) REVERT: A 463 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7891 (p) REVERT: A 531 GLN cc_start: 0.7635 (tt0) cc_final: 0.7260 (mt0) REVERT: A 556 ASN cc_start: 0.8583 (m-40) cc_final: 0.8366 (m110) REVERT: A 564 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8352 (tp30) REVERT: E 334 ASN cc_start: 0.7533 (t0) cc_final: 0.6759 (p0) REVERT: E 335 LEU cc_start: 0.7886 (mt) cc_final: 0.7442 (mt) outliers start: 22 outliers final: 16 residues processed: 113 average time/residue: 0.1550 time to fit residues: 24.5436 Evaluate side-chains 113 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 68 optimal weight: 0.0270 chunk 72 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6676 Z= 0.180 Angle : 0.581 10.801 9078 Z= 0.296 Chirality : 0.043 0.197 963 Planarity : 0.003 0.036 1172 Dihedral : 5.211 52.882 969 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.30 % Allowed : 14.94 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 789 helix: 0.72 (0.27), residues: 404 sheet: -0.36 (0.70), residues: 49 loop : 0.10 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 302 HIS 0.002 0.001 HIS A 535 PHE 0.018 0.001 PHE A 308 TYR 0.012 0.001 TYR E 508 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 0.768 Fit side-chains REVERT: A 26 LYS cc_start: 0.8476 (mttt) cc_final: 0.8220 (mtpt) REVERT: A 62 MET cc_start: 0.8500 (tmm) cc_final: 0.8072 (tpt) REVERT: A 222 LEU cc_start: 0.8023 (tp) cc_final: 0.7763 (tp) REVERT: A 295 ASP cc_start: 0.7919 (m-30) cc_final: 0.7697 (t0) REVERT: A 299 ASP cc_start: 0.7965 (t0) cc_final: 0.7677 (t0) REVERT: A 463 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7866 (p) REVERT: A 531 GLN cc_start: 0.7600 (tt0) cc_final: 0.7275 (mt0) REVERT: E 334 ASN cc_start: 0.7556 (t0) cc_final: 0.6714 (p0) REVERT: E 335 LEU cc_start: 0.7888 (mt) cc_final: 0.7427 (mt) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 0.1760 time to fit residues: 27.3016 Evaluate side-chains 113 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.2980 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6676 Z= 0.157 Angle : 0.564 10.267 9078 Z= 0.286 Chirality : 0.043 0.233 963 Planarity : 0.003 0.035 1172 Dihedral : 4.907 57.371 969 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.87 % Allowed : 15.37 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.53 (0.30), residues: 789 helix: 0.83 (0.27), residues: 403 sheet: -0.34 (0.73), residues: 49 loop : 0.04 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 594 HIS 0.002 0.000 HIS A 535 PHE 0.015 0.001 PHE A 308 TYR 0.012 0.001 TYR E 508 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.773 Fit side-chains REVERT: A 26 LYS cc_start: 0.8540 (mttt) cc_final: 0.8309 (mtpt) REVERT: A 62 MET cc_start: 0.8476 (tmm) cc_final: 0.8044 (tpt) REVERT: A 222 LEU cc_start: 0.7991 (tp) cc_final: 0.7723 (tp) REVERT: A 295 ASP cc_start: 0.7708 (m-30) cc_final: 0.7505 (t0) REVERT: A 299 ASP cc_start: 0.7847 (t0) cc_final: 0.7571 (t0) REVERT: A 463 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7870 (p) REVERT: A 482 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7370 (mtp180) REVERT: E 334 ASN cc_start: 0.7484 (t0) cc_final: 0.6705 (p0) REVERT: E 335 LEU cc_start: 0.7838 (mt) cc_final: 0.7408 (mt) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.1733 time to fit residues: 26.9466 Evaluate side-chains 113 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6676 Z= 0.157 Angle : 0.553 9.954 9078 Z= 0.281 Chirality : 0.042 0.199 963 Planarity : 0.003 0.035 1172 Dihedral : 4.824 56.052 969 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.87 % Allowed : 16.09 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.58 (0.30), residues: 789 helix: 0.90 (0.27), residues: 403 sheet: -0.40 (0.73), residues: 49 loop : 0.03 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 302 HIS 0.003 0.000 HIS A 535 PHE 0.013 0.001 PHE E 429 TYR 0.014 0.001 TYR A 207 ARG 0.004 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.804 Fit side-chains REVERT: A 26 LYS cc_start: 0.8496 (mttt) cc_final: 0.8243 (mtpt) REVERT: A 62 MET cc_start: 0.8510 (tmm) cc_final: 0.8069 (tpt) REVERT: A 222 LEU cc_start: 0.7967 (tp) cc_final: 0.6994 (tt) REVERT: A 295 ASP cc_start: 0.7657 (m-30) cc_final: 0.7419 (t0) REVERT: A 299 ASP cc_start: 0.7870 (t0) cc_final: 0.7573 (t0) REVERT: A 463 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 482 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7399 (mtp180) REVERT: E 334 ASN cc_start: 0.7506 (t0) cc_final: 0.6654 (p0) REVERT: E 335 LEU cc_start: 0.7849 (mt) cc_final: 0.7568 (mt) REVERT: E 420 ASP cc_start: 0.8320 (m-30) cc_final: 0.7842 (t0) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.1708 time to fit residues: 26.1970 Evaluate side-chains 113 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 0.0040 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.166331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.134017 restraints weight = 15527.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.140090 restraints weight = 18012.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.142238 restraints weight = 6596.722| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6676 Z= 0.178 Angle : 0.566 9.715 9078 Z= 0.287 Chirality : 0.042 0.203 963 Planarity : 0.003 0.036 1172 Dihedral : 4.944 58.696 969 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.02 % Allowed : 15.66 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.57 (0.30), residues: 789 helix: 0.93 (0.27), residues: 403 sheet: -0.52 (0.73), residues: 49 loop : -0.02 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 302 HIS 0.003 0.001 HIS A 535 PHE 0.013 0.001 PHE E 429 TYR 0.012 0.001 TYR E 508 ARG 0.003 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.16 seconds wall clock time: 36 minutes 30.67 seconds (2190.67 seconds total)