Starting phenix.real_space_refine on Mon Mar 11 00:28:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqu_15590/03_2024/8aqu_15590.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqu_15590/03_2024/8aqu_15590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqu_15590/03_2024/8aqu_15590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqu_15590/03_2024/8aqu_15590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqu_15590/03_2024/8aqu_15590.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqu_15590/03_2024/8aqu_15590.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 37 5.16 5 C 4049 2.51 5 N 1062 2.21 5 O 1192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4744 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 557} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1554 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "C" 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: "B" 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: 3.84, per 1000 atoms: 0.61 Number of scatterers: 6340 At special positions: 0 Unit cell: (96.4503, 81.9309, 113.044, 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 37 16.00 O 1192 8.00 N 1062 7.00 C 4049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 526 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 49.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.512A pdb=" N ALA A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 88 removed outlier: 4.859A pdb=" N SER A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N GLN A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N GLU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 5.539A pdb=" N LYS A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.652A pdb=" N GLN A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.872A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 4.471A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 4.636A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.727A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.634A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Proline residue: A 280 - end of helix No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.977A pdb=" N ASN A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.723A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.943A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.011A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ARG A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix removed outlier: 5.879A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.839A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.607A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.865A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.268A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 removed outlier: 4.980A pdb=" N SER A 502 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N PHE A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N HIS A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.529A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 575 removed outlier: 4.000A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Proline residue: A 565 - end of helix removed outlier: 6.348A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.949A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Proline residue: A 590 - end of helix removed outlier: 5.375A pdb=" N ASP A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.865A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.425A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.236A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 421' 177 hydrogen bonds defined for protein. 531 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: 1.40 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2039 1.35 - 1.47: 1681 1.47 - 1.59: 2737 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6515 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C1 NAG B 526 " pdb=" O5 NAG B 526 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.440 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C2 NAG B 526 " pdb=" N2 NAG B 526 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.59e+00 ... (remaining 6510 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 208 107.15 - 113.86: 3476 113.86 - 120.58: 2684 120.58 - 127.29: 2390 127.29 - 134.01: 89 Bond angle restraints: 8847 Sorted by residual: angle pdb=" C ALA A 107 " pdb=" CA ALA A 107 " pdb=" CB ALA A 107 " ideal model delta sigma weight residual 115.89 110.49 5.40 1.32e+00 5.74e-01 1.67e+01 angle pdb=" N GLU A 471 " pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 114.56 109.81 4.75 1.27e+00 6.20e-01 1.40e+01 angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 111.81 109.20 2.61 8.60e-01 1.35e+00 9.24e+00 angle pdb=" C THR A 55 " pdb=" N GLU A 56 " pdb=" CA GLU A 56 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.65e+00 angle pdb=" C ARG B 457 " pdb=" N LYS B 458 " pdb=" CA LYS B 458 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.39e+00 ... (remaining 8842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 3621 22.87 - 45.74: 232 45.74 - 68.61: 22 68.61 - 91.48: 12 91.48 - 114.35: 17 Dihedral angle restraints: 3904 sinusoidal: 1614 harmonic: 2290 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -29.20 -56.80 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C5 NAG C 2 " ideal model delta sinusoidal sigma weight residual -62.96 51.39 -114.35 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C3 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sinusoidal sigma weight residual -55.55 55.41 -110.96 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 3901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 592 0.035 - 0.070: 253 0.070 - 0.105: 76 0.105 - 0.139: 9 0.139 - 0.174: 2 Chirality restraints: 932 Sorted by residual: chirality pdb=" C2 NAG B 526 " pdb=" C1 NAG B 526 " pdb=" C3 NAG B 526 " pdb=" N2 NAG B 526 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA PRO B 337 " pdb=" N PRO B 337 " pdb=" C PRO B 337 " pdb=" CB PRO B 337 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 929 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO B 337 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 56 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C GLU A 56 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 56 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 134 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 135 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.025 5.00e-02 4.00e+02 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1190 2.77 - 3.30: 6104 3.30 - 3.84: 9943 3.84 - 4.37: 11280 4.37 - 4.90: 19334 Nonbonded interactions: 47851 Sorted by model distance: nonbonded pdb=" O SER A 77 " pdb=" NE2 GLN A 81 " model vdw 2.240 2.520 nonbonded pdb=" O ARG A 273 " pdb=" OG1 THR A 445 " model vdw 2.240 2.440 nonbonded pdb=" O ASN A 53 " pdb=" ND2 ASN A 58 " model vdw 2.260 2.520 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.311 2.440 nonbonded pdb=" NH1 ARG B 454 " pdb=" O ASP B 467 " model vdw 2.311 2.520 ... (remaining 47846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 9.200 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.920 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 0.062 6515 Z= 0.182 Angle : 0.616 7.988 8847 Z= 0.340 Chirality : 0.040 0.174 932 Planarity : 0.005 0.073 1145 Dihedral : 16.844 114.347 2414 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.31), residues: 773 helix: 0.63 (0.33), residues: 274 sheet: -2.59 (0.83), residues: 37 loop : -1.94 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.002 0.001 HIS A 378 PHE 0.017 0.001 PHE B 497 TYR 0.015 0.001 TYR B 495 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LEU cc_start: 0.6302 (pp) cc_final: 0.6079 (mp) REVERT: A 455 MET cc_start: 0.7447 (ppp) cc_final: 0.7055 (ppp) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2018 time to fit residues: 34.4191 Evaluate side-chains 89 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.0040 chunk 39 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 265 HIS A 345 HIS A 388 GLN A 442 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6515 Z= 0.160 Angle : 0.603 9.578 8847 Z= 0.291 Chirality : 0.042 0.241 932 Planarity : 0.005 0.073 1145 Dihedral : 11.812 106.117 915 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.89 % Allowed : 10.21 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.31), residues: 773 helix: 0.39 (0.32), residues: 287 sheet: -2.28 (0.83), residues: 36 loop : -1.97 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.016 0.001 PHE A 452 TYR 0.036 0.001 TYR A 535 ARG 0.005 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6828 (tt0) REVERT: A 236 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3895 (mt) REVERT: A 270 MET cc_start: 0.0819 (tpt) cc_final: 0.0413 (tpt) REVERT: A 455 MET cc_start: 0.7244 (ppp) cc_final: 0.6859 (ppp) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.1666 time to fit residues: 20.3918 Evaluate side-chains 85 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 345 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6515 Z= 0.183 Angle : 0.585 9.611 8847 Z= 0.286 Chirality : 0.041 0.247 932 Planarity : 0.005 0.069 1145 Dihedral : 8.122 93.274 914 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.37 % Allowed : 12.28 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.31), residues: 773 helix: 0.31 (0.31), residues: 298 sheet: -2.25 (0.74), residues: 46 loop : -2.07 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.010 0.001 PHE A 369 TYR 0.018 0.001 TYR A 535 ARG 0.003 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6979 (tt0) REVERT: A 208 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5968 (mm-30) REVERT: A 236 LEU cc_start: 0.4370 (OUTLIER) cc_final: 0.3966 (mt) REVERT: A 270 MET cc_start: 0.0760 (tpt) cc_final: 0.0389 (tpt) REVERT: A 455 MET cc_start: 0.7258 (ppp) cc_final: 0.6855 (ppp) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 0.1418 time to fit residues: 19.1761 Evaluate side-chains 88 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6515 Z= 0.175 Angle : 0.580 9.663 8847 Z= 0.282 Chirality : 0.041 0.248 932 Planarity : 0.005 0.065 1145 Dihedral : 7.676 87.522 914 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.25 % Allowed : 13.46 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.31), residues: 773 helix: 0.27 (0.31), residues: 298 sheet: -2.11 (0.75), residues: 46 loop : -2.03 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE A 369 TYR 0.013 0.001 TYR A 535 ARG 0.002 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.811 Fit side-chains REVERT: A 102 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7001 (tt0) REVERT: A 208 GLU cc_start: 0.6224 (tm-30) cc_final: 0.5920 (mm-30) REVERT: A 229 THR cc_start: 0.1593 (t) cc_final: 0.0868 (m) REVERT: A 236 LEU cc_start: 0.4297 (OUTLIER) cc_final: 0.3917 (mt) REVERT: A 270 MET cc_start: 0.0511 (tpt) cc_final: 0.0156 (tpt) REVERT: A 455 MET cc_start: 0.7203 (ppp) cc_final: 0.6772 (ppp) outliers start: 22 outliers final: 15 residues processed: 100 average time/residue: 0.1536 time to fit residues: 21.5645 Evaluate side-chains 94 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.0040 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6515 Z= 0.165 Angle : 0.579 9.686 8847 Z= 0.280 Chirality : 0.041 0.249 932 Planarity : 0.004 0.062 1145 Dihedral : 7.213 81.570 914 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.85 % Allowed : 14.79 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.31), residues: 773 helix: 0.30 (0.31), residues: 298 sheet: -1.85 (0.75), residues: 47 loop : -2.07 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE A 369 TYR 0.011 0.001 TYR A 535 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.765 Fit side-chains REVERT: A 183 TYR cc_start: 0.5969 (t80) cc_final: 0.5717 (t80) REVERT: A 208 GLU cc_start: 0.6233 (tm-30) cc_final: 0.5919 (mm-30) REVERT: A 229 THR cc_start: 0.1839 (t) cc_final: 0.1090 (m) REVERT: A 236 LEU cc_start: 0.4192 (OUTLIER) cc_final: 0.3860 (mt) REVERT: A 270 MET cc_start: 0.0627 (tpt) cc_final: 0.0289 (tpt) REVERT: A 455 MET cc_start: 0.7211 (ppp) cc_final: 0.6776 (ppp) outliers start: 26 outliers final: 16 residues processed: 104 average time/residue: 0.1529 time to fit residues: 22.9837 Evaluate side-chains 97 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6515 Z= 0.188 Angle : 0.599 9.725 8847 Z= 0.289 Chirality : 0.041 0.250 932 Planarity : 0.005 0.059 1145 Dihedral : 7.090 78.965 914 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.85 % Allowed : 15.68 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.31), residues: 773 helix: 0.28 (0.31), residues: 298 sheet: -1.70 (0.77), residues: 47 loop : -2.09 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE A 369 TYR 0.009 0.001 TYR A 535 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 0.643 Fit side-chains REVERT: A 102 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6866 (tt0) REVERT: A 208 GLU cc_start: 0.6314 (tm-30) cc_final: 0.5987 (mm-30) REVERT: A 229 THR cc_start: 0.2267 (t) cc_final: 0.1491 (m) REVERT: A 236 LEU cc_start: 0.4258 (OUTLIER) cc_final: 0.3914 (mt) REVERT: A 270 MET cc_start: 0.0657 (tpt) cc_final: 0.0334 (tpt) REVERT: A 455 MET cc_start: 0.6737 (ppp) cc_final: 0.6368 (ppp) outliers start: 26 outliers final: 19 residues processed: 107 average time/residue: 0.1407 time to fit residues: 21.5060 Evaluate side-chains 100 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.0020 chunk 34 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 397 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6515 Z= 0.152 Angle : 0.576 9.692 8847 Z= 0.277 Chirality : 0.040 0.247 932 Planarity : 0.004 0.059 1145 Dihedral : 6.777 74.752 914 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.25 % Allowed : 16.57 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.31), residues: 773 helix: 0.39 (0.31), residues: 304 sheet: -1.76 (0.89), residues: 38 loop : -2.09 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.002 0.001 HIS A 378 PHE 0.008 0.001 PHE A 369 TYR 0.009 0.001 TYR A 535 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.627 Fit side-chains REVERT: A 102 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6744 (tt0) REVERT: A 152 MET cc_start: 0.0223 (ttt) cc_final: -0.0731 (ptp) REVERT: A 208 GLU cc_start: 0.6305 (tm-30) cc_final: 0.5986 (mm-30) REVERT: A 229 THR cc_start: 0.2290 (t) cc_final: 0.1510 (m) REVERT: A 236 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.3994 (mt) REVERT: A 270 MET cc_start: 0.0640 (tpt) cc_final: 0.0319 (tpt) REVERT: A 455 MET cc_start: 0.6722 (ppp) cc_final: 0.6350 (ppp) REVERT: A 592 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.5131 (t80) outliers start: 22 outliers final: 18 residues processed: 102 average time/residue: 0.1401 time to fit residues: 20.6786 Evaluate side-chains 99 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6515 Z= 0.181 Angle : 0.604 10.227 8847 Z= 0.289 Chirality : 0.041 0.249 932 Planarity : 0.005 0.060 1145 Dihedral : 6.663 72.152 914 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.55 % Allowed : 16.12 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.31), residues: 773 helix: 0.25 (0.31), residues: 314 sheet: -1.70 (0.89), residues: 38 loop : -2.15 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 459 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE A 369 TYR 0.008 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.706 Fit side-chains REVERT: A 102 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6850 (tt0) REVERT: A 152 MET cc_start: 0.0233 (ttt) cc_final: -0.0721 (ptp) REVERT: A 183 TYR cc_start: 0.5959 (t80) cc_final: 0.5714 (t80) REVERT: A 208 GLU cc_start: 0.6483 (tm-30) cc_final: 0.6168 (mm-30) REVERT: A 229 THR cc_start: 0.2867 (t) cc_final: 0.2090 (m) REVERT: A 236 LEU cc_start: 0.4209 (OUTLIER) cc_final: 0.3912 (mt) REVERT: A 270 MET cc_start: 0.0697 (tpt) cc_final: 0.0391 (tpt) REVERT: A 455 MET cc_start: 0.6783 (ppp) cc_final: 0.6406 (ppp) REVERT: A 579 MET cc_start: 0.6120 (mtm) cc_final: 0.5853 (mtt) REVERT: A 592 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5167 (t80) REVERT: B 495 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7940 (m-10) outliers start: 24 outliers final: 18 residues processed: 102 average time/residue: 0.1414 time to fit residues: 20.7610 Evaluate side-chains 102 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.0170 chunk 65 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 44 optimal weight: 9.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6515 Z= 0.150 Angle : 0.580 10.737 8847 Z= 0.278 Chirality : 0.040 0.246 932 Planarity : 0.005 0.059 1145 Dihedral : 6.377 67.141 914 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.11 % Allowed : 16.72 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.31), residues: 773 helix: 0.37 (0.31), residues: 312 sheet: -1.61 (0.89), residues: 38 loop : -2.06 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 378 PHE 0.007 0.001 PHE A 369 TYR 0.007 0.001 TYR A 535 ARG 0.001 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.642 Fit side-chains REVERT: A 152 MET cc_start: 0.0214 (ttt) cc_final: -0.0705 (ptp) REVERT: A 208 GLU cc_start: 0.6391 (tm-30) cc_final: 0.6118 (mm-30) REVERT: A 229 THR cc_start: 0.2891 (t) cc_final: 0.2122 (m) REVERT: A 236 LEU cc_start: 0.4208 (OUTLIER) cc_final: 0.3935 (mt) REVERT: A 270 MET cc_start: 0.0751 (tpt) cc_final: 0.0443 (tpt) REVERT: A 455 MET cc_start: 0.6634 (ppp) cc_final: 0.6247 (ppp) REVERT: A 592 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5100 (t80) REVERT: B 495 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7861 (m-10) outliers start: 21 outliers final: 16 residues processed: 102 average time/residue: 0.1395 time to fit residues: 20.4494 Evaluate side-chains 98 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6515 Z= 0.188 Angle : 0.609 11.203 8847 Z= 0.291 Chirality : 0.041 0.249 932 Planarity : 0.005 0.058 1145 Dihedral : 6.269 63.328 914 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.11 % Allowed : 17.31 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.31), residues: 773 helix: 0.25 (0.31), residues: 317 sheet: -1.51 (0.78), residues: 47 loop : -2.05 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 459 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE A 369 TYR 0.008 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.693 Fit side-chains REVERT: A 102 GLN cc_start: 0.7412 (mm-40) cc_final: 0.6807 (tt0) REVERT: A 152 MET cc_start: 0.0321 (ttt) cc_final: -0.0620 (ptp) REVERT: A 208 GLU cc_start: 0.6434 (tm-30) cc_final: 0.6166 (mm-30) REVERT: A 236 LEU cc_start: 0.4082 (OUTLIER) cc_final: 0.3875 (mt) REVERT: A 270 MET cc_start: 0.0659 (tpt) cc_final: 0.0322 (tpt) REVERT: A 455 MET cc_start: 0.6496 (ppp) cc_final: 0.6098 (ppp) REVERT: A 592 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.5098 (t80) REVERT: B 495 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7934 (m-10) outliers start: 21 outliers final: 16 residues processed: 99 average time/residue: 0.1369 time to fit residues: 19.4787 Evaluate side-chains 97 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 62 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.228578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.194690 restraints weight = 9305.073| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 3.37 r_work: 0.4058 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6515 Z= 0.148 Angle : 0.605 11.458 8847 Z= 0.285 Chirality : 0.041 0.245 932 Planarity : 0.005 0.058 1145 Dihedral : 5.967 57.503 914 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.66 % Allowed : 17.60 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.31), residues: 773 helix: 0.37 (0.31), residues: 315 sheet: -1.77 (0.76), residues: 48 loop : -2.03 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 459 HIS 0.003 0.001 HIS A 505 PHE 0.007 0.001 PHE A 308 TYR 0.007 0.001 TYR A 41 ARG 0.001 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.76 seconds wall clock time: 33 minutes 25.05 seconds (2005.05 seconds total)