Starting phenix.real_space_refine on Fri Mar 14 04:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zay_14582/03_2025/7zay_14582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zay_14582/03_2025/7zay_14582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2025/7zay_14582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2025/7zay_14582.map" model { file = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2025/7zay_14582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2025/7zay_14582.cif" } resolution = 2.8 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= 0.002 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 P 2 5.49 5 S 46 5.16 5 C 6010 2.51 5 N 1571 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4573 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4688 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 6.65, per 1000 atoms: 0.71 Number of scatterers: 9339 At special positions: 0 Unit cell: (97.44, 102.48, 102.48, 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) S 46 16.00 P 2 15.00 O 1710 8.00 N 1571 7.00 C 6010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 800 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 37.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 removed outlier: 4.026A pdb=" N LYS A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.765A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A 387 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.885A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 447' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.969A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 551 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.606A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.550A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 699 through 713 Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.704A pdb=" N ALA B 150 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 removed outlier: 3.548A pdb=" N THR B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.994A pdb=" N LYS B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 4.206A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 314' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.971A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.686A pdb=" N ILE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 400 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 removed outlier: 3.826A pdb=" N GLY B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.581A pdb=" N ASN B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 524 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.589A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.721A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.853A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 removed outlier: 3.705A pdb=" N CYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.341A pdb=" N TYR A 117 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA A 219 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 194 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 216 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 234 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 218 " --> pdb=" O ILE A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295 removed outlier: 4.039A pdb=" N LEU A 335 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 267 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 360 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.696A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 726 removed outlier: 6.991A pdb=" N VAL B 643 " --> pdb=" O HIS B 694 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 696 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS B 645 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 563 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 646 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 565 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR B 457 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE B 537 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 459 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 512 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP B 489 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218 removed outlier: 4.680A pdb=" N PHE B 217 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 283 removed outlier: 6.153A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 316 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 342 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 583 removed outlier: 3.589A pdb=" N LEU B 572 " --> pdb=" O LYS B 581 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 813 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: 3.14 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2958 1.34 - 1.46: 2340 1.46 - 1.58: 4214 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 9585 Sorted by residual: bond pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.80e-02 3.09e+03 6.21e+00 bond pdb=" C1 NAG A 800 " pdb=" O5 NAG A 800 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 9580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 12930 2.89 - 5.77: 87 5.77 - 8.66: 9 8.66 - 11.54: 2 11.54 - 14.43: 1 Bond angle restraints: 13029 Sorted by residual: angle pdb=" C GLY B 260 " pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O1A UDP A 801 " ideal model delta sigma weight residual 106.70 111.08 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 105.97 110.23 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" N LEU B 261 " pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " ideal model delta sigma weight residual 110.49 117.47 -6.98 1.69e+00 3.50e-01 1.70e+01 angle pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " pdb=" CG LEU B 261 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 ... (remaining 13024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 5486 21.82 - 43.64: 256 43.64 - 65.46: 37 65.46 - 87.28: 12 87.28 - 109.10: 6 Dihedral angle restraints: 5797 sinusoidal: 2410 harmonic: 3387 Sorted by residual: dihedral pdb=" CD ARG A 723 " pdb=" NE ARG A 723 " pdb=" CZ ARG A 723 " pdb=" NH1 ARG A 723 " ideal model delta sinusoidal sigma weight residual 0.00 71.37 -71.37 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA ALA B 202 " pdb=" C ALA B 202 " pdb=" N LEU B 203 " pdb=" CA LEU B 203 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.61 109.10 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 5794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1178 0.054 - 0.108: 217 0.108 - 0.161: 34 0.161 - 0.215: 3 0.215 - 0.269: 1 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA PRO B 263 " pdb=" N PRO B 263 " pdb=" C PRO B 263 " pdb=" CB PRO B 263 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1430 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 723 " 0.882 9.50e-02 1.11e+02 3.97e-01 1.07e+02 pdb=" NE ARG A 723 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 723 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 723 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 723 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 562 " -0.225 9.50e-02 1.11e+02 1.02e-01 8.22e+00 pdb=" NE ARG B 562 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 562 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 562 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 562 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 196 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO B 197 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 197 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 197 " 0.025 5.00e-02 4.00e+02 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 865 2.74 - 3.28: 9521 3.28 - 3.82: 15843 3.82 - 4.36: 19801 4.36 - 4.90: 32647 Nonbonded interactions: 78677 Sorted by model distance: nonbonded pdb=" O ILE B 376 " pdb=" OG SER B 379 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 271 " pdb=" O3B UDP A 801 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 223 " pdb=" NE2 HIS B 88 " model vdw 2.238 3.120 nonbonded pdb=" O PRO B 560 " pdb=" ND1 HIS B 601 " model vdw 2.253 3.120 nonbonded pdb=" OH TYR A 626 " pdb=" NE2 HIS A 631 " model vdw 2.261 3.120 ... (remaining 78672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 0.045 9585 Z= 0.161 Angle : 0.611 14.426 13029 Z= 0.310 Chirality : 0.044 0.269 1433 Planarity : 0.011 0.397 1650 Dihedral : 13.247 109.101 3579 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.82 % Favored : 92.01 % Rotamer: Outliers : 1.09 % Allowed : 7.42 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.32 (0.25), residues: 1126 helix: 0.29 (0.29), residues: 354 sheet: -2.14 (0.49), residues: 105 loop : -1.33 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 711 HIS 0.010 0.001 HIS B 694 PHE 0.009 0.001 PHE B 400 TYR 0.009 0.001 TYR A 608 ARG 0.060 0.001 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7245 (m-80) cc_final: 0.7040 (m-80) REVERT: A 420 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 478 SER cc_start: 0.7735 (p) cc_final: 0.7275 (t) REVERT: A 670 ILE cc_start: 0.8002 (mm) cc_final: 0.7766 (mm) REVERT: B 388 MET cc_start: 0.7140 (mtp) cc_final: 0.6859 (mtp) REVERT: B 484 LYS cc_start: 0.4508 (OUTLIER) cc_final: 0.4284 (ttmm) REVERT: B 695 ARG cc_start: 0.7137 (ptt-90) cc_final: 0.6737 (ptt-90) outliers start: 11 outliers final: 1 residues processed: 264 average time/residue: 1.1239 time to fit residues: 319.3629 Evaluate side-chains 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 484 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0270 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 471 ASN B 162 GLN B 200 ASN B 262 HIS B 389 GLN B 412 GLN B 454 GLN B 550 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.237938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.206466 restraints weight = 11197.347| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 2.66 r_work: 0.4473 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9585 Z= 0.207 Angle : 0.672 12.113 13029 Z= 0.334 Chirality : 0.045 0.219 1433 Planarity : 0.005 0.068 1650 Dihedral : 9.313 89.909 1379 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 3.07 % Allowed : 15.23 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.10 (0.25), residues: 1126 helix: 0.34 (0.28), residues: 365 sheet: -1.96 (0.50), residues: 101 loop : -1.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 711 HIS 0.006 0.001 HIS B 694 PHE 0.014 0.001 PHE B 680 TYR 0.013 0.001 TYR A 592 ARG 0.008 0.001 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7638 (m-80) cc_final: 0.7311 (m-80) REVERT: A 420 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 478 SER cc_start: 0.7844 (p) cc_final: 0.7322 (t) REVERT: B 281 LEU cc_start: 0.7554 (tt) cc_final: 0.7311 (tt) REVERT: B 388 MET cc_start: 0.7099 (mtp) cc_final: 0.6757 (mtp) REVERT: B 441 SER cc_start: 0.8088 (p) cc_final: 0.7782 (t) REVERT: B 452 GLN cc_start: 0.7089 (mt0) cc_final: 0.6768 (mp10) REVERT: B 592 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7158 (mtm) REVERT: B 624 MET cc_start: 0.7446 (mmm) cc_final: 0.7179 (mmt) REVERT: B 695 ARG cc_start: 0.7555 (ptt-90) cc_final: 0.7338 (ptt-90) outliers start: 31 outliers final: 14 residues processed: 222 average time/residue: 1.0224 time to fit residues: 247.0765 Evaluate side-chains 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 397 HIS A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 313 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.232771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.200420 restraints weight = 11422.974| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 2.72 r_work: 0.4407 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9585 Z= 0.305 Angle : 0.683 10.426 13029 Z= 0.344 Chirality : 0.047 0.266 1433 Planarity : 0.005 0.050 1650 Dihedral : 8.708 88.668 1375 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.63 % Rotamer: Outliers : 4.06 % Allowed : 17.01 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1126 helix: 0.15 (0.27), residues: 368 sheet: -1.86 (0.52), residues: 99 loop : -1.12 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 711 HIS 0.003 0.001 HIS A 597 PHE 0.019 0.002 PHE B 604 TYR 0.023 0.002 TYR B 107 ARG 0.006 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7693 (m-80) cc_final: 0.7362 (m-80) REVERT: A 420 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 478 SER cc_start: 0.7872 (p) cc_final: 0.7358 (t) REVERT: B 314 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7791 (mp0) REVERT: B 388 MET cc_start: 0.7116 (mtp) cc_final: 0.6799 (mtp) REVERT: B 441 SER cc_start: 0.8153 (p) cc_final: 0.7838 (t) REVERT: B 452 GLN cc_start: 0.7158 (mt0) cc_final: 0.6864 (mp10) REVERT: B 561 ASP cc_start: 0.7152 (p0) cc_final: 0.6860 (t0) REVERT: B 624 MET cc_start: 0.7514 (mmm) cc_final: 0.7226 (mmm) outliers start: 41 outliers final: 19 residues processed: 211 average time/residue: 1.0163 time to fit residues: 233.2807 Evaluate side-chains 189 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 3 optimal weight: 0.0070 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 287 HIS A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.232546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.200412 restraints weight = 11341.943| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.68 r_work: 0.4412 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9585 Z= 0.272 Angle : 0.680 11.203 13029 Z= 0.338 Chirality : 0.047 0.340 1433 Planarity : 0.004 0.044 1650 Dihedral : 8.411 88.559 1375 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.93 % Favored : 92.90 % Rotamer: Outliers : 3.36 % Allowed : 18.69 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.18 (0.25), residues: 1126 helix: 0.14 (0.27), residues: 366 sheet: -2.00 (0.48), residues: 114 loop : -1.08 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 394 HIS 0.003 0.001 HIS A 285 PHE 0.019 0.002 PHE B 604 TYR 0.018 0.002 TYR A 592 ARG 0.007 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7709 (m-80) cc_final: 0.7372 (m-80) REVERT: A 420 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 478 SER cc_start: 0.7871 (p) cc_final: 0.7364 (t) REVERT: B 388 MET cc_start: 0.7118 (mtp) cc_final: 0.6769 (mtp) REVERT: B 441 SER cc_start: 0.8159 (p) cc_final: 0.7855 (t) REVERT: B 452 GLN cc_start: 0.7123 (mt0) cc_final: 0.6859 (mp-120) REVERT: B 624 MET cc_start: 0.7541 (mmm) cc_final: 0.7297 (mmt) outliers start: 34 outliers final: 19 residues processed: 196 average time/residue: 1.2380 time to fit residues: 264.4667 Evaluate side-chains 186 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 587 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN B 161 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.234728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.202714 restraints weight = 11268.259| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 2.70 r_work: 0.4439 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9585 Z= 0.213 Angle : 0.651 10.906 13029 Z= 0.322 Chirality : 0.046 0.318 1433 Planarity : 0.004 0.044 1650 Dihedral : 8.132 85.613 1375 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 3.46 % Allowed : 19.19 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.04 (0.25), residues: 1126 helix: 0.26 (0.27), residues: 366 sheet: -1.91 (0.49), residues: 114 loop : -1.00 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 200 HIS 0.003 0.001 HIS B 88 PHE 0.020 0.001 PHE B 98 TYR 0.016 0.001 TYR A 467 ARG 0.008 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7678 (m-80) cc_final: 0.7327 (m-80) REVERT: A 420 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 478 SER cc_start: 0.7887 (p) cc_final: 0.7354 (t) REVERT: B 80 ARG cc_start: 0.7183 (ttm110) cc_final: 0.6827 (tpp-160) REVERT: B 192 LEU cc_start: 0.8114 (mt) cc_final: 0.7912 (mt) REVERT: B 314 GLU cc_start: 0.7801 (mp0) cc_final: 0.6691 (mp0) REVERT: B 388 MET cc_start: 0.7149 (mtp) cc_final: 0.6796 (mtp) REVERT: B 441 SER cc_start: 0.8092 (p) cc_final: 0.7798 (t) REVERT: B 452 GLN cc_start: 0.7098 (mt0) cc_final: 0.6848 (mp-120) REVERT: B 561 ASP cc_start: 0.7105 (p0) cc_final: 0.6698 (t0) outliers start: 35 outliers final: 19 residues processed: 207 average time/residue: 0.9886 time to fit residues: 222.8475 Evaluate side-chains 189 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.231676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.199319 restraints weight = 11394.468| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 2.71 r_work: 0.4403 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9585 Z= 0.289 Angle : 0.696 11.951 13029 Z= 0.345 Chirality : 0.047 0.372 1433 Planarity : 0.004 0.043 1650 Dihedral : 8.205 85.150 1375 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.84 % Favored : 92.90 % Rotamer: Outliers : 3.96 % Allowed : 19.58 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.19 (0.25), residues: 1126 helix: -0.01 (0.26), residues: 381 sheet: -1.67 (0.54), residues: 102 loop : -1.10 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 200 HIS 0.003 0.001 HIS A 285 PHE 0.018 0.002 PHE B 98 TYR 0.028 0.002 TYR B 107 ARG 0.009 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7688 (m-80) cc_final: 0.7376 (m-80) REVERT: A 420 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 478 SER cc_start: 0.7905 (p) cc_final: 0.7409 (t) REVERT: B 80 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6861 (tpp-160) REVERT: B 310 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 388 MET cc_start: 0.7130 (mtp) cc_final: 0.6798 (mtp) REVERT: B 441 SER cc_start: 0.8162 (p) cc_final: 0.7870 (t) REVERT: B 452 GLN cc_start: 0.7123 (mt0) cc_final: 0.6910 (mp-120) REVERT: B 592 MET cc_start: 0.7680 (mtp) cc_final: 0.7340 (mtm) REVERT: B 624 MET cc_start: 0.7522 (mmm) cc_final: 0.7217 (mmm) outliers start: 40 outliers final: 25 residues processed: 200 average time/residue: 1.0391 time to fit residues: 226.8297 Evaluate side-chains 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.232267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.200037 restraints weight = 11495.491| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 2.70 r_work: 0.4406 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9585 Z= 0.266 Angle : 0.690 10.608 13029 Z= 0.342 Chirality : 0.047 0.360 1433 Planarity : 0.004 0.041 1650 Dihedral : 8.149 84.250 1375 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.57 % Favored : 93.16 % Rotamer: Outliers : 3.56 % Allowed : 20.47 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.07 (0.25), residues: 1126 helix: 0.07 (0.27), residues: 375 sheet: -1.64 (0.54), residues: 102 loop : -1.00 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 200 HIS 0.003 0.001 HIS A 285 PHE 0.018 0.002 PHE A 577 TYR 0.025 0.002 TYR A 467 ARG 0.008 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7715 (m-80) cc_final: 0.7399 (m-80) REVERT: A 420 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 478 SER cc_start: 0.7889 (p) cc_final: 0.7379 (t) REVERT: B 80 ARG cc_start: 0.7211 (ttm110) cc_final: 0.6858 (tpp-160) REVERT: B 310 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 388 MET cc_start: 0.7127 (mtp) cc_final: 0.6781 (mtp) REVERT: B 441 SER cc_start: 0.8146 (p) cc_final: 0.7857 (t) REVERT: B 592 MET cc_start: 0.7745 (mtp) cc_final: 0.7420 (mtm) REVERT: B 624 MET cc_start: 0.7600 (mmm) cc_final: 0.7317 (mmm) outliers start: 36 outliers final: 25 residues processed: 203 average time/residue: 0.9830 time to fit residues: 217.0955 Evaluate side-chains 189 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN A 721 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 389 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.233842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.201999 restraints weight = 11567.059| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 2.70 r_work: 0.4430 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9585 Z= 0.225 Angle : 0.693 10.202 13029 Z= 0.341 Chirality : 0.046 0.331 1433 Planarity : 0.004 0.044 1650 Dihedral : 8.009 81.428 1375 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.66 % Favored : 93.07 % Rotamer: Outliers : 3.07 % Allowed : 20.67 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -0.99 (0.25), residues: 1126 helix: 0.18 (0.27), residues: 373 sheet: -1.64 (0.54), residues: 102 loop : -0.96 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 PHE 0.018 0.001 PHE A 577 TYR 0.025 0.001 TYR A 467 ARG 0.009 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7657 (m-80) cc_final: 0.7321 (m-80) REVERT: A 420 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 478 SER cc_start: 0.7900 (p) cc_final: 0.7362 (t) REVERT: B 80 ARG cc_start: 0.7190 (ttm110) cc_final: 0.6834 (tpp-160) REVERT: B 276 HIS cc_start: 0.4633 (OUTLIER) cc_final: 0.4046 (p90) REVERT: B 310 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 388 MET cc_start: 0.7124 (mtp) cc_final: 0.6770 (mtp) REVERT: B 441 SER cc_start: 0.8092 (p) cc_final: 0.7800 (t) REVERT: B 561 ASP cc_start: 0.7065 (p0) cc_final: 0.6808 (t0) REVERT: B 592 MET cc_start: 0.7654 (mtp) cc_final: 0.7398 (mtm) REVERT: B 624 MET cc_start: 0.7587 (mmm) cc_final: 0.7318 (mmm) outliers start: 31 outliers final: 22 residues processed: 200 average time/residue: 0.9570 time to fit residues: 208.4207 Evaluate side-chains 194 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 94 optimal weight: 0.0060 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.234222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.202294 restraints weight = 11324.864| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 2.70 r_work: 0.4432 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9585 Z= 0.228 Angle : 0.695 9.743 13029 Z= 0.342 Chirality : 0.046 0.326 1433 Planarity : 0.004 0.041 1650 Dihedral : 7.937 79.361 1375 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.39 % Favored : 93.25 % Rotamer: Outliers : 3.07 % Allowed : 20.97 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -0.94 (0.25), residues: 1126 helix: 0.14 (0.27), residues: 377 sheet: -1.57 (0.54), residues: 102 loop : -0.89 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 200 HIS 0.003 0.001 HIS A 285 PHE 0.017 0.001 PHE A 577 TYR 0.031 0.001 TYR A 467 ARG 0.008 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7634 (m-80) cc_final: 0.7346 (m-80) REVERT: A 420 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 478 SER cc_start: 0.7899 (p) cc_final: 0.7360 (t) REVERT: B 80 ARG cc_start: 0.7199 (ttm110) cc_final: 0.6841 (tpp-160) REVERT: B 276 HIS cc_start: 0.4592 (OUTLIER) cc_final: 0.4026 (p90) REVERT: B 310 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 388 MET cc_start: 0.7125 (mtp) cc_final: 0.6775 (mtp) REVERT: B 436 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7888 (mtmm) REVERT: B 441 SER cc_start: 0.8071 (p) cc_final: 0.7790 (t) REVERT: B 561 ASP cc_start: 0.7070 (p0) cc_final: 0.6783 (t0) REVERT: B 592 MET cc_start: 0.7635 (mtp) cc_final: 0.7321 (mtm) REVERT: B 624 MET cc_start: 0.7591 (mmm) cc_final: 0.7330 (mmm) outliers start: 31 outliers final: 22 residues processed: 194 average time/residue: 1.0551 time to fit residues: 223.2113 Evaluate side-chains 193 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 91 optimal weight: 0.1980 chunk 101 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.235003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.202869 restraints weight = 11510.162| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 2.72 r_work: 0.4443 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9585 Z= 0.227 Angle : 0.705 9.395 13029 Z= 0.347 Chirality : 0.046 0.312 1433 Planarity : 0.004 0.041 1650 Dihedral : 7.856 77.173 1375 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.31 % Favored : 93.43 % Rotamer: Outliers : 2.27 % Allowed : 21.86 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -0.89 (0.25), residues: 1126 helix: 0.25 (0.27), residues: 374 sheet: -1.73 (0.50), residues: 114 loop : -0.83 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 PHE 0.016 0.001 PHE A 577 TYR 0.033 0.001 TYR A 467 ARG 0.006 0.000 ARG A 595 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7615 (m-80) cc_final: 0.7281 (m-80) REVERT: A 420 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 478 SER cc_start: 0.7901 (p) cc_final: 0.7366 (t) REVERT: B 80 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6859 (tpp-160) REVERT: B 388 MET cc_start: 0.7117 (mtp) cc_final: 0.6777 (mtp) REVERT: B 436 LYS cc_start: 0.8093 (ttmt) cc_final: 0.7833 (mtmm) REVERT: B 441 SER cc_start: 0.8070 (p) cc_final: 0.7790 (t) REVERT: B 561 ASP cc_start: 0.7137 (p0) cc_final: 0.6773 (t0) REVERT: B 592 MET cc_start: 0.7623 (mtp) cc_final: 0.7387 (mtm) REVERT: B 624 MET cc_start: 0.7581 (mmm) cc_final: 0.7314 (mmm) outliers start: 23 outliers final: 17 residues processed: 190 average time/residue: 0.9619 time to fit residues: 199.1419 Evaluate side-chains 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 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 254 ASN A 431 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.234561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.202395 restraints weight = 11371.251| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 2.70 r_work: 0.4432 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9585 Z= 0.238 Angle : 0.708 9.944 13029 Z= 0.350 Chirality : 0.047 0.305 1433 Planarity : 0.004 0.041 1650 Dihedral : 7.801 75.004 1375 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.31 % Favored : 93.43 % Rotamer: Outliers : 2.47 % Allowed : 21.76 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -0.89 (0.25), residues: 1126 helix: 0.22 (0.27), residues: 377 sheet: -1.72 (0.50), residues: 114 loop : -0.82 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 200 HIS 0.004 0.001 HIS B 571 PHE 0.017 0.001 PHE A 577 TYR 0.039 0.002 TYR A 467 ARG 0.006 0.000 ARG A 595 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7040.63 seconds wall clock time: 123 minutes 30.43 seconds (7410.43 seconds total)