Starting phenix.real_space_refine on Sun May 11 08:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4h_41031/05_2025/8t4h_41031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4h_41031/05_2025/8t4h_41031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4h_41031/05_2025/8t4h_41031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4h_41031/05_2025/8t4h_41031.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4h_41031/05_2025/8t4h_41031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4h_41031/05_2025/8t4h_41031.cif" } resolution = 3.8 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= 0.027 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 31 5.16 5 C 4874 2.51 5 N 1354 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7702 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 3442 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 406 Chain: "B" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4186 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Time building chain proxies: 5.99, per 1000 atoms: 0.78 Number of scatterers: 7702 At special positions: 0 Unit cell: (68.798, 112.426, 135.918, 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 31 16.00 O 1443 8.00 N 1354 7.00 C 4874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 73.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 183 through 202 removed outlier: 4.451A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 4.154A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 250 removed outlier: 4.016A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 292 through 323 Processing helix chain 'A' and resid 324 through 373 removed outlier: 3.735A pdb=" N THR A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 4.074A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 3.703A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.619A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 482 removed outlier: 3.713A pdb=" N LEU A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 4.100A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 542 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.514A pdb=" N ILE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.728A pdb=" N GLY A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 659 removed outlier: 3.583A pdb=" N ARG A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.709A pdb=" N LEU A 705 " --> pdb=" O HIS A 702 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 708 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 148 through 182 removed outlier: 3.680A pdb=" N GLY B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 185 through 235 removed outlier: 3.626A pdb=" N GLY B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.854A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 removed outlier: 3.579A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 289 removed outlier: 4.099A pdb=" N VAL B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 338 removed outlier: 3.598A pdb=" N THR B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.702A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 402 removed outlier: 4.583A pdb=" N LEU B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 448 removed outlier: 3.824A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.243A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.576A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.800A pdb=" N VAL B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 3.751A pdb=" N GLU B 591 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.986A pdb=" N THR B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 623 removed outlier: 3.723A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.437A pdb=" N ASP B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 524 removed outlier: 6.664A pdb=" N PHE A 510 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 522 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 508 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 524 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 503 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 519 through 524 removed outlier: 6.664A pdb=" N PHE A 510 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 522 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 508 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 524 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.614A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 716 removed outlier: 6.425A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 484 through 493 removed outlier: 7.374A pdb=" N VAL B 485 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA B 476 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 471 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 526 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.891A pdb=" N VAL B 547 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASP B 631 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 549 " --> pdb=" O ASP B 631 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.23 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: 2608 1.34 - 1.46: 1670 1.46 - 1.58: 3493 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7824 Sorted by residual: bond pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.27e-02 6.20e+03 3.02e+00 bond pdb=" CB THR A 235 " pdb=" CG2 THR A 235 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.50e+00 bond pdb=" CA MET B 285 " pdb=" C MET B 285 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.30e-02 5.92e+03 2.47e+00 bond pdb=" CA ASN A 251 " pdb=" CB ASN A 251 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.69e-02 3.50e+03 1.85e+00 bond pdb=" SD MET B 196 " pdb=" CE MET B 196 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.77e+00 ... (remaining 7819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 10539 2.83 - 5.67: 81 5.67 - 8.50: 27 8.50 - 11.33: 6 11.33 - 14.17: 3 Bond angle restraints: 10656 Sorted by residual: angle pdb=" C VAL B 576 " pdb=" N MET B 577 " pdb=" CA MET B 577 " ideal model delta sigma weight residual 121.58 112.36 9.22 1.95e+00 2.63e-01 2.24e+01 angle pdb=" CB MET A 420 " pdb=" CG MET A 420 " pdb=" SD MET A 420 " ideal model delta sigma weight residual 112.70 98.53 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N LEU B 286 " pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 111.07 106.13 4.94 1.07e+00 8.73e-01 2.13e+01 angle pdb=" CB MET B 260 " pdb=" CG MET B 260 " pdb=" SD MET B 260 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CB MET B 592 " pdb=" CG MET B 592 " pdb=" SD MET B 592 " ideal model delta sigma weight residual 112.70 124.34 -11.64 3.00e+00 1.11e-01 1.51e+01 ... (remaining 10651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4101 16.79 - 33.57: 423 33.57 - 50.36: 113 50.36 - 67.15: 21 67.15 - 83.93: 11 Dihedral angle restraints: 4669 sinusoidal: 1554 harmonic: 3115 Sorted by residual: dihedral pdb=" CA MET A 420 " pdb=" C MET A 420 " pdb=" N LEU A 421 " pdb=" CA LEU A 421 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP B 237 " pdb=" CB ASP B 237 " pdb=" CG ASP B 237 " pdb=" OD1 ASP B 237 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ILE A 319 " pdb=" C ILE A 319 " pdb=" N MET A 320 " pdb=" CA MET A 320 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 917 0.039 - 0.078: 264 0.078 - 0.116: 77 0.116 - 0.155: 12 0.155 - 0.194: 6 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA MET B 577 " pdb=" N MET B 577 " pdb=" C MET B 577 " pdb=" CB MET B 577 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1273 not shown) Planarity restraints: 1391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 251 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASN A 251 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 251 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 252 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 257 " -0.011 2.00e-02 2.50e+03 1.58e-02 3.74e+00 pdb=" CG HIS A 257 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 257 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS A 257 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS A 257 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 257 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 404 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" CD GLU A 404 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 404 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 404 " 0.011 2.00e-02 2.50e+03 ... (remaining 1388 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1938 2.79 - 3.32: 7749 3.32 - 3.85: 12888 3.85 - 4.37: 12954 4.37 - 4.90: 23270 Nonbonded interactions: 58799 Sorted by model distance: nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.267 3.040 nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.295 3.040 nonbonded pdb=" O ASN A 443 " pdb=" OG1 THR A 446 " model vdw 2.331 3.040 nonbonded pdb=" NH1 ARG A 186 " pdb=" OG1 THR A 252 " model vdw 2.337 3.120 nonbonded pdb=" NH2 ARG A 378 " pdb=" O GLN B 236 " model vdw 2.340 3.120 ... (remaining 58794 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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 : 0.004 0.052 7824 Z= 0.175 Angle : 0.760 14.168 10656 Z= 0.371 Chirality : 0.042 0.194 1276 Planarity : 0.004 0.044 1391 Dihedral : 15.551 83.931 2663 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.57 % Allowed : 20.43 % Favored : 79.01 % 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: 1.54 (0.25), residues: 1076 helix: 1.78 (0.19), residues: 720 sheet: -1.23 (0.75), residues: 54 loop : -0.31 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 322 HIS 0.021 0.002 HIS A 257 PHE 0.011 0.001 PHE A 224 TYR 0.010 0.001 TYR B 422 ARG 0.009 0.000 ARG C 2 Details of bonding type rmsd hydrogen bonds : bond 0.13765 ( 582) hydrogen bonds : angle 5.41427 ( 1713) covalent geometry : bond 0.00360 ( 7824) covalent geometry : angle 0.76034 (10656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.8048 (mmm) cc_final: 0.7595 (mmt) REVERT: A 339 PHE cc_start: 0.7991 (m-80) cc_final: 0.7595 (m-10) REVERT: A 408 TYR cc_start: 0.8111 (t80) cc_final: 0.7789 (t80) REVERT: B 166 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7723 (mt-10) REVERT: B 269 ASN cc_start: 0.8235 (t0) cc_final: 0.7876 (t0) REVERT: B 294 LEU cc_start: 0.7505 (mt) cc_final: 0.7088 (tp) REVERT: B 298 LEU cc_start: 0.8840 (mm) cc_final: 0.8466 (mp) outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.2299 time to fit residues: 39.3333 Evaluate side-chains 91 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.143212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113516 restraints weight = 13443.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116945 restraints weight = 6762.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119143 restraints weight = 4269.959| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7824 Z= 0.134 Angle : 0.537 7.117 10656 Z= 0.276 Chirality : 0.037 0.142 1276 Planarity : 0.003 0.029 1391 Dihedral : 3.730 34.942 1157 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.26 % Allowed : 20.28 % Favored : 76.45 % 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: 2.09 (0.26), residues: 1076 helix: 2.22 (0.19), residues: 736 sheet: -1.04 (0.77), residues: 54 loop : -0.30 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 322 HIS 0.009 0.001 HIS A 257 PHE 0.022 0.001 PHE A 224 TYR 0.010 0.001 TYR A 309 ARG 0.003 0.000 ARG B 561 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 582) hydrogen bonds : angle 4.09323 ( 1713) covalent geometry : bond 0.00284 ( 7824) covalent geometry : angle 0.53746 (10656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.837 Fit side-chains REVERT: A 202 MET cc_start: 0.7418 (tpp) cc_final: 0.7090 (ttm) REVERT: A 338 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8807 (tt) REVERT: A 339 PHE cc_start: 0.7768 (m-80) cc_final: 0.7425 (m-10) REVERT: A 420 MET cc_start: 0.7863 (ttt) cc_final: 0.7525 (mtp) REVERT: B 298 LEU cc_start: 0.8507 (mm) cc_final: 0.8259 (mp) REVERT: B 390 LEU cc_start: 0.8559 (tt) cc_final: 0.8344 (tp) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 0.1731 time to fit residues: 26.9141 Evaluate side-chains 102 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112684 restraints weight = 13620.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116137 restraints weight = 6765.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118412 restraints weight = 4232.382| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7824 Z= 0.135 Angle : 0.513 6.495 10656 Z= 0.265 Chirality : 0.037 0.132 1276 Planarity : 0.003 0.032 1391 Dihedral : 3.567 33.219 1157 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.69 % Allowed : 20.85 % Favored : 75.46 % 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: 2.30 (0.26), residues: 1076 helix: 2.37 (0.19), residues: 736 sheet: -0.99 (0.77), residues: 54 loop : -0.19 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.006 0.001 HIS A 257 PHE 0.024 0.001 PHE A 224 TYR 0.014 0.001 TYR A 408 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 582) hydrogen bonds : angle 3.95259 ( 1713) covalent geometry : bond 0.00291 ( 7824) covalent geometry : angle 0.51338 (10656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.967 Fit side-chains REVERT: A 202 MET cc_start: 0.7469 (tpp) cc_final: 0.6971 (ttm) REVERT: A 231 MET cc_start: 0.8545 (ttp) cc_final: 0.8334 (ttp) REVERT: A 338 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8878 (tt) REVERT: A 339 PHE cc_start: 0.7794 (m-80) cc_final: 0.7500 (m-80) REVERT: B 260 MET cc_start: 0.7311 (mmp) cc_final: 0.6997 (mmp) REVERT: B 298 LEU cc_start: 0.8497 (mm) cc_final: 0.8232 (mp) REVERT: B 399 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7343 (ttt) outliers start: 26 outliers final: 14 residues processed: 112 average time/residue: 0.1744 time to fit residues: 27.9464 Evaluate side-chains 99 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 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 = 0.3931 r_free = 0.3931 target = 0.139155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109250 restraints weight = 13480.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.112602 restraints weight = 6860.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114750 restraints weight = 4353.712| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7824 Z= 0.166 Angle : 0.557 8.793 10656 Z= 0.285 Chirality : 0.039 0.128 1276 Planarity : 0.003 0.034 1391 Dihedral : 3.625 32.158 1157 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.82 % Allowed : 20.28 % Favored : 74.89 % 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: 2.25 (0.26), residues: 1076 helix: 2.35 (0.19), residues: 735 sheet: -1.15 (0.76), residues: 54 loop : -0.23 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 322 HIS 0.011 0.001 HIS A 257 PHE 0.020 0.002 PHE A 224 TYR 0.015 0.002 TYR A 408 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 582) hydrogen bonds : angle 3.95889 ( 1713) covalent geometry : bond 0.00373 ( 7824) covalent geometry : angle 0.55673 (10656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.863 Fit side-chains REVERT: A 199 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8565 (mm) REVERT: A 214 TRP cc_start: 0.8079 (t60) cc_final: 0.7848 (t60) REVERT: A 338 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 339 PHE cc_start: 0.7869 (m-80) cc_final: 0.7504 (m-80) REVERT: B 294 LEU cc_start: 0.7894 (mt) cc_final: 0.7634 (tp) REVERT: B 298 LEU cc_start: 0.8592 (mm) cc_final: 0.8277 (mp) REVERT: B 399 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7939 (ttm) outliers start: 34 outliers final: 24 residues processed: 114 average time/residue: 0.1712 time to fit residues: 27.7629 Evaluate side-chains 105 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 66 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113011 restraints weight = 13536.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.116529 restraints weight = 6714.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118780 restraints weight = 4181.485| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7824 Z= 0.119 Angle : 0.521 7.780 10656 Z= 0.260 Chirality : 0.037 0.149 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.383 31.915 1156 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.84 % Allowed : 23.55 % Favored : 73.62 % 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: 2.49 (0.26), residues: 1076 helix: 2.60 (0.19), residues: 729 sheet: -1.08 (0.75), residues: 54 loop : -0.27 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 322 HIS 0.002 0.001 HIS B 543 PHE 0.019 0.001 PHE A 224 TYR 0.014 0.001 TYR A 408 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 582) hydrogen bonds : angle 3.72667 ( 1713) covalent geometry : bond 0.00242 ( 7824) covalent geometry : angle 0.52100 (10656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7991 (t60) cc_final: 0.7765 (t60) REVERT: A 338 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8934 (tt) REVERT: A 339 PHE cc_start: 0.7923 (m-80) cc_final: 0.7699 (m-80) REVERT: B 298 LEU cc_start: 0.8615 (mm) cc_final: 0.8388 (mp) REVERT: B 399 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8030 (ttm) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.1799 time to fit residues: 28.4153 Evaluate side-chains 98 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109730 restraints weight = 13495.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113102 restraints weight = 6797.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115270 restraints weight = 4295.393| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7824 Z= 0.161 Angle : 0.559 7.758 10656 Z= 0.283 Chirality : 0.039 0.141 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.464 32.073 1156 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.11 % Allowed : 22.27 % Favored : 72.62 % 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: 2.42 (0.26), residues: 1076 helix: 2.53 (0.19), residues: 729 sheet: -1.19 (0.75), residues: 54 loop : -0.24 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 322 HIS 0.005 0.001 HIS A 257 PHE 0.017 0.001 PHE A 224 TYR 0.014 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 582) hydrogen bonds : angle 3.84634 ( 1713) covalent geometry : bond 0.00364 ( 7824) covalent geometry : angle 0.55902 (10656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8599 (mm) REVERT: A 338 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8863 (tt) REVERT: A 339 PHE cc_start: 0.7971 (m-80) cc_final: 0.7709 (m-80) REVERT: B 298 LEU cc_start: 0.8650 (mm) cc_final: 0.8407 (mp) REVERT: B 399 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8126 (ttm) outliers start: 36 outliers final: 28 residues processed: 121 average time/residue: 0.1688 time to fit residues: 29.0260 Evaluate side-chains 114 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.0030 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 30.0000 chunk 37 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** A 451 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 = 0.3979 r_free = 0.3979 target = 0.142870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113436 restraints weight = 13487.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.116947 restraints weight = 6650.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.119221 restraints weight = 4134.639| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7824 Z= 0.117 Angle : 0.532 7.426 10656 Z= 0.264 Chirality : 0.037 0.134 1276 Planarity : 0.003 0.032 1391 Dihedral : 3.348 29.585 1156 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.69 % Allowed : 24.40 % Favored : 71.91 % 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: 2.60 (0.26), residues: 1076 helix: 2.71 (0.19), residues: 724 sheet: -1.10 (0.74), residues: 54 loop : -0.26 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.005 0.001 HIS A 257 PHE 0.017 0.001 PHE A 224 TYR 0.014 0.001 TYR A 465 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 582) hydrogen bonds : angle 3.69707 ( 1713) covalent geometry : bond 0.00236 ( 7824) covalent geometry : angle 0.53156 (10656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.838 Fit side-chains REVERT: A 199 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 338 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8915 (tt) REVERT: A 347 LYS cc_start: 0.7862 (mmmm) cc_final: 0.7550 (mtmt) REVERT: B 298 LEU cc_start: 0.8518 (mm) cc_final: 0.8198 (mp) REVERT: B 399 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8064 (ttm) REVERT: C 1 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7783 (ptp90) outliers start: 26 outliers final: 17 residues processed: 110 average time/residue: 0.1732 time to fit residues: 26.9051 Evaluate side-chains 104 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 16 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 30.0000 chunk 15 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.139252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109273 restraints weight = 13729.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112627 restraints weight = 6889.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.114879 restraints weight = 4371.326| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7824 Z= 0.163 Angle : 0.576 7.679 10656 Z= 0.288 Chirality : 0.039 0.147 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.479 29.487 1156 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.40 % Allowed : 23.83 % Favored : 71.77 % 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: 2.42 (0.26), residues: 1076 helix: 2.57 (0.19), residues: 723 sheet: -1.20 (0.73), residues: 54 loop : -0.28 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 322 HIS 0.006 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.017 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 582) hydrogen bonds : angle 3.86360 ( 1713) covalent geometry : bond 0.00369 ( 7824) covalent geometry : angle 0.57633 (10656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.913 Fit side-chains REVERT: A 199 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 329 MET cc_start: 0.7490 (mmt) cc_final: 0.7220 (tpp) REVERT: A 338 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8848 (tt) REVERT: B 298 LEU cc_start: 0.8659 (mm) cc_final: 0.8377 (mp) REVERT: B 390 LEU cc_start: 0.8665 (tt) cc_final: 0.8424 (tp) REVERT: B 399 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7903 (ttt) REVERT: B 551 GLN cc_start: 0.5399 (OUTLIER) cc_final: 0.4975 (tt0) REVERT: C 6 THR cc_start: 0.8923 (t) cc_final: 0.8691 (p) outliers start: 31 outliers final: 25 residues processed: 115 average time/residue: 0.1785 time to fit residues: 28.8045 Evaluate side-chains 112 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 551 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.0470 chunk 41 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.141966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112329 restraints weight = 13668.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115783 restraints weight = 6707.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.118069 restraints weight = 4199.044| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7824 Z= 0.125 Angle : 0.561 7.802 10656 Z= 0.278 Chirality : 0.037 0.146 1276 Planarity : 0.003 0.034 1391 Dihedral : 3.388 29.411 1156 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.69 % Allowed : 25.11 % Favored : 71.21 % 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: 2.54 (0.26), residues: 1076 helix: 2.67 (0.19), residues: 725 sheet: -1.16 (0.73), residues: 54 loop : -0.27 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.006 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.012 0.001 TYR A 408 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 582) hydrogen bonds : angle 3.70633 ( 1713) covalent geometry : bond 0.00260 ( 7824) covalent geometry : angle 0.56070 (10656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8521 (mm) REVERT: A 338 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8814 (tt) REVERT: B 298 LEU cc_start: 0.8600 (mm) cc_final: 0.8340 (mp) REVERT: B 399 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8039 (ttm) outliers start: 26 outliers final: 20 residues processed: 110 average time/residue: 0.2052 time to fit residues: 31.5496 Evaluate side-chains 105 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 67 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 30.0000 chunk 85 optimal weight: 0.0770 chunk 97 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 chunk 45 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.143400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113966 restraints weight = 13580.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.117572 restraints weight = 6644.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.119870 restraints weight = 4100.427| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7824 Z= 0.119 Angle : 0.559 8.692 10656 Z= 0.276 Chirality : 0.037 0.147 1276 Planarity : 0.003 0.038 1391 Dihedral : 3.215 12.738 1154 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.12 % Allowed : 25.39 % Favored : 71.49 % 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: 2.63 (0.26), residues: 1076 helix: 2.73 (0.19), residues: 726 sheet: -1.08 (0.73), residues: 54 loop : -0.24 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.006 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.018 0.001 TYR B 430 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 582) hydrogen bonds : angle 3.65199 ( 1713) covalent geometry : bond 0.00243 ( 7824) covalent geometry : angle 0.55887 (10656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 338 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8881 (tt) REVERT: B 298 LEU cc_start: 0.8654 (mm) cc_final: 0.8323 (mp) REVERT: B 399 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8016 (ttm) outliers start: 22 outliers final: 19 residues processed: 108 average time/residue: 0.1645 time to fit residues: 25.4108 Evaluate side-chains 109 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.143367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113880 restraints weight = 13554.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.117463 restraints weight = 6669.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119789 restraints weight = 4139.568| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7824 Z= 0.124 Angle : 0.572 8.514 10656 Z= 0.282 Chirality : 0.038 0.150 1276 Planarity : 0.003 0.037 1391 Dihedral : 3.216 15.246 1154 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.55 % Allowed : 25.11 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.26), residues: 1076 helix: 2.73 (0.19), residues: 726 sheet: -1.03 (0.74), residues: 54 loop : -0.22 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 322 HIS 0.004 0.001 HIS A 257 PHE 0.016 0.001 PHE B 412 TYR 0.012 0.001 TYR A 408 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 582) hydrogen bonds : angle 3.64668 ( 1713) covalent geometry : bond 0.00261 ( 7824) covalent geometry : angle 0.57171 (10656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.63 seconds wall clock time: 45 minutes 0.84 seconds (2700.84 seconds total)