Starting phenix.real_space_refine
on Fri Aug 22 20:41:03 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8t4h_41031/08_2025/8t4h_41031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t4h_41031/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t4h_41031/08_2025/8t4h_41031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t4h_41031/08_2025/8t4h_41031.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t4h_41031/08_2025/8t4h_41031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t4h_41031/08_2025/8t4h_41031.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'PHE:plan': 7, 'HIS:plan': 7, 'GLU:plan': 16, 'GLN:plan1': 24, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 11, 'TRP:plan': 1}
          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: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1}
          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: 2.04, per 1000 atoms: 0.26
  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: 0.67
  Conformation dependent library (CDL) restraints added in 441.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.28
  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: 1.27

  Time building geometry restraints manager: 0.90 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.780
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.090
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.440
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.000   ARG C   2 
 TYR   0.010   0.001   TYR B 422 
 PHE   0.011   0.001   PHE A 224 
 TRP   0.009   0.001   TRP A 322 
 HIS   0.021   0.002   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7824)
  covalent geometry    : angle       0.76034 (10656)
  hydrogen bonds       : bond        0.13765 (  582)
  hydrogen bonds       : angle       5.41427 ( 1713)

*********************** 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  : 0.302 
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: 0.7594 (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: 0.1015
  time to fit residues: 17.4624
Evaluate side-chains
  92 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 49 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:   30.0000
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 257 HIS
A 401 ASN
** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.142665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.112739 restraints weight = 13528.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.116159 restraints weight = 6784.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.118430 restraints weight = 4294.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.119840 restraints weight = 3166.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.120562 restraints weight = 2603.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1209

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= 0.143
  Angle     :  0.544   6.978  10656  Z= 0.280
  Chirality :  0.037   0.143   1276
  Planarity :  0.003   0.030   1391
  Dihedral  :  3.744  34.256   1157
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.14 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.26), residues: 1076
  helix:  2.19 (0.19), residues: 736
  sheet: -1.05 (0.77), residues: 54
  loop : -0.31 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 561 
 TYR   0.010   0.001   TYR A 309 
 PHE   0.022   0.001   PHE A 224 
 TRP   0.015   0.001   TRP A 322 
 HIS   0.009   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7824)
  covalent geometry    : angle       0.54419 (10656)
  hydrogen bonds       : bond        0.04877 (  582)
  hydrogen bonds       : angle       4.13654 ( 1713)

*********************** 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
  120 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  202 MET cc_start: 0.7429 (tpp) cc_final: 0.7190 (ttm)
REVERT: A  319 ILE cc_start: 0.9182 (tt) cc_final: 0.8979 (tt)
REVERT: A  338 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8817 (tt)
REVERT: A  339 PHE cc_start: 0.7703 (m-80) cc_final: 0.7353 (m-10)
REVERT: A  420 MET cc_start: 0.7866 (ttt) cc_final: 0.7527 (mtp)
REVERT: B  294 LEU cc_start: 0.7681 (mt) cc_final: 0.7449 (tp)
REVERT: B  298 LEU cc_start: 0.8503 (mm) cc_final: 0.8224 (mp)
REVERT: B  390 LEU cc_start: 0.8580 (tt) cc_final: 0.8370 (tp)
  outliers start: 27
  outliers final: 17
  residues processed: 112
  average time/residue: 0.0820
  time to fit residues: 13.3828
Evaluate side-chains
  104 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  414 THR
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  382 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 42 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.139348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.109405 restraints weight = 13481.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.112737 restraints weight = 6843.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.114919 restraints weight = 4362.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.116315 restraints weight = 3248.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.117035 restraints weight = 2668.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7824  Z= 0.172
  Angle     :  0.549   6.462  10656  Z= 0.286
  Chirality :  0.039   0.129   1276
  Planarity :  0.003   0.033   1391
  Dihedral  :  3.685  33.370   1157
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 20.43 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.26), residues: 1076
  helix:  2.23 (0.19), residues: 735
  sheet: -1.13 (0.77), residues: 54
  loop : -0.22 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 252 
 TYR   0.017   0.001   TYR A 408 
 PHE   0.024   0.002   PHE A 224 
 TRP   0.016   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7824)
  covalent geometry    : angle       0.54896 (10656)
  hydrogen bonds       : bond        0.05150 (  582)
  hydrogen bonds       : angle       4.08147 ( 1713)

*********************** 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
  128 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  202 MET cc_start: 0.7612 (tpp) cc_final: 0.7252 (ttm)
REVERT: A  231 MET cc_start: 0.8521 (ttp) cc_final: 0.8261 (ttp)
REVERT: A  338 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8836 (tt)
REVERT: A  339 PHE cc_start: 0.7797 (m-80) cc_final: 0.7459 (m-80)
REVERT: A  401 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7404 (t0)
REVERT: A  420 MET cc_start: 0.7764 (ttt) cc_final: 0.7271 (mtt)
REVERT: B  298 LEU cc_start: 0.8566 (mm) cc_final: 0.8254 (mp)
REVERT: B  300 MET cc_start: 0.8219 (tpp) cc_final: 0.8008 (tpp)
  outliers start: 34
  outliers final: 23
  residues processed: 118
  average time/residue: 0.0782
  time to fit residues: 13.4594
Evaluate side-chains
  110 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  244 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  401 ASN
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 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  387 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain C residue    4 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 41 optimal weight:   20.0000
   chunk 98 optimal weight:    3.9990
   chunk 52 optimal weight:   40.0000
   chunk 89 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 106 optimal weight:   10.0000
   chunk 105 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.140719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.110906 restraints weight = 13664.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.114329 restraints weight = 6788.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.116590 restraints weight = 4283.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.117922 restraints weight = 3151.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.118764 restraints weight = 2593.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7824  Z= 0.136
  Angle     :  0.522   9.048  10656  Z= 0.266
  Chirality :  0.038   0.129   1276
  Planarity :  0.003   0.034   1391
  Dihedral  :  3.463  30.606   1156
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 21.13 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.26), residues: 1076
  helix:  2.42 (0.19), residues: 735
  sheet: -1.09 (0.76), residues: 54
  loop : -0.27 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.015   0.001   TYR A 408 
 PHE   0.021   0.001   PHE A 224 
 TRP   0.014   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7824)
  covalent geometry    : angle       0.52204 (10656)
  hydrogen bonds       : bond        0.04764 (  582)
  hydrogen bonds       : angle       3.88252 ( 1713)

*********************** 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
  123 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  199 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8516 (mm)
REVERT: A  338 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8858 (tt)
REVERT: A  339 PHE cc_start: 0.7843 (m-80) cc_final: 0.7498 (m-80)
REVERT: A  401 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7889 (t0)
REVERT: A  420 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7565 (mtt)
REVERT: B  298 LEU cc_start: 0.8579 (mm) cc_final: 0.8282 (mp)
REVERT: B  388 GLN cc_start: 0.8442 (tp40) cc_final: 0.8161 (tp40)
REVERT: B  399 MET cc_start: 0.8868 (ttt) cc_final: 0.8664 (ttt)
  outliers start: 29
  outliers final: 19
  residues processed: 115
  average time/residue: 0.0826
  time to fit residues: 13.6070
Evaluate side-chains
  108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  368 ILE
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  420 MET
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  387 VAL
Chi-restraints excluded: chain B residue  396 LEU
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 C residue    4 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 31 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
A 257 HIS
B 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.136149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.105982 restraints weight = 13789.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.109310 restraints weight = 7058.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111428 restraints weight = 4510.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.112784 restraints weight = 3363.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.113625 restraints weight = 2783.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7824  Z= 0.216
  Angle     :  0.605   7.731  10656  Z= 0.312
  Chirality :  0.041   0.131   1276
  Planarity :  0.004   0.036   1391
  Dihedral  :  3.724  30.576   1156
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 20.00 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.26), residues: 1076
  helix:  2.26 (0.19), residues: 722
  sheet: -1.33 (0.74), residues: 54
  loop : -0.40 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 252 
 TYR   0.020   0.002   TYR B 282 
 PHE   0.019   0.002   PHE A 224 
 TRP   0.020   0.002   TRP A 322 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 7824)
  covalent geometry    : angle       0.60478 (10656)
  hydrogen bonds       : bond        0.05541 (  582)
  hydrogen bonds       : angle       4.13141 ( 1713)

*********************** 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
  140 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 90
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  199 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8679 (mm)
REVERT: A  338 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8790 (tt)
REVERT: A  417 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8110 (tp)
REVERT: B  298 LEU cc_start: 0.8738 (mm) cc_final: 0.8436 (mp)
  outliers start: 50
  outliers final: 33
  residues processed: 129
  average time/residue: 0.0775
  time to fit residues: 14.4301
Evaluate side-chains
  119 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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  268 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  321 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  414 THR
Chi-restraints excluded: chain A residue  417 ILE
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  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  286 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  387 VAL
Chi-restraints excluded: chain B residue  396 LEU
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  467 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  571 CYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 29 optimal weight:   30.0000
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
** 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 = 0.3913 r_free = 0.3913 target = 0.137774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.107572 restraints weight = 13861.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.110965 restraints weight = 6995.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.113142 restraints weight = 4408.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.114557 restraints weight = 3266.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.115097 restraints weight = 2683.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7824  Z= 0.169
  Angle     :  0.569   8.563  10656  Z= 0.291
  Chirality :  0.039   0.145   1276
  Planarity :  0.003   0.037   1391
  Dihedral  :  3.655  28.118   1156
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 22.13 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.26), residues: 1076
  helix:  2.30 (0.19), residues: 727
  sheet: -1.30 (0.75), residues: 54
  loop : -0.37 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 252 
 TYR   0.016   0.001   TYR B 282 
 PHE   0.018   0.001   PHE A 224 
 TRP   0.014   0.001   TRP A 322 
 HIS   0.003   0.001   HIS B 543 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 7824)
  covalent geometry    : angle       0.56865 (10656)
  hydrogen bonds       : bond        0.05271 (  582)
  hydrogen bonds       : angle       4.02128 ( 1713)

*********************** 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
  128 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 89
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  199 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8623 (mm)
REVERT: A  329 MET cc_start: 0.7411 (mmt) cc_final: 0.7153 (tpp)
REVERT: A  338 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8763 (tt)
REVERT: A  339 PHE cc_start: 0.8002 (m-80) cc_final: 0.7665 (m-80)
REVERT: A  401 ASN cc_start: 0.7576 (t0) cc_final: 0.7167 (t0)
REVERT: B  298 LEU cc_start: 0.8703 (mm) cc_final: 0.8407 (mp)
REVERT: B  388 GLN cc_start: 0.8471 (tp40) cc_final: 0.8250 (tp40)
REVERT: B  551 GLN cc_start: 0.5370 (OUTLIER) cc_final: 0.4947 (tt0)
  outliers start: 39
  outliers final: 29
  residues processed: 120
  average time/residue: 0.0814
  time to fit residues: 14.0298
Evaluate side-chains
  116 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 84
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
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 A residue  468 VAL
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  200 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  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  391 MET
Chi-restraints excluded: chain B residue  396 LEU
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  551 GLN
Chi-restraints excluded: chain B residue  571 CYS
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 28 optimal weight:    0.9980
   chunk 51 optimal weight:   50.0000
   chunk 99 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 81 optimal weight:    0.1980
   chunk 75 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
** 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 = 0.3938 r_free = 0.3938 target = 0.139783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.109936 restraints weight = 13547.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.113352 restraints weight = 6743.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.115541 restraints weight = 4245.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.116925 restraints weight = 3129.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.117699 restraints weight = 2581.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7824  Z= 0.134
  Angle     :  0.535   8.105  10656  Z= 0.272
  Chirality :  0.038   0.143   1276
  Planarity :  0.003   0.036   1391
  Dihedral  :  3.376  14.421   1154
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 22.70 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.26), residues: 1076
  helix:  2.56 (0.19), residues: 722
  sheet: -1.24 (0.74), residues: 54
  loop : -0.32 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.014   0.001   TYR A 408 
 PHE   0.017   0.001   PHE A 224 
 TRP   0.009   0.001   TRP A 322 
 HIS   0.002   0.001   HIS B 543 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7824)
  covalent geometry    : angle       0.53547 (10656)
  hydrogen bonds       : bond        0.04747 (  582)
  hydrogen bonds       : angle       3.83927 ( 1713)

*********************** 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
  133 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8472 (mm)
REVERT: A  202 MET cc_start: 0.7508 (tpp) cc_final: 0.6986 (ttm)
REVERT: A  329 MET cc_start: 0.7446 (mmt) cc_final: 0.7178 (tpp)
REVERT: A  338 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8852 (tt)
REVERT: A  339 PHE cc_start: 0.7926 (m-80) cc_final: 0.7592 (m-80)
REVERT: A  401 ASN cc_start: 0.7540 (t0) cc_final: 0.7226 (t0)
REVERT: B  298 LEU cc_start: 0.8710 (mm) cc_final: 0.8422 (mp)
REVERT: B  551 GLN cc_start: 0.5373 (OUTLIER) cc_final: 0.4934 (tt0)
  outliers start: 36
  outliers final: 29
  residues processed: 128
  average time/residue: 0.0777
  time to fit residues: 14.3081
Evaluate side-chains
  120 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 88
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  244 VAL
Chi-restraints excluded: chain A residue  321 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  421 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  468 VAL
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  200 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  387 VAL
Chi-restraints excluded: chain B residue  396 LEU
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
Chi-restraints excluded: chain B residue  573 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 93 optimal weight:    0.4980
   chunk 60 optimal weight:    0.5980
   chunk 104 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 39 optimal weight:    8.9990
   chunk 12 optimal weight:    0.1980
   chunk 68 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
A 257 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.141389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.111619 restraints weight = 13634.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.115188 restraints weight = 6804.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.117432 restraints weight = 4206.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.118869 restraints weight = 3077.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.119781 restraints weight = 2499.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2281

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= 0.123
  Angle     :  0.544   8.598  10656  Z= 0.271
  Chirality :  0.037   0.133   1276
  Planarity :  0.003   0.035   1391
  Dihedral  :  3.321  13.861   1154
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 24.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.26), residues: 1076
  helix:  2.67 (0.19), residues: 721
  sheet: -1.37 (0.72), residues: 56
  loop : -0.17 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.014   0.001   TYR A 408 
 PHE   0.016   0.001   PHE A 224 
 TRP   0.010   0.001   TRP A 322 
 HIS   0.002   0.001   HIS B 543 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7824)
  covalent geometry    : angle       0.54405 (10656)
  hydrogen bonds       : bond        0.04486 (  582)
  hydrogen bonds       : angle       3.75127 ( 1713)

*********************** 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
  124 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8544 (mm)
REVERT: A  329 MET cc_start: 0.7418 (mmt) cc_final: 0.7160 (tpp)
REVERT: A  338 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8835 (tt)
REVERT: A  339 PHE cc_start: 0.7894 (m-80) cc_final: 0.7625 (m-80)
REVERT: A  401 ASN cc_start: 0.7481 (t0) cc_final: 0.7174 (t0)
REVERT: A  417 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8117 (tp)
REVERT: B  298 LEU cc_start: 0.8678 (mm) cc_final: 0.8398 (mp)
REVERT: B  551 GLN cc_start: 0.5422 (OUTLIER) cc_final: 0.4945 (tt0)
  outliers start: 30
  outliers final: 23
  residues processed: 118
  average time/residue: 0.0896
  time to fit residues: 14.7618
Evaluate side-chains
  119 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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  338 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  468 VAL
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  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  387 VAL
Chi-restraints excluded: chain B residue  396 LEU
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
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 59 optimal weight:    0.5980
   chunk 103 optimal weight:    8.9990
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 50 optimal weight:   30.0000
   chunk 57 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
** 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 = 0.3954 r_free = 0.3954 target = 0.140966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.111075 restraints weight = 13652.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.114564 restraints weight = 6743.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.116810 restraints weight = 4229.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.118261 restraints weight = 3099.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.118997 restraints weight = 2539.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7824  Z= 0.133
  Angle     :  0.562   8.215  10656  Z= 0.279
  Chirality :  0.038   0.140   1276
  Planarity :  0.003   0.039   1391
  Dihedral  :  3.327  13.639   1154
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 24.26 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.26), residues: 1076
  helix:  2.63 (0.19), residues: 723
  sheet: -1.38 (0.71), residues: 56
  loop : -0.19 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.017   0.001   TYR B 430 
 PHE   0.017   0.001   PHE B 412 
 TRP   0.013   0.001   TRP A 322 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7824)
  covalent geometry    : angle       0.56184 (10656)
  hydrogen bonds       : bond        0.04582 (  582)
  hydrogen bonds       : angle       3.77523 ( 1713)

*********************** 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
  127 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8551 (mm)
REVERT: A  329 MET cc_start: 0.7433 (mmt) cc_final: 0.7182 (tpp)
REVERT: A  338 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8830 (tt)
REVERT: A  339 PHE cc_start: 0.7886 (m-80) cc_final: 0.7675 (m-80)
REVERT: A  401 ASN cc_start: 0.7608 (t0) cc_final: 0.7227 (t0)
REVERT: B  298 LEU cc_start: 0.8665 (mm) cc_final: 0.8385 (mp)
REVERT: B  551 GLN cc_start: 0.5417 (OUTLIER) cc_final: 0.4940 (tt0)
  outliers start: 32
  outliers final: 26
  residues processed: 122
  average time/residue: 0.0778
  time to fit residues: 13.6892
Evaluate side-chains
  119 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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  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  464 ILE
Chi-restraints excluded: chain A residue  468 VAL
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  254 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  396 LEU
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
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain C residue    4 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0170
   chunk 79 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 88 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0870
   overall best weight:    0.4996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
** 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 = 0.3981 r_free = 0.3981 target = 0.143000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.113460 restraints weight = 13494.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.116935 restraints weight = 6592.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.119255 restraints weight = 4117.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.120736 restraints weight = 3002.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.121513 restraints weight = 2439.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7824  Z= 0.120
  Angle     :  0.559   8.604  10656  Z= 0.277
  Chirality :  0.037   0.155   1276
  Planarity :  0.003   0.037   1391
  Dihedral  :  3.284  14.759   1154
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 25.53 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.26), residues: 1076
  helix:  2.71 (0.19), residues: 725
  sheet: -1.34 (0.71), residues: 56
  loop : -0.18 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.016   0.001   PHE A 224 
 TRP   0.009   0.001   TRP A 322 
 HIS   0.006   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7824)
  covalent geometry    : angle       0.55910 (10656)
  hydrogen bonds       : bond        0.04287 (  582)
  hydrogen bonds       : angle       3.70033 ( 1713)

********************** 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
  117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: A  338 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8821 (tt)
REVERT: A  339 PHE cc_start: 0.7808 (m-80) cc_final: 0.7607 (m-80)
REVERT: A  401 ASN cc_start: 0.7522 (t0) cc_final: 0.7184 (t0)
REVERT: B  298 LEU cc_start: 0.8675 (mm) cc_final: 0.8398 (mp)
REVERT: B  551 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.4942 (tt0)
  outliers start: 24
  outliers final: 21
  residues processed: 113
  average time/residue: 0.0795
  time to fit residues: 12.9515
Evaluate side-chains
  113 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  244 VAL
Chi-restraints excluded: chain A residue  251 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  468 VAL
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  391 MET
Chi-restraints excluded: chain B residue  396 LEU
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
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   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 251 ASN
** 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 = 0.3951 r_free = 0.3951 target = 0.140644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.110796 restraints weight = 13551.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.114283 restraints weight = 6704.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.116372 restraints weight = 4180.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.117966 restraints weight = 3102.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.118790 restraints weight = 2518.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7824  Z= 0.155
  Angle     :  0.605  11.958  10656  Z= 0.301
  Chirality :  0.039   0.155   1276
  Planarity :  0.003   0.038   1391
  Dihedral  :  3.349  14.885   1154
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 25.11 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.26), residues: 1076
  helix:  2.58 (0.19), residues: 725
  sheet: -1.42 (0.71), residues: 56
  loop : -0.22 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 252 
 TYR   0.017   0.001   TYR B 430 
 PHE   0.018   0.001   PHE B 412 
 TRP   0.017   0.001   TRP A 322 
 HIS   0.009   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7824)
  covalent geometry    : angle       0.60539 (10656)
  hydrogen bonds       : bond        0.04679 (  582)
  hydrogen bonds       : angle       3.78881 ( 1713)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1462.49 seconds
wall clock time: 25 minutes 59.56 seconds (1559.56 seconds total)