Starting phenix.real_space_refine
on Wed Sep 17 18:10:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xs0_38612/09_2025/8xs0_38612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xs0_38612/09_2025/8xs0_38612.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xs0_38612/09_2025/8xs0_38612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xs0_38612/09_2025/8xs0_38612.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xs0_38612/09_2025/8xs0_38612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xs0_38612/09_2025/8xs0_38612.map"
  }
  resolution = 3.89
  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=   0.008 sd=   0.057
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      30      5.16       5
     C    6826      2.51       5
     N    1696      2.21       5
     O    1801      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10353
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 688, 5129
          Classifications: {'peptide': 688}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 30, 'TRANS': 657}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 387
          Unresolved non-hydrogen angles: 482
          Unresolved non-hydrogen dihedrals: 325
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'PHE:plan': 5, 'TRP:plan': 2, 'ARG:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 19, 'GLN:plan1': 8, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 230
    Chain: "B"
      Number of atoms: 5224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 700, 5224
          Classifications: {'peptide': 700}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 31, 'TRANS': 668}
          Unresolved non-hydrogen bonds: 387
          Unresolved non-hydrogen angles: 482
          Unresolved non-hydrogen dihedrals: 325
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'PHE:plan': 5, 'TRP:plan': 2, 'ARG:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 19, 'GLN:plan1': 8, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 230
  Time building chain proxies: 2.77, per 1000 atoms: 0.27
  Number of scatterers: 10353
  At special positions: 0
  Unit cell: (88.62, 138.205, 103.39, 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      30     16.00
     O    1801      8.00
     N    1696      7.00
     C    6826      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.16
  Conformation dependent library (CDL) restraints added in 554.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2656

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 2 sheets defined
      71.0% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 26
    Processing helix  chain 'A' and resid 36 through 42
      removed outlier: 3.742A  pdb=" N   ILE A  42 " --> pdb=" O   TYR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 68
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 78 through 112
      removed outlier: 3.781A  pdb=" N   ALA A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      Proline residue:  A 104  - end of helix
      removed outlier: 4.099A  pdb=" N   LEU A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      Proline residue:  A 108  - end of helix
    Processing helix  chain 'A' and resid 117 through 125
      removed outlier: 6.183A  pdb=" N   ALA A 122 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 142
      removed outlier: 6.845A  pdb=" N   MET A 139 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE A 142 " --> pdb=" O   MET A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 151
    Processing helix  chain 'A' and resid 152 through 184
    Processing helix  chain 'A' and resid 207 through 220
    Processing helix  chain 'A' and resid 233 through 252
    Processing helix  chain 'A' and resid 253 through 256
    Processing helix  chain 'A' and resid 279 through 305
      removed outlier: 3.967A  pdb=" N   THR A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 286 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU A 287 " --> pdb=" O   TYR A 283 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 325
    Processing helix  chain 'A' and resid 355 through 377
    Processing helix  chain 'A' and resid 377 through 387
      removed outlier: 4.237A  pdb=" N   ILE A 381 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   PHE A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 396
      removed outlier: 3.586A  pdb=" N   ILE A 396 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 438
      Proline residue:  A 418  - end of helix
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 444 through 468
      removed outlier: 3.748A  pdb=" N   ALA A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ILE A 466 " --> pdb=" O   PHE A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 492
    Processing helix  chain 'A' and resid 492 through 523
      removed outlier: 3.723A  pdb=" N   THR A 496 " --> pdb=" O   ASN A 492 " (cutoff:3.500A)
      Proline residue:  A 499  - end of helix
      removed outlier: 3.959A  pdb=" N   PHE A 514 " --> pdb=" O   ALA A 510 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLY A 516 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   TYR A 517 " --> pdb=" O   PHE A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 536
    Processing helix  chain 'A' and resid 540 through 548
      removed outlier: 3.764A  pdb=" N   TRP A 548 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 572
      removed outlier: 3.540A  pdb=" N   VAL A 559 " --> pdb=" O   TYR A 555 " (cutoff:3.500A)
      Proline residue:  A 560  - end of helix
      removed outlier: 3.584A  pdb=" N   TYR A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 601
      removed outlier: 4.029A  pdb=" N   PHE A 582 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 610
      removed outlier: 4.314A  pdb=" N   GLY A 610 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 607 through 610'
    Processing helix  chain 'A' and resid 611 through 638
      removed outlier: 4.544A  pdb=" N   HIS A 615 " --> pdb=" O   ARG A 611 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 616 " --> pdb=" O   MET A 612 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ARG A 619 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA A 622 " --> pdb=" O   GLN A 618 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 637 " --> pdb=" O   GLY A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 665
      removed outlier: 3.608A  pdb=" N   ILE A 651 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   THR A 652 " --> pdb=" O   PRO A 648 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 670
      removed outlier: 3.670A  pdb=" N   GLU A 669 " --> pdb=" O   TYR A 665 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   HIS A 670 " --> pdb=" O   GLY A 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 665 through 670'
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.865A  pdb=" N   CYS A 677 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 694
      removed outlier: 3.837A  pdb=" N   PHE A 690 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ARG A 691 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   ALA A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 27
      removed outlier: 4.170A  pdb=" N   LEU B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 42
    Processing helix  chain 'B' and resid 59 through 67
    Processing helix  chain 'B' and resid 69 through 77
    Processing helix  chain 'B' and resid 78 through 112
      removed outlier: 3.618A  pdb=" N   ALA B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      Proline residue:  B 104  - end of helix
      removed outlier: 3.808A  pdb=" N   LEU B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      Proline residue:  B 108  - end of helix
    Processing helix  chain 'B' and resid 117 through 125
      removed outlier: 3.643A  pdb=" N   ASN B 121 " --> pdb=" O   ASN B 118 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ALA B 122 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 184
      removed outlier: 3.610A  pdb=" N   VAL B 156 " --> pdb=" O   PHE B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 218
    Processing helix  chain 'B' and resid 233 through 255
    Processing helix  chain 'B' and resid 274 through 278
      removed outlier: 3.623A  pdb=" N   GLN B 277 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   VAL B 278 " --> pdb=" O   GLY B 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 274 through 278'
    Processing helix  chain 'B' and resid 279 through 303
      removed outlier: 3.617A  pdb=" N   TYR B 284 " --> pdb=" O   SER B 280 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   THR B 285 " --> pdb=" O   ILE B 281 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLU B 286 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 287 " --> pdb=" O   TYR B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 325
      removed outlier: 3.525A  pdb=" N   ALA B 325 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 376
    Processing helix  chain 'B' and resid 377 through 387
      removed outlier: 4.253A  pdb=" N   ILE B 381 " --> pdb=" O   TYR B 377 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   PHE B 383 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 391
    Processing helix  chain 'B' and resid 392 through 396
    Processing helix  chain 'B' and resid 401 through 408
      removed outlier: 4.012A  pdb=" N   GLU B 405 " --> pdb=" O   LYS B 401 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE B 406 " --> pdb=" O   PRO B 402 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   THR B 407 " --> pdb=" O   VAL B 403 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ALA B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 401 through 408'
    Processing helix  chain 'B' and resid 409 through 440
      removed outlier: 3.673A  pdb=" N   GLU B 414 " --> pdb=" O   ARG B 410 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   SER B 415 " --> pdb=" O   THR B 411 " (cutoff:3.500A)
      Proline residue:  B 418  - end of helix
      removed outlier: 3.764A  pdb=" N   PHE B 425 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      Proline residue:  B 430  - end of helix
      removed outlier: 3.505A  pdb=" N   ALA B 439 " --> pdb=" O   PHE B 435 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLU B 440 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 468
      removed outlier: 3.778A  pdb=" N   ALA B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 484
      removed outlier: 3.645A  pdb=" N   LYS B 479 " --> pdb=" O   ASN B 476 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE B 481 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA B 482 " --> pdb=" O   LYS B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 523
      removed outlier: 4.186A  pdb=" N   ILE B 490 " --> pdb=" O   LYS B 486 " (cutoff:3.500A)
      Proline residue:  B 499  - end of helix
    Processing helix  chain 'B' and resid 523 through 536
    Processing helix  chain 'B' and resid 540 through 547
    Processing helix  chain 'B' and resid 554 through 572
      removed outlier: 3.888A  pdb=" N   VAL B 559 " --> pdb=" O   TYR B 555 " (cutoff:3.500A)
      Proline residue:  B 560  - end of helix
      removed outlier: 3.648A  pdb=" N   TYR B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 601
      removed outlier: 4.110A  pdb=" N   ILE B 581 " --> pdb=" O   PRO B 577 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE B 582 " --> pdb=" O   LEU B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 611
      removed outlier: 4.398A  pdb=" N   GLY B 610 " --> pdb=" O   GLU B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 638
    Processing helix  chain 'B' and resid 642 through 665
      Proline residue:  B 648  - end of helix
    Processing helix  chain 'B' and resid 665 through 670
      removed outlier: 3.556A  pdb=" N   GLU B 669 " --> pdb=" O   TYR B 665 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   HIS B 670 " --> pdb=" O   GLY B 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 665 through 670'
    Processing helix  chain 'B' and resid 673 through 678
    Processing helix  chain 'B' and resid 686 through 694
      removed outlier: 4.148A  pdb=" N   PHE B 690 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ALA B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229
      removed outlier: 3.655A  pdb=" N   ILE A 194 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 228 through 231
      removed outlier: 5.534A  pdb=" N   ALA B 310 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL B 313 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)

    644 hydrogen bonds defined for protein.
    1845 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: 1.71

  Time building geometry restraints manager: 1.48 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: 3164
        1.34 -     1.46: 2275
        1.46 -     1.58: 5131
        1.58 -     1.70: 0
        1.70 -     1.81: 46
  Bond restraints: 10616
  Sorted by residual:
  bond pdb=" CA  LEU B 348 "
       pdb=" CB  LEU B 348 "
    ideal  model  delta    sigma   weight residual
    1.528  1.486  0.042 2.61e-02 1.47e+03 2.63e+00
  bond pdb=" CA  LEU B 195 "
       pdb=" CB  LEU B 195 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.022 1.46e-02 4.69e+03 2.21e+00
  bond pdb=" C   TYR B 549 "
       pdb=" N   PRO B 550 "
    ideal  model  delta    sigma   weight residual
    1.336  1.319  0.017 1.20e-02 6.94e+03 1.94e+00
  bond pdb=" CG  LEU A 649 "
       pdb=" CD2 LEU A 649 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.43e+00
  bond pdb=" CA  ILE B 689 "
       pdb=" CB  ILE B 689 "
    ideal  model  delta    sigma   weight residual
    1.545  1.534  0.012 1.05e-02 9.07e+03 1.26e+00
  ... (remaining 10611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 14145
        2.34 -     4.68: 317
        4.68 -     7.02: 48
        7.02 -     9.36: 6
        9.36 -    11.70: 1
  Bond angle restraints: 14517
  Sorted by residual:
  angle pdb=" C   THR B 223 "
        pdb=" N   PHE B 224 "
        pdb=" CA  PHE B 224 "
      ideal   model   delta    sigma   weight residual
     121.54  130.33   -8.79 1.91e+00 2.74e-01 2.12e+01
  angle pdb=" N   VAL A 675 "
        pdb=" CA  VAL A 675 "
        pdb=" C   VAL A 675 "
      ideal   model   delta    sigma   weight residual
     112.80  107.70    5.10 1.15e+00 7.56e-01 1.97e+01
  angle pdb=" N   GLU A 679 "
        pdb=" CA  GLU A 679 "
        pdb=" C   GLU A 679 "
      ideal   model   delta    sigma   weight residual
     110.06  115.77   -5.71 1.43e+00 4.89e-01 1.60e+01
  angle pdb=" N   GLU B 241 "
        pdb=" CA  GLU B 241 "
        pdb=" CB  GLU B 241 "
      ideal   model   delta    sigma   weight residual
     110.28  115.98   -5.70 1.55e+00 4.16e-01 1.35e+01
  angle pdb=" C   LYS B 663 "
        pdb=" N   PHE B 664 "
        pdb=" CA  PHE B 664 "
      ideal   model   delta    sigma   weight residual
     122.08  116.61    5.47 1.53e+00 4.27e-01 1.28e+01
  ... (remaining 14512 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.83: 5570
       15.83 -    31.66: 504
       31.66 -    47.49: 114
       47.49 -    63.32: 16
       63.32 -    79.15: 4
  Dihedral angle restraints: 6208
    sinusoidal: 2115
      harmonic: 4093
  Sorted by residual:
  dihedral pdb=" CA  ALA B  34 "
           pdb=" C   ALA B  34 "
           pdb=" N   PRO B  35 "
           pdb=" CA  PRO B  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -129.23  -50.77     0      5.00e+00 4.00e-02 1.03e+02
  dihedral pdb=" CA  ALA A  34 "
           pdb=" C   ALA A  34 "
           pdb=" N   PRO A  35 "
           pdb=" CA  PRO A  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.98  -49.02     0      5.00e+00 4.00e-02 9.61e+01
  dihedral pdb=" CA  GLY B 441 "
           pdb=" C   GLY B 441 "
           pdb=" N   ILE B 442 "
           pdb=" CA  ILE B 442 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.66   33.34     0      5.00e+00 4.00e-02 4.45e+01
  ... (remaining 6205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1579
       0.076 -    0.153: 169
       0.153 -    0.229: 2
       0.229 -    0.306: 1
       0.306 -    0.382: 1
  Chirality restraints: 1752
  Sorted by residual:
  chirality pdb=" CB  ILE A 256 "
            pdb=" CA  ILE A 256 "
            pdb=" CG1 ILE A 256 "
            pdb=" CG2 ILE A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.65e+00
  chirality pdb=" CG  LEU A 564 "
            pdb=" CB  LEU A 564 "
            pdb=" CD1 LEU A 564 "
            pdb=" CD2 LEU A 564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  TRP A 613 "
            pdb=" N   TRP A 613 "
            pdb=" C   TRP A 613 "
            pdb=" CB  TRP A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 1749 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 341 "    0.046 5.00e-02 4.00e+02   6.96e-02 7.76e+00
        pdb=" N   PRO A 342 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 342 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 342 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  38 "    0.043 5.00e-02 4.00e+02   6.60e-02 6.96e+00
        pdb=" N   PRO A  39 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A  39 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  39 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 103 "   -0.036 5.00e-02 4.00e+02   5.55e-02 4.93e+00
        pdb=" N   PRO B 104 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 104 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 104 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 410
        2.71 -     3.26: 11714
        3.26 -     3.80: 16624
        3.80 -     4.35: 19230
        4.35 -     4.90: 31855
  Nonbonded interactions: 79833
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 164 "
            pdb=" OG  SER B 653 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" O   ASN A 136 "
            pdb=" ND2 ASN A 141 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" O   ASN A 114 "
            pdb=" OG1 THR A 119 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" ND2 ASN A 351 "
            pdb=" O   LYS A 438 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" O   LYS B 144 "
            pdb=" OG1 THR B 639 "
     model   vdw
     2.210 3.040
  ... (remaining 79828 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 3 through 473 or resid 486 through 702))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.910
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
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   0.042  10616  Z= 0.203
  Angle     :  0.839  11.703  14517  Z= 0.468
  Chirality :  0.046   0.382   1752
  Planarity :  0.006   0.070   1794
  Dihedral  : 12.990  79.155   3552
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.60 %
    Favored  : 86.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.30 %

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: -0.93 (0.24), residues: 1382
  helix:  0.86 (0.19), residues: 799
  sheet: -5.70 (0.64), residues: 10
  loop : -2.81 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 611 
 TYR   0.017   0.002   TYR B 693 
 PHE   0.026   0.002   PHE A 664 
 TRP   0.020   0.002   TRP B 336 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (10616)
  covalent geometry    : angle       0.83892 (14517)
  hydrogen bonds       : bond        0.14741 (  644)
  hydrogen bonds       : angle       5.49981 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8067 (ptt180) cc_final: 0.7759 (tmm-80)
REVERT: A  248 LYS cc_start: 0.9653 (mmpt) cc_final: 0.9389 (mmmt)
REVERT: A  513 PHE cc_start: 0.7369 (m-80) cc_final: 0.6780 (m-80)
REVERT: B  237 ASN cc_start: 0.8800 (m110) cc_final: 0.8592 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0919
  time to fit residues: 27.0945
Evaluate side-chains
  159 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.4980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 308 GLN
B 353 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.153791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.112751 restraints weight = 19970.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.111256 restraints weight = 17358.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.111832 restraints weight = 14456.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112766 restraints weight = 12092.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112793 restraints weight = 10278.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10616  Z= 0.158
  Angle     :  0.756   9.692  14517  Z= 0.382
  Chirality :  0.045   0.339   1752
  Planarity :  0.005   0.069   1794
  Dihedral  :  5.801  47.303   1475
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.16 %
    Favored  : 87.70 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.94 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.30 %

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: -0.84 (0.24), residues: 1382
  helix:  0.91 (0.18), residues: 830
  sheet: -5.21 (0.79), residues: 10
  loop : -2.94 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 595 
 TYR   0.024   0.002   TYR A 171 
 PHE   0.024   0.002   PHE B 514 
 TRP   0.010   0.001   TRP B  61 
 HIS   0.006   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10616)
  covalent geometry    : angle       0.75614 (14517)
  hydrogen bonds       : bond        0.04700 (  644)
  hydrogen bonds       : angle       4.63669 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 176
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  115 ASN cc_start: 0.8741 (m110) cc_final: 0.8515 (m-40)
REVERT: A  248 LYS cc_start: 0.9562 (mmpt) cc_final: 0.9353 (mmmt)
REVERT: A  377 TYR cc_start: 0.6307 (p90) cc_final: 0.5050 (p90)
REVERT: A  378 MET cc_start: 0.7419 (mmp) cc_final: 0.6644 (mmm)
REVERT: B  437 SER cc_start: 0.9117 (t) cc_final: 0.8874 (t)
REVERT: B  589 LEU cc_start: 0.8365 (mp) cc_final: 0.8144 (mp)
  outliers start: 26
  outliers final: 16
  residues processed: 187
  average time/residue: 0.0911
  time to fit residues: 25.4350
Evaluate side-chains
  164 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  630 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 131 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 130 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 104 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 308 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.154662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.113346 restraints weight = 20141.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.111359 restraints weight = 17716.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112059 restraints weight = 13811.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112924 restraints weight = 12547.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112991 restraints weight = 10838.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10616  Z= 0.150
  Angle     :  0.725  10.085  14517  Z= 0.363
  Chirality :  0.044   0.315   1752
  Planarity :  0.005   0.067   1794
  Dihedral  :  5.614  48.159   1475
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.79 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.47 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.30 %

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: -0.56 (0.24), residues: 1382
  helix:  1.06 (0.18), residues: 830
  sheet:  None (None), residues: 0
  loop : -2.77 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 611 
 TYR   0.027   0.001   TYR A 171 
 PHE   0.035   0.002   PHE B 514 
 TRP   0.012   0.001   TRP B  61 
 HIS   0.005   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10616)
  covalent geometry    : angle       0.72461 (14517)
  hydrogen bonds       : bond        0.04222 (  644)
  hydrogen bonds       : angle       4.49132 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LYS cc_start: 0.9593 (mmpt) cc_final: 0.9374 (mmmt)
REVERT: B  231 THR cc_start: 0.8239 (p) cc_final: 0.7812 (p)
REVERT: B  308 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7406 (pm20)
REVERT: B  432 LEU cc_start: 0.9152 (tt) cc_final: 0.8943 (tp)
REVERT: B  437 SER cc_start: 0.9091 (t) cc_final: 0.8803 (t)
  outliers start: 26
  outliers final: 12
  residues processed: 183
  average time/residue: 0.0867
  time to fit residues: 24.2422
Evaluate side-chains
  168 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  308 GLN
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  630 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 129 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 136 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS
** B 308 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 = 0.3955 r_free = 0.3955 target = 0.155287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.115516 restraints weight = 20229.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.112032 restraints weight = 17370.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112785 restraints weight = 14074.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.113591 restraints weight = 11834.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.113830 restraints weight = 10522.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10616  Z= 0.147
  Angle     :  0.708   9.889  14517  Z= 0.354
  Chirality :  0.043   0.292   1752
  Planarity :  0.005   0.066   1794
  Dihedral  :  5.478  48.505   1475
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.29 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 17.24 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.30 %

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: -0.48 (0.24), residues: 1382
  helix:  1.11 (0.19), residues: 833
  sheet:  None (None), residues: 0
  loop : -2.73 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 611 
 TYR   0.050   0.001   TYR A 171 
 PHE   0.031   0.002   PHE B 513 
 TRP   0.009   0.001   TRP A 548 
 HIS   0.005   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10616)
  covalent geometry    : angle       0.70812 (14517)
  hydrogen bonds       : bond        0.04042 (  644)
  hydrogen bonds       : angle       4.42680 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  248 LYS cc_start: 0.9578 (mmpt) cc_final: 0.9376 (mmmt)
REVERT: A  306 LYS cc_start: 0.8631 (pttp) cc_final: 0.8328 (pttp)
REVERT: A  377 TYR cc_start: 0.6364 (p90) cc_final: 0.4924 (p90)
REVERT: B  231 THR cc_start: 0.8189 (p) cc_final: 0.7769 (p)
REVERT: B  308 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7463 (pm20)
REVERT: B  369 PHE cc_start: 0.8800 (t80) cc_final: 0.8571 (t80)
REVERT: B  437 SER cc_start: 0.9085 (t) cc_final: 0.8769 (t)
REVERT: B  505 PHE cc_start: 0.8845 (m-10) cc_final: 0.8637 (m-80)
REVERT: B  595 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8631 (ttt90)
  outliers start: 35
  outliers final: 20
  residues processed: 185
  average time/residue: 0.0891
  time to fit residues: 25.0592
Evaluate side-chains
  171 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  308 GLN
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  511 LEU
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  630 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 30 optimal weight:    0.0000
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    0.4980
   chunk 95 optimal weight:   10.0000
   chunk 33 optimal weight:    0.4980
   chunk 98 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.6024

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.156554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.117425 restraints weight = 20025.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.114771 restraints weight = 18345.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.115696 restraints weight = 14773.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.116387 restraints weight = 12036.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.116597 restraints weight = 10715.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10616  Z= 0.137
  Angle     :  0.701  10.784  14517  Z= 0.348
  Chirality :  0.043   0.278   1752
  Planarity :  0.005   0.066   1794
  Dihedral  :  5.350  48.054   1475
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.78 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 18.42 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.23 %

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: -0.37 (0.24), residues: 1382
  helix:  1.21 (0.19), residues: 831
  sheet: -0.17 (2.85), residues: 5
  loop : -2.71 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 619 
 TYR   0.042   0.001   TYR A 171 
 PHE   0.026   0.001   PHE A 513 
 TRP   0.010   0.001   TRP B  61 
 HIS   0.005   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10616)
  covalent geometry    : angle       0.70061 (14517)
  hydrogen bonds       : bond        0.03838 (  644)
  hydrogen bonds       : angle       4.35573 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 162
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A  351 ASN cc_start: 0.8681 (t0) cc_final: 0.8445 (t0)
REVERT: A  378 MET cc_start: 0.7741 (mmm) cc_final: 0.7083 (mmm)
REVERT: B  432 LEU cc_start: 0.9079 (tt) cc_final: 0.8875 (tp)
REVERT: B  437 SER cc_start: 0.9116 (t) cc_final: 0.8850 (t)
  outliers start: 45
  outliers final: 25
  residues processed: 190
  average time/residue: 0.0892
  time to fit residues: 26.0060
Evaluate side-chains
  174 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  511 LEU
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  694 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 117 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0270
   chunk 86 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
** B 353 ASN ** 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 = 0.3966 r_free = 0.3966 target = 0.156179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.115302 restraints weight = 20589.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.112556 restraints weight = 16344.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.113504 restraints weight = 12953.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.113943 restraints weight = 11309.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.114048 restraints weight = 10044.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10616  Z= 0.137
  Angle     :  0.699  10.400  14517  Z= 0.344
  Chirality :  0.042   0.207   1752
  Planarity :  0.005   0.066   1794
  Dihedral  :  5.232  47.982   1475
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.00 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 19.51 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.23 %

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: -0.31 (0.24), residues: 1382
  helix:  1.26 (0.19), residues: 830
  sheet:  0.14 (2.77), residues: 5
  loop : -2.69 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 661 
 TYR   0.036   0.001   TYR A 171 
 PHE   0.028   0.001   PHE A 513 
 TRP   0.011   0.001   TRP B  61 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10616)
  covalent geometry    : angle       0.69914 (14517)
  hydrogen bonds       : bond        0.03760 (  644)
  hydrogen bonds       : angle       4.31341 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 157
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TRP cc_start: 0.7274 (m100) cc_final: 0.7016 (m100)
REVERT: A  351 ASN cc_start: 0.8641 (t0) cc_final: 0.8413 (t0)
REVERT: A  377 TYR cc_start: 0.6359 (p90) cc_final: 0.5988 (p90)
REVERT: A  378 MET cc_start: 0.7815 (mmm) cc_final: 0.7504 (mmm)
REVERT: B   86 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8877 (p)
REVERT: B  437 SER cc_start: 0.9047 (t) cc_final: 0.8736 (t)
  outliers start: 42
  outliers final: 29
  residues processed: 185
  average time/residue: 0.0850
  time to fit residues: 24.2629
Evaluate side-chains
  183 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  693 TYR
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  511 LEU
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  694 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 68 optimal weight:   30.0000
   chunk 75 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 117 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B 353 ASN ** 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 = 0.3970 r_free = 0.3970 target = 0.156436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.115314 restraints weight = 19868.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.114147 restraints weight = 16044.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.115009 restraints weight = 12429.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.115391 restraints weight = 10979.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.115650 restraints weight = 10132.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10616  Z= 0.142
  Angle     :  0.697  10.698  14517  Z= 0.344
  Chirality :  0.043   0.321   1752
  Planarity :  0.005   0.064   1794
  Dihedral  :  5.210  48.037   1475
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.93 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 20.00 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.15 %

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: -0.25 (0.24), residues: 1382
  helix:  1.33 (0.19), residues: 825
  sheet: -0.33 (1.97), residues: 10
  loop : -2.65 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 661 
 TYR   0.034   0.001   TYR A 586 
 PHE   0.028   0.001   PHE B 513 
 TRP   0.011   0.001   TRP B  61 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (10616)
  covalent geometry    : angle       0.69672 (14517)
  hydrogen bonds       : bond        0.03756 (  644)
  hydrogen bonds       : angle       4.32883 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 155
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TRP cc_start: 0.7177 (m100) cc_final: 0.6949 (m100)
REVERT: A  351 ASN cc_start: 0.8591 (t0) cc_final: 0.8367 (t0)
REVERT: B  437 SER cc_start: 0.9093 (t) cc_final: 0.8766 (t)
  outliers start: 41
  outliers final: 30
  residues processed: 180
  average time/residue: 0.0831
  time to fit residues: 23.2372
Evaluate side-chains
  178 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  693 TYR
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  628 GLN
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  694 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 129 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 112 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 93 optimal weight:   10.0000
   chunk 102 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 308 GLN
A 353 ASN
** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.117403 restraints weight = 20024.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.114900 restraints weight = 17976.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.116175 restraints weight = 14221.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.116785 restraints weight = 11495.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.116991 restraints weight = 10413.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10616  Z= 0.142
  Angle     :  0.725  16.200  14517  Z= 0.352
  Chirality :  0.043   0.244   1752
  Planarity :  0.005   0.064   1794
  Dihedral  :  5.198  48.022   1475
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.93 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.87 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.15 %

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: -0.24 (0.24), residues: 1382
  helix:  1.31 (0.19), residues: 824
  sheet: -0.23 (1.95), residues: 10
  loop : -2.61 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 661 
 TYR   0.033   0.002   TYR A 171 
 PHE   0.027   0.001   PHE B 513 
 TRP   0.012   0.001   TRP B  61 
 HIS   0.003   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10616)
  covalent geometry    : angle       0.72491 (14517)
  hydrogen bonds       : bond        0.03829 (  644)
  hydrogen bonds       : angle       4.30829 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 151
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  351 ASN cc_start: 0.8598 (t0) cc_final: 0.8370 (t0)
REVERT: A  513 PHE cc_start: 0.7047 (m-80) cc_final: 0.6521 (m-80)
REVERT: A  517 TYR cc_start: 0.8539 (m-10) cc_final: 0.8199 (m-80)
REVERT: B  437 SER cc_start: 0.9083 (t) cc_final: 0.8729 (t)
  outliers start: 38
  outliers final: 28
  residues processed: 173
  average time/residue: 0.0826
  time to fit residues: 22.2241
Evaluate side-chains
  176 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  628 GLN
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  694 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0170
   chunk 7 optimal weight:    0.8980
   chunk 68 optimal weight:   30.0000
   chunk 28 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9990
   chunk 105 optimal weight:    0.1980
   overall best weight:    0.6220

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

Flipped N/Q/H residues before XYZ refinement:
** B 353 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.157682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.117220 restraints weight = 19776.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.116787 restraints weight = 15044.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.116871 restraints weight = 11968.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.117163 restraints weight = 11695.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.117599 restraints weight = 10581.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10616  Z= 0.134
  Angle     :  0.709  12.912  14517  Z= 0.345
  Chirality :  0.043   0.221   1752
  Planarity :  0.005   0.063   1794
  Dihedral  :  5.152  47.722   1475
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.64 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.97 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.15 %

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: -0.21 (0.24), residues: 1382
  helix:  1.30 (0.19), residues: 829
  sheet: -1.03 (3.00), residues: 5
  loop : -2.54 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 661 
 TYR   0.030   0.001   TYR A 171 
 PHE   0.029   0.002   PHE B 513 
 TRP   0.013   0.001   TRP B  61 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10616)
  covalent geometry    : angle       0.70945 (14517)
  hydrogen bonds       : bond        0.03721 (  644)
  hydrogen bonds       : angle       4.26135 ( 1845)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (t80)
REVERT: A  351 ASN cc_start: 0.8540 (t0) cc_final: 0.8335 (t0)
REVERT: A  517 TYR cc_start: 0.8500 (m-10) cc_final: 0.8174 (m-80)
REVERT: A  563 MET cc_start: 0.8160 (mtp) cc_final: 0.7797 (mtm)
REVERT: B  224 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7234 (m-80)
REVERT: B  437 SER cc_start: 0.9032 (t) cc_final: 0.8675 (t)
  outliers start: 33
  outliers final: 26
  residues processed: 169
  average time/residue: 0.0834
  time to fit residues: 21.8807
Evaluate side-chains
  175 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  171 TYR
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  693 TYR
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  631 MET
Chi-restraints excluded: chain B residue  694 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 129 optimal weight:    0.5980
   chunk 104 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 51 optimal weight:    0.1980
   chunk 71 optimal weight:    0.1980
   chunk 118 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0980
   chunk 81 optimal weight:    0.8980
   chunk 122 optimal weight:    0.3980
   chunk 38 optimal weight:    7.9990
   overall best weight:    0.2980

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
B 351 ASN
** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.159581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.118377 restraints weight = 19541.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.118747 restraints weight = 13009.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.118648 restraints weight = 10439.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.119400 restraints weight = 9947.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.119446 restraints weight = 9101.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10616  Z= 0.130
  Angle     :  0.737  20.342  14517  Z= 0.352
  Chirality :  0.043   0.233   1752
  Planarity :  0.005   0.064   1794
  Dihedral  :  5.121  47.118   1475
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.27 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.27 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.15 %

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: -0.13 (0.24), residues: 1382
  helix:  1.35 (0.19), residues: 827
  sheet: -1.11 (2.92), residues: 5
  loop : -2.45 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 661 
 TYR   0.028   0.001   TYR A 171 
 PHE   0.042   0.001   PHE B 505 
 TRP   0.015   0.001   TRP B  61 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10616)
  covalent geometry    : angle       0.73735 (14517)
  hydrogen bonds       : bond        0.03607 (  644)
  hydrogen bonds       : angle       4.27361 ( 1845)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8511 (t80)
REVERT: A  351 ASN cc_start: 0.8522 (t0) cc_final: 0.8312 (t0)
REVERT: A  513 PHE cc_start: 0.6994 (m-80) cc_final: 0.6351 (m-80)
REVERT: A  517 TYR cc_start: 0.8504 (m-10) cc_final: 0.8157 (m-80)
REVERT: A  564 LEU cc_start: 0.8641 (tp) cc_final: 0.8425 (tp)
REVERT: B  224 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7318 (m-80)
REVERT: B  300 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8332 (ptpp)
REVERT: B  563 MET cc_start: 0.8379 (tpp) cc_final: 0.7841 (ttt)
  outliers start: 31
  outliers final: 27
  residues processed: 176
  average time/residue: 0.0804
  time to fit residues: 21.8077
Evaluate side-chains
  180 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  171 TYR
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  693 TYR
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  527 LEU
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  631 MET
Chi-restraints excluded: chain B residue  694 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 68 optimal weight:   30.0000
   chunk 53 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 137 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 131 optimal weight:    2.9990
   chunk 40 optimal weight:   50.0000
   chunk 22 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B 353 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.156128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.115413 restraints weight = 20153.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.113974 restraints weight = 15377.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.114232 restraints weight = 12958.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.114909 restraints weight = 11291.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.115188 restraints weight = 10339.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10616  Z= 0.155
  Angle     :  0.728  16.565  14517  Z= 0.353
  Chirality :  0.043   0.209   1752
  Planarity :  0.005   0.063   1794
  Dihedral  :  5.112  47.391   1475
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.56 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.56 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.28 %
    Twisted General : 0.15 %

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: -0.10 (0.24), residues: 1382
  helix:  1.37 (0.19), residues: 828
  sheet: -1.24 (1.12), residues: 20
  loop : -2.46 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 661 
 TYR   0.033   0.001   TYR A 171 
 PHE   0.028   0.002   PHE A 416 
 TRP   0.011   0.001   TRP B  61 
 HIS   0.003   0.001   HIS B 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10616)
  covalent geometry    : angle       0.72780 (14517)
  hydrogen bonds       : bond        0.03651 (  644)
  hydrogen bonds       : angle       4.25968 ( 1845)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1690.54 seconds
wall clock time: 30 minutes 10.10 seconds (1810.10 seconds total)