Starting phenix.real_space_refine
on Tue Jul 29 03:03:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lby_23267/07_2025/7lby_23267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lby_23267/07_2025/7lby_23267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lby_23267/07_2025/7lby_23267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lby_23267/07_2025/7lby_23267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lby_23267/07_2025/7lby_23267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lby_23267/07_2025/7lby_23267.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2664 atoms to isotropic.
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      23      5.16       5
     C    5441      2.51       5
     N    1624      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8800
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 755, 3724
          Classifications: {'peptide': 755}
          Incomplete info: {'truncation_to_alanine': 648}
          Link IDs: {'PTRANS': 40, 'TRANS': 714}
          Chain breaks: 2
          Unresolved chain link angles: 40
          Unresolved non-hydrogen bonds: 2559
          Unresolved non-hydrogen angles: 3319
          Unresolved non-hydrogen dihedrals: 2205
          Unresolved non-hydrogen chiralities: 231
          Planarities with less than four sites: {'GLN:plan1': 28, 'ASP:plan': 25, 'TYR:plan': 28, 'ASN:plan1': 28, 'TRP:plan': 22, 'HIS:plan': 24, 'PHE:plan': 40, 'GLU:plan': 32, 'ARG:plan': 54}
          Unresolved non-hydrogen planarities: 1423
    Chain: "B"
      Number of atoms: 5076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5076
          Classifications: {'peptide': 663}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 612}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Time building chain proxies: 6.36, per 1000 atoms: 0.72
  Number of scatterers: 8800
  At special positions: 0
  Unit cell: (135, 150.12, 124.2, 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      23     16.00
     O    1712      8.00
     N    1624      7.00
     C    5441      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 182 " - pdb=" SG  CYS B 500 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2648

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 13 sheets defined
      40.6% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 42
    Processing helix  chain 'A' and resid 124 through 142
      Proline residue:  A 129  - end of helix
      Proline residue:  A 133  - end of helix
      removed outlier: 3.859A  pdb=" N   HIS A 142 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
      removed outlier: 3.510A  pdb=" N   SER A 152 " --> pdb=" O   HIS A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 178 through 191
    Processing helix  chain 'A' and resid 196 through 219
      removed outlier: 3.894A  pdb=" N   MET A 200 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 222 through 227
    Processing helix  chain 'A' and resid 228 through 256
      Proline residue:  A 250  - end of helix
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 287 through 300
      removed outlier: 3.576A  pdb=" N   SER A 300 " --> pdb=" O   TRP A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 328
    Processing helix  chain 'A' and resid 343 through 352
    Processing helix  chain 'A' and resid 353 through 355
      No H-bonds generated for 'chain 'A' and resid 353 through 355'
    Processing helix  chain 'A' and resid 373 through 377
      removed outlier: 3.632A  pdb=" N   SER A 376 " --> pdb=" O   ILE A 373 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 377 " --> pdb=" O   TYR A 374 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 373 through 377'
    Processing helix  chain 'A' and resid 400 through 407
    Processing helix  chain 'A' and resid 416 through 421
    Processing helix  chain 'A' and resid 422 through 430
      removed outlier: 3.703A  pdb=" N   ASN A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 468
      removed outlier: 3.825A  pdb=" N   GLN A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU A 463 " --> pdb=" O   LYS A 459 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLN A 467 " --> pdb=" O   LEU A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 513
    Processing helix  chain 'A' and resid 519 through 551
      removed outlier: 3.903A  pdb=" N   THR A 535 " --> pdb=" O   VAL A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 582
    Processing helix  chain 'A' and resid 589 through 610
      removed outlier: 4.249A  pdb=" N   GLY A 593 " --> pdb=" O   ASN A 589 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG A 601 " --> pdb=" O   LYS A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 659
      Proline residue:  A 646  - end of helix
    Processing helix  chain 'A' and resid 663 through 688
      Proline residue:  A 670  - end of helix
    Processing helix  chain 'A' and resid 791 through 802
      removed outlier: 3.822A  pdb=" N   ARG A 802 " --> pdb=" O   ARG A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 831
      removed outlier: 3.592A  pdb=" N   GLY A 830 " --> pdb=" O   PHE A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 838 through 860
    Processing helix  chain 'A' and resid 861 through 863
      No H-bonds generated for 'chain 'A' and resid 861 through 863'
    Processing helix  chain 'B' and resid 145 through 149
      removed outlier: 3.692A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 259
    Processing helix  chain 'B' and resid 260 through 262
      No H-bonds generated for 'chain 'B' and resid 260 through 262'
    Processing helix  chain 'B' and resid 321 through 335
    Processing helix  chain 'B' and resid 532 through 538
    Processing helix  chain 'B' and resid 560 through 578
      removed outlier: 3.558A  pdb=" N   MET B 564 " --> pdb=" O   ASN B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 614
      No H-bonds generated for 'chain 'B' and resid 612 through 614'
    Processing helix  chain 'B' and resid 615 through 630
      removed outlier: 3.907A  pdb=" N   LEU B 619 " --> pdb=" O   LYS B 615 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B 620 " --> pdb=" O   GLN B 616 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   VAL B 621 " --> pdb=" O   ILE B 617 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN B 622 " --> pdb=" O   ASP B 618 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TRP B 627 " --> pdb=" O   ALA B 623 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR B 630 " --> pdb=" O   SER B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 697
      removed outlier: 3.517A  pdb=" N   TYR B 688 " --> pdb=" O   SER B 684 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASP B 697 " --> pdb=" O   ASP B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 743
      removed outlier: 4.047A  pdb=" N   VAL B 736 " --> pdb=" O   TRP B 732 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   TRP B 737 " --> pdb=" O   PHE B 733 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR B 738 " --> pdb=" O   GLU B 734 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ASN B 742 " --> pdb=" O   TYR B 738 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   HIS B 743 " --> pdb=" O   ALA B 739 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 743 through 772
    Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 282
      removed outlier: 3.766A  pdb=" N   ALA A 279 " --> pdb=" O   SER A 309 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 311 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392
      removed outlier: 3.546A  pdb=" N   PHE A 478 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 700 through 704
      removed outlier: 6.586A  pdb=" N   TYR A 702 " --> pdb=" O   THR A 722 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   THR A 722 " --> pdb=" O   TYR A 702 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA A 704 " --> pdb=" O   ASN A 720 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   GLU A 729 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 716 through 717
    Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 101
      removed outlier: 4.078A  pdb=" N   PHE B 100 " --> pdb=" O   ASN B 168 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ASN B 168 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU B 173 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL B 132 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   GLY B 140 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 159
      removed outlier: 4.207A  pdb=" N   THR B 153 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   TYR B 117 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ALA B 111 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LYS B 110 " --> pdb=" O   THR B 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 267 through 269
      removed outlier: 4.116A  pdb=" N   LEU B 268 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE B 235 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   VAL B 234 " --> pdb=" O   PHE B 280 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   VAL B 279 " --> pdb=" O   VAL B 317 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL B 316 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 384
    Processing sheet with id=AB1, first strand: chain 'B' and resid 395 through 396
      removed outlier: 3.942A  pdb=" N   LEU B 396 " --> pdb=" O   ASN B 480 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASN B 480 " --> pdb=" O   LEU B 396 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442
      removed outlier: 3.880A  pdb=" N   GLN B 439 " --> pdb=" O   ILE B 431 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET B 429 " --> pdb=" O   PHE B 441 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG B 428 " --> pdb=" O   GLU B 487 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLU B 487 " --> pdb=" O   ARG B 428 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ASP B 430 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ASP B 485 " --> pdb=" O   ASP B 430 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 527 through 528
      removed outlier: 4.022A  pdb=" N   ILE B 527 " --> pdb=" O   VAL B 727 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL B 727 " --> pdb=" O   ILE B 527 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 586 through 588
      removed outlier: 6.163A  pdb=" N   THR B 553 " --> pdb=" O   THR B 588 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE B 552 " --> pdb=" O   MET B 602 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   ILE B 604 " --> pdb=" O   ILE B 552 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   VAL B 554 " --> pdb=" O   ILE B 604 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ILE B 601 " --> pdb=" O   SER B 676 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE B 678 " --> pdb=" O   ILE B 601 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA B 662 " --> pdb=" O   ILE B 711 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 710 " --> pdb=" O   ASN B 717 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN B 717 " --> pdb=" O   VAL B 710 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1269 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 2.63 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 3201
        1.34 -     1.46: 1632
        1.46 -     1.58: 4037
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 8914
  Sorted by residual:
  bond pdb=" CA  VAL A 343 "
       pdb=" CB  VAL A 343 "
    ideal  model  delta    sigma   weight residual
    1.537  1.508  0.028 5.00e-03 4.00e+04 3.22e+01
  bond pdb=" C   THR A 540 "
       pdb=" O   THR A 540 "
    ideal  model  delta    sigma   weight residual
    1.236  1.272 -0.036 1.15e-02 7.56e+03 9.71e+00
  bond pdb=" N   THR A 540 "
       pdb=" CA  THR A 540 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.031 1.19e-02 7.06e+03 6.89e+00
  bond pdb=" N   SER A 635 "
       pdb=" CA  SER A 635 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.28e-02 6.10e+03 6.04e+00
  bond pdb=" N   GLY A 636 "
       pdb=" CA  GLY A 636 "
    ideal  model  delta    sigma   weight residual
    1.454  1.481 -0.027 1.24e-02 6.50e+03 4.60e+00
  ... (remaining 8909 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 11846
        1.82 -     3.65: 307
        3.65 -     5.47: 45
        5.47 -     7.30: 37
        7.30 -     9.12: 13
  Bond angle restraints: 12248
  Sorted by residual:
  angle pdb=" N   PRO A 445 "
        pdb=" CA  PRO A 445 "
        pdb=" CB  PRO A 445 "
      ideal   model   delta    sigma   weight residual
     102.25  110.63   -8.38 7.00e-01 2.04e+00 1.43e+02
  angle pdb=" N   PRO A 764 "
        pdb=" CA  PRO A 764 "
        pdb=" CB  PRO A 764 "
      ideal   model   delta    sigma   weight residual
     103.36  110.96   -7.60 8.30e-01 1.45e+00 8.38e+01
  angle pdb=" N   PRO A 337 "
        pdb=" CA  PRO A 337 "
        pdb=" CB  PRO A 337 "
      ideal   model   delta    sigma   weight residual
     103.36  110.62   -7.26 8.30e-01 1.45e+00 7.66e+01
  angle pdb=" N   PRO A 706 "
        pdb=" CA  PRO A 706 "
        pdb=" CB  PRO A 706 "
      ideal   model   delta    sigma   weight residual
     103.25  112.37   -9.12 1.05e+00 9.07e-01 7.55e+01
  angle pdb=" N   PRO A 763 "
        pdb=" CA  PRO A 763 "
        pdb=" CB  PRO A 763 "
      ideal   model   delta    sigma   weight residual
     103.08  111.30   -8.22 9.70e-01 1.06e+00 7.18e+01
  ... (remaining 12243 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 5008
       17.93 -    35.86: 233
       35.86 -    53.79: 43
       53.79 -    71.71: 13
       71.71 -    89.64: 7
  Dihedral angle restraints: 5304
    sinusoidal: 1226
      harmonic: 4078
  Sorted by residual:
  dihedral pdb=" N   PRO A 342 "
           pdb=" C   PRO A 342 "
           pdb=" CA  PRO A 342 "
           pdb=" CB  PRO A 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  124.59   -9.49     0      2.50e+00 1.60e-01 1.44e+01
  dihedral pdb=" CB  GLU B 183 "
           pdb=" CG  GLU B 183 "
           pdb=" CD  GLU B 183 "
           pdb=" OE1 GLU B 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.64  -89.64     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" N   PRO A 307 "
           pdb=" C   PRO A 307 "
           pdb=" CA  PRO A 307 "
           pdb=" CB  PRO A 307 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  123.23   -8.13     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 5301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1195
       0.052 -    0.104: 227
       0.104 -    0.155: 31
       0.155 -    0.207: 11
       0.207 -    0.259: 33
  Chirality restraints: 1497
  Sorted by residual:
  chirality pdb=" CA  PRO A 307 "
            pdb=" N   PRO A 307 "
            pdb=" C   PRO A 307 "
            pdb=" CB  PRO A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  PRO A 342 "
            pdb=" N   PRO A 342 "
            pdb=" C   PRO A 342 "
            pdb=" CB  PRO A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  PRO A 660 "
            pdb=" N   PRO A 660 "
            pdb=" C   PRO A 660 "
            pdb=" CB  PRO A 660 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1494 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  83 "   -0.047 5.00e-02 4.00e+02   7.15e-02 8.19e+00
        pdb=" N   PRO B  84 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B  84 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B  84 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 538 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.66e+00
        pdb=" C   ALA A 538 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ALA A 538 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   HIS A 539 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 537 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   ASP A 537 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASP A 537 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A 538 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 174
        2.70 -     3.25: 8609
        3.25 -     3.80: 13241
        3.80 -     4.35: 14118
        4.35 -     4.90: 24343
  Nonbonded interactions: 60485
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 705 "
            pdb=" OG  SER B 718 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" ND2 ASN B 569 "
            pdb=" OD1 ASN B 692 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OG  SER B 432 "
            pdb=" O   ARG B 483 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR B 118 "
            pdb=" OD1 ASP B 193 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   ASN B  67 "
            pdb=" OH  TYR B 311 "
     model   vdw
     2.289 3.040
  ... (remaining 60480 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.540
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8915  Z= 0.217
  Angle     :  0.780   9.122  12250  Z= 0.603
  Chirality :  0.054   0.259   1497
  Planarity :  0.003   0.072   1689
  Dihedral  : 12.333  89.643   2653
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  :  6.19 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1406
  helix:  2.83 (0.22), residues: 539
  sheet: -1.18 (0.40), residues: 194
  loop : -2.55 (0.23), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.000   TRP B 253 
 HIS   0.001   0.000   HIS B 509 
 PHE   0.024   0.001   PHE B 289 
 TYR   0.005   0.001   TYR B 524 
 ARG   0.005   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17919 (  434)
  hydrogen bonds       : angle       5.94837 ( 1269)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.05338 (    2)
  covalent geometry    : bond        0.00300 ( 8914)
  covalent geometry    : angle       0.78034 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
REVERT: B  172 LEU cc_start: 0.8714 (mp) cc_final: 0.8465 (mt)
REVERT: B  338 LEU cc_start: 0.8362 (pt) cc_final: 0.7991 (pp)
REVERT: B  429 MET cc_start: 0.8745 (tmm) cc_final: 0.8237 (tmm)
REVERT: B  482 LEU cc_start: 0.8744 (tp) cc_final: 0.8481 (tt)
REVERT: B  676 SER cc_start: 0.8473 (p) cc_final: 0.7910 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1723
  time to fit residues: 38.7794
Evaluate side-chains
  115 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 72 optimal weight:   30.0000
   chunk 57 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0470
   chunk 82 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9990
   overall best weight:    1.1484

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 ASN
B 729 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.173782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.157159 restraints weight = 20596.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.153556 restraints weight = 32885.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.153500 restraints weight = 39758.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8915  Z= 0.161
  Angle     :  0.538   5.437  12250  Z= 0.286
  Chirality :  0.043   0.149   1497
  Planarity :  0.004   0.071   1689
  Dihedral  :  3.556  18.022   1460
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.26 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.54 %
    Favored  : 94.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.24), residues: 1406
  helix:  3.14 (0.22), residues: 556
  sheet: -1.18 (0.44), residues: 165
  loop : -2.54 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 737 
 HIS   0.003   0.001   HIS B 177 
 PHE   0.017   0.001   PHE B 221 
 TYR   0.010   0.001   TYR B 416 
 ARG   0.003   0.001   ARG B 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  434)
  hydrogen bonds       : angle       4.39970 ( 1269)
  SS BOND              : bond        0.00393 (    1)
  SS BOND              : angle       0.88736 (    2)
  covalent geometry    : bond        0.00348 ( 8914)
  covalent geometry    : angle       0.53745 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 1.065 
Fit side-chains
REVERT: B   88 VAL cc_start: 0.8255 (t) cc_final: 0.7983 (m)
REVERT: B  258 SER cc_start: 0.9053 (t) cc_final: 0.8669 (t)
REVERT: B  338 LEU cc_start: 0.8532 (pt) cc_final: 0.8301 (pp)
REVERT: B  372 PHE cc_start: 0.7435 (m-80) cc_final: 0.6985 (m-80)
REVERT: B  466 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7051 (ttmm)
REVERT: B  482 LEU cc_start: 0.8978 (tp) cc_final: 0.8710 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 136
  average time/residue: 0.1855
  time to fit residues: 36.7645
Evaluate side-chains
  114 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 20 optimal weight:    0.4980
   chunk 135 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 30 optimal weight:   20.0000
   chunk 24 optimal weight:    0.0370
   overall best weight:    1.1062

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

Flipped N/Q/H residues before XYZ refinement:
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 569 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 = 0.4298 r_free = 0.4298 target = 0.171741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.156777 restraints weight = 21161.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.153951 restraints weight = 46181.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.151962 restraints weight = 40036.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6916
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8915  Z= 0.152
  Angle     :  0.531   6.842  12250  Z= 0.281
  Chirality :  0.043   0.143   1497
  Planarity :  0.004   0.071   1689
  Dihedral  :  3.665  22.536   1460
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.33 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.24), residues: 1406
  helix:  3.15 (0.22), residues: 562
  sheet: -1.33 (0.42), residues: 170
  loop : -2.57 (0.23), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 191 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.023   0.002   PHE B 254 
 TYR   0.017   0.001   TYR B 378 
 ARG   0.003   0.001   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  434)
  hydrogen bonds       : angle       4.02427 ( 1269)
  SS BOND              : bond        0.00426 (    1)
  SS BOND              : angle       0.77999 (    2)
  covalent geometry    : bond        0.00329 ( 8914)
  covalent geometry    : angle       0.53109 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.062 
Fit side-chains
REVERT: B  263 GLN cc_start: 0.8860 (mp10) cc_final: 0.8457 (mp10)
REVERT: B  466 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7571 (ttmm)
REVERT: B  482 LEU cc_start: 0.9104 (tp) cc_final: 0.8803 (tt)
REVERT: B  522 LYS cc_start: 0.6699 (tttm) cc_final: 0.6498 (tttt)
REVERT: B  547 ASP cc_start: 0.8408 (p0) cc_final: 0.8110 (p0)
REVERT: B  580 PHE cc_start: 0.8741 (t80) cc_final: 0.8349 (t80)
REVERT: B  690 MET cc_start: 0.7503 (ptt) cc_final: 0.7137 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1796
  time to fit residues: 34.6766
Evaluate side-chains
  108 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 124 optimal weight:    0.5980
   chunk 117 optimal weight:    0.0980
   chunk 14 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:   20.0000
   chunk 80 optimal weight:    0.2980
   chunk 128 optimal weight:    0.0020
   chunk 120 optimal weight:    0.9990
   overall best weight:    0.3388

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 ASN
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.174679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.159369 restraints weight = 21225.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.158431 restraints weight = 44858.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.157599 restraints weight = 41177.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8915  Z= 0.091
  Angle     :  0.497   6.660  12250  Z= 0.257
  Chirality :  0.042   0.152   1497
  Planarity :  0.004   0.071   1689
  Dihedral  :  3.479  19.598   1460
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.90 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.24), residues: 1406
  helix:  3.20 (0.22), residues: 563
  sheet: -1.34 (0.42), residues: 168
  loop : -2.48 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B 627 
 HIS   0.002   0.000   HIS B 306 
 PHE   0.010   0.001   PHE B 221 
 TYR   0.021   0.001   TYR B 378 
 ARG   0.006   0.000   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02625 (  434)
  hydrogen bonds       : angle       3.84594 ( 1269)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       0.46665 (    2)
  covalent geometry    : bond        0.00191 ( 8914)
  covalent geometry    : angle       0.49698 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.984 
Fit side-chains
REVERT: B  116 GLU cc_start: 0.6628 (mp0) cc_final: 0.6167 (mp0)
REVERT: B  263 GLN cc_start: 0.8515 (mp10) cc_final: 0.8298 (mp10)
REVERT: B  466 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7360 (ttmm)
REVERT: B  482 LEU cc_start: 0.8948 (tp) cc_final: 0.8695 (tt)
REVERT: B  547 ASP cc_start: 0.8056 (p0) cc_final: 0.7843 (p0)
REVERT: B  602 MET cc_start: 0.7262 (ttt) cc_final: 0.6972 (ttt)
REVERT: B  676 SER cc_start: 0.8375 (p) cc_final: 0.8047 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1851
  time to fit residues: 36.7398
Evaluate side-chains
  110 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 127 optimal weight:    2.9990
   chunk 73 optimal weight:   30.0000
   chunk 56 optimal weight:   30.0000
   chunk 133 optimal weight:    0.0370
   chunk 32 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 60 optimal weight:   40.0000
   overall best weight:    1.5464

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

Flipped N/Q/H residues before XYZ refinement:
B 244 GLN
B 397 ASN
** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 696 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 = 0.4257 r_free = 0.4257 target = 0.168163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 106)---------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.148100 restraints weight = 20849.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.143494 restraints weight = 40880.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.143605 restraints weight = 40201.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
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      :  0.004   0.043   8915  Z= 0.199
  Angle     :  0.587   7.594  12250  Z= 0.311
  Chirality :  0.045   0.152   1497
  Planarity :  0.005   0.071   1689
  Dihedral  :  3.988  20.816   1460
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.97 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1406
  helix:  3.20 (0.22), residues: 562
  sheet: -1.70 (0.40), residues: 168
  loop : -2.59 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 191 
 HIS   0.004   0.001   HIS B 729 
 PHE   0.016   0.002   PHE B 580 
 TYR   0.017   0.002   TYR B 378 
 ARG   0.009   0.001   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03021 (  434)
  hydrogen bonds       : angle       3.89743 ( 1269)
  SS BOND              : bond        0.00609 (    1)
  SS BOND              : angle       0.85896 (    2)
  covalent geometry    : bond        0.00441 ( 8914)
  covalent geometry    : angle       0.58742 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: B  112 MET cc_start: 0.7428 (tpp) cc_final: 0.7223 (mtt)
REVERT: B  210 LYS cc_start: 0.7758 (pttp) cc_final: 0.7219 (tppt)
REVERT: B  466 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7726 (ttmm)
REVERT: B  565 GLU cc_start: 0.8068 (pp20) cc_final: 0.7857 (tm-30)
REVERT: B  675 ARG cc_start: 0.6819 (mmt90) cc_final: 0.6294 (mmt180)
REVERT: B  690 MET cc_start: 0.7665 (ptt) cc_final: 0.7459 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1786
  time to fit residues: 32.5544
Evaluate side-chains
  108 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 4 optimal weight:    0.1980
   chunk 51 optimal weight:   20.0000
   chunk 139 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 62 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 126 optimal weight:    0.4980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 696 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 = 0.4270 r_free = 0.4270 target = 0.169392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.156057 restraints weight = 20901.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.153075 restraints weight = 47095.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.150670 restraints weight = 42459.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8915  Z= 0.143
  Angle     :  0.543   6.523  12250  Z= 0.285
  Chirality :  0.044   0.158   1497
  Planarity :  0.004   0.072   1689
  Dihedral  :  3.892  20.130   1460
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.33 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1406
  helix:  3.19 (0.22), residues: 563
  sheet: -1.44 (0.42), residues: 158
  loop : -2.56 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 191 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.013   0.001   PHE B 221 
 TYR   0.014   0.001   TYR B 378 
 ARG   0.004   0.001   ARG B 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02766 (  434)
  hydrogen bonds       : angle       3.79156 ( 1269)
  SS BOND              : bond        0.00357 (    1)
  SS BOND              : angle       0.66656 (    2)
  covalent geometry    : bond        0.00313 ( 8914)
  covalent geometry    : angle       0.54287 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  412 MET cc_start: 0.8377 (mmm) cc_final: 0.8114 (mmp)
REVERT: B  466 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7791 (ttmm)
REVERT: B  547 ASP cc_start: 0.8091 (p0) cc_final: 0.7856 (p0)
REVERT: B  565 GLU cc_start: 0.7928 (pp20) cc_final: 0.7703 (pp20)
REVERT: B  627 TRP cc_start: 0.8791 (t-100) cc_final: 0.8544 (t-100)
REVERT: B  675 ARG cc_start: 0.6778 (mmt90) cc_final: 0.6337 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1830
  time to fit residues: 34.8080
Evaluate side-chains
  105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 94 optimal weight:    0.7980
   chunk 128 optimal weight:    0.1980
   chunk 19 optimal weight:   20.0000
   chunk 131 optimal weight:    0.3980
   chunk 118 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   chunk 22 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 42 optimal weight:   50.0000
   chunk 69 optimal weight:    5.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 696 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 = 0.4259 r_free = 0.4259 target = 0.168492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.155121 restraints weight = 21043.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.152444 restraints weight = 46558.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.150322 restraints weight = 38822.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8915  Z= 0.153
  Angle     :  0.569  10.904  12250  Z= 0.296
  Chirality :  0.044   0.177   1497
  Planarity :  0.004   0.076   1689
  Dihedral  :  3.915  21.753   1460
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.61 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1406
  helix:  3.24 (0.22), residues: 557
  sheet: -1.62 (0.40), residues: 169
  loop : -2.59 (0.22), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 191 
 HIS   0.002   0.001   HIS B 306 
 PHE   0.016   0.002   PHE B 540 
 TYR   0.027   0.001   TYR B 378 
 ARG   0.008   0.001   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02817 (  434)
  hydrogen bonds       : angle       3.75056 ( 1269)
  SS BOND              : bond        0.00454 (    1)
  SS BOND              : angle       0.73934 (    2)
  covalent geometry    : bond        0.00338 ( 8914)
  covalent geometry    : angle       0.56883 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.950 
Fit side-chains
REVERT: B  263 GLN cc_start: 0.8533 (mp10) cc_final: 0.8248 (mp10)
REVERT: B  466 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7866 (ttmm)
REVERT: B  547 ASP cc_start: 0.8125 (p0) cc_final: 0.7916 (p0)
REVERT: B  565 GLU cc_start: 0.7901 (pp20) cc_final: 0.7664 (pp20)
REVERT: B  627 TRP cc_start: 0.8835 (t-100) cc_final: 0.8576 (t-100)
REVERT: B  675 ARG cc_start: 0.6901 (mmt90) cc_final: 0.6639 (mmt180)
REVERT: B  690 MET cc_start: 0.7265 (ptt) cc_final: 0.6937 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1597
  time to fit residues: 29.5195
Evaluate side-chains
  102 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 113 optimal weight:    5.9990
   chunk 92 optimal weight:    0.2980
   chunk 59 optimal weight:    0.0980
   chunk 12 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 140 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 131 optimal weight:    0.0060
   chunk 62 optimal weight:    7.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    0.9998

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 696 ASN ** 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 = 0.4260 r_free = 0.4260 target = 0.168526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.152463 restraints weight = 21299.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.150776 restraints weight = 48707.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.151051 restraints weight = 46125.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8915  Z= 0.142
  Angle     :  0.571  10.969  12250  Z= 0.293
  Chirality :  0.043   0.167   1497
  Planarity :  0.004   0.074   1689
  Dihedral  :  3.912  21.913   1460
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.97 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1406
  helix:  3.25 (0.22), residues: 558
  sheet: -1.48 (0.43), residues: 144
  loop : -2.51 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 760 
 HIS   0.002   0.001   HIS B 306 
 PHE   0.021   0.001   PHE B 667 
 TYR   0.020   0.001   TYR B 725 
 ARG   0.006   0.000   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02727 (  434)
  hydrogen bonds       : angle       3.75304 ( 1269)
  SS BOND              : bond        0.00412 (    1)
  SS BOND              : angle       0.70643 (    2)
  covalent geometry    : bond        0.00313 ( 8914)
  covalent geometry    : angle       0.57081 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: B  466 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7871 (ttmm)
REVERT: B  547 ASP cc_start: 0.8175 (p0) cc_final: 0.7948 (p0)
REVERT: B  565 GLU cc_start: 0.7920 (pp20) cc_final: 0.7674 (pp20)
REVERT: B  627 TRP cc_start: 0.8873 (t-100) cc_final: 0.8607 (t-100)
REVERT: B  661 MET cc_start: 0.7534 (mmp) cc_final: 0.7314 (mmp)
REVERT: B  675 ARG cc_start: 0.6848 (mmt90) cc_final: 0.6289 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1693
  time to fit residues: 31.1259
Evaluate side-chains
  101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 139 optimal weight:    1.9990
   chunk 34 optimal weight:   20.0000
   chunk 138 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 124 optimal weight:    0.1980
   chunk 100 optimal weight:    0.6980
   chunk 21 optimal weight:   20.0000
   chunk 112 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.168204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 125)---------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.142898 restraints weight = 21264.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.136902 restraints weight = 27086.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.136755 restraints weight = 35096.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8915  Z= 0.134
  Angle     :  0.574   8.687  12250  Z= 0.295
  Chirality :  0.044   0.165   1497
  Planarity :  0.004   0.073   1689
  Dihedral  :  3.901  21.933   1460
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.18 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.24), residues: 1406
  helix:  3.24 (0.22), residues: 557
  sheet: -1.48 (0.42), residues: 153
  loop : -2.55 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 191 
 HIS   0.004   0.001   HIS B 177 
 PHE   0.015   0.002   PHE B 540 
 TYR   0.015   0.001   TYR B 725 
 ARG   0.006   0.000   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02743 (  434)
  hydrogen bonds       : angle       3.68184 ( 1269)
  SS BOND              : bond        0.00355 (    1)
  SS BOND              : angle       0.69235 (    2)
  covalent geometry    : bond        0.00299 ( 8914)
  covalent geometry    : angle       0.57424 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  395 SER cc_start: 0.8330 (m) cc_final: 0.7402 (m)
REVERT: B  466 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8074 (ttmm)
REVERT: B  547 ASP cc_start: 0.8574 (p0) cc_final: 0.8273 (p0)
REVERT: B  565 GLU cc_start: 0.8354 (pp20) cc_final: 0.8037 (pp20)
REVERT: B  627 TRP cc_start: 0.8998 (t-100) cc_final: 0.8659 (t-100)
REVERT: B  675 ARG cc_start: 0.7127 (mmt90) cc_final: 0.6396 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1527
  time to fit residues: 28.9179
Evaluate side-chains
  99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 125 optimal weight:    0.5980
   chunk 112 optimal weight:    0.3980
   chunk 76 optimal weight:    0.8980
   chunk 51 optimal weight:   20.0000
   chunk 139 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 168 ASN
** B 550 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 = 0.4264 r_free = 0.4264 target = 0.168822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.155320 restraints weight = 21165.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.152862 restraints weight = 45824.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.150590 restraints weight = 39386.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8915  Z= 0.111
  Angle     :  0.559   9.049  12250  Z= 0.285
  Chirality :  0.043   0.163   1497
  Planarity :  0.004   0.073   1689
  Dihedral  :  3.822  21.837   1460
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.33 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1406
  helix:  3.26 (0.22), residues: 558
  sheet: -1.46 (0.43), residues: 151
  loop : -2.53 (0.22), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B 760 
 HIS   0.002   0.001   HIS B 306 
 PHE   0.014   0.001   PHE B 221 
 TYR   0.017   0.001   TYR B 378 
 ARG   0.006   0.000   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02609 (  434)
  hydrogen bonds       : angle       3.64255 ( 1269)
  SS BOND              : bond        0.00308 (    1)
  SS BOND              : angle       0.55230 (    2)
  covalent geometry    : bond        0.00246 ( 8914)
  covalent geometry    : angle       0.55901 (12248)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.974 
Fit side-chains
REVERT: B  466 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7923 (ttmm)
REVERT: B  547 ASP cc_start: 0.8079 (p0) cc_final: 0.7872 (p0)
REVERT: B  565 GLU cc_start: 0.7899 (pp20) cc_final: 0.7678 (pp20)
REVERT: B  627 TRP cc_start: 0.8853 (t-100) cc_final: 0.8626 (t-100)
REVERT: B  675 ARG cc_start: 0.6704 (mmt90) cc_final: 0.6298 (mmt180)
REVERT: B  690 MET cc_start: 0.7557 (ptt) cc_final: 0.7277 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1609
  time to fit residues: 29.8892
Evaluate side-chains
  98 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 123 optimal weight:    0.0970
   chunk 94 optimal weight:    0.4980
   chunk 65 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 110 optimal weight:    0.0370
   chunk 97 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0980
   chunk 31 optimal weight:   50.0000
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
B 381 GLN
** B 550 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 = 0.4263 r_free = 0.4263 target = 0.168729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.155243 restraints weight = 21186.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.153963 restraints weight = 43667.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.150881 restraints weight = 39122.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8915  Z= 0.116
  Angle     :  0.563  10.563  12250  Z= 0.286
  Chirality :  0.043   0.173   1497
  Planarity :  0.004   0.073   1689
  Dihedral  :  3.800  24.083   1460
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.54 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1406
  helix:  3.26 (0.22), residues: 558
  sheet: -1.54 (0.40), residues: 170
  loop : -2.56 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B 760 
 HIS   0.002   0.001   HIS B 177 
 PHE   0.015   0.001   PHE B 221 
 TYR   0.012   0.001   TYR B 725 
 ARG   0.006   0.000   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02594 (  434)
  hydrogen bonds       : angle       3.59362 ( 1269)
  SS BOND              : bond        0.00332 (    1)
  SS BOND              : angle       0.50668 (    2)
  covalent geometry    : bond        0.00258 ( 8914)
  covalent geometry    : angle       0.56315 (12248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2940.20 seconds
wall clock time: 51 minutes 24.99 seconds (3084.99 seconds total)