Starting phenix.real_space_refine
on Wed Sep 25 21:21:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/09_2024/8toi_41453.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/09_2024/8toi_41453.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/09_2024/8toi_41453.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/09_2024/8toi_41453.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/09_2024/8toi_41453.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/09_2024/8toi_41453.cif"
  }
  resolution = 2.64
  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=   0.057 sd=   0.508
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: 6
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     P      34      5.49       5
     S      40      5.16       5
     C    7502      2.51       5
     N    1724      2.21       5
     O    2110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 11414
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 649, 5160
          Classifications: {'peptide': 649}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 28, 'TRANS': 620}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "A"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 547
          Unusual residues: {' CA': 2, 'PGW': 18}
          Classifications: {'undetermined': 20}
          Link IDs: {None: 19}
          Unresolved non-hydrogen bonds: 373
          Unresolved non-hydrogen angles: 394
          Unresolved non-hydrogen dihedrals: 425
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'PGW:plan-3': 9}
          Unresolved non-hydrogen planarities: 27
  Restraints were copied for chains:
    B
  Time building chain proxies: 11.30, per 1000 atoms: 0.99
  Number of scatterers: 11414
  At special positions: 0
  Unit cell: (91.575, 137.775, 106.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      4     19.99
     S      40     16.00
     P      34     15.00
     O    2110      8.00
     N    1724      7.00
     C    7502      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: 2.56
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2460

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      73.3% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 47
      removed outlier: 3.644A  pdb=" N   GLY A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.618A  pdb=" N   PHE A  76 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.833A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN A 106 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 126 through 130
      removed outlier: 3.552A  pdb=" N   GLU A 129 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 165
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.813A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 199
      removed outlier: 3.549A  pdb=" N   ALA A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 246
    Processing helix  chain 'A' and resid 250 through 254
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.578A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 320
    Processing helix  chain 'A' and resid 330 through 358
      Proline residue:  A 341  - end of helix
    Processing helix  chain 'A' and resid 362 through 392
      removed outlier: 6.230A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.627A  pdb=" N   LEU A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   THR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 3.793A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR A 443 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE A 449 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU A 452 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 477 through 481
      removed outlier: 3.584A  pdb=" N   GLU A 480 " --> pdb=" O   GLU A 477 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLU A 481 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 477 through 481'
    Processing helix  chain 'A' and resid 482 through 493
    Processing helix  chain 'A' and resid 499 through 518
      removed outlier: 4.318A  pdb=" N   ASP A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 545
      removed outlier: 3.987A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.705A  pdb=" N   GLY A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER A 584 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASN A 585 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 625
      removed outlier: 3.506A  pdb=" N   LEU A 602 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 642
    Processing helix  chain 'A' and resid 667 through 685
    Processing helix  chain 'A' and resid 689 through 694
    Processing helix  chain 'A' and resid 701 through 716
      removed outlier: 3.653A  pdb=" N   ILE A 705 " --> pdb=" O   MET A 701 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 716 " --> pdb=" O   ILE A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 47
      removed outlier: 3.644A  pdb=" N   GLY B  39 " --> pdb=" O   GLU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.618A  pdb=" N   PHE B  76 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 107
      removed outlier: 3.834A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN B 106 " --> pdb=" O   GLN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 126 through 130
      removed outlier: 3.552A  pdb=" N   GLU B 129 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 165
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.813A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 199
      removed outlier: 3.549A  pdb=" N   ALA B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 246
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.578A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 320
    Processing helix  chain 'B' and resid 330 through 358
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 362 through 392
      removed outlier: 6.230A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 413
      removed outlier: 3.627A  pdb=" N   LEU B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   THR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 3.793A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR B 443 " --> pdb=" O   TYR B 439 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU B 452 " --> pdb=" O   ASN B 448 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 466
    Processing helix  chain 'B' and resid 477 through 481
      removed outlier: 3.584A  pdb=" N   GLU B 480 " --> pdb=" O   GLU B 477 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLU B 481 " --> pdb=" O   ASP B 478 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 477 through 481'
    Processing helix  chain 'B' and resid 482 through 493
    Processing helix  chain 'B' and resid 499 through 518
      removed outlier: 4.317A  pdb=" N   ASP B 503 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 545
      removed outlier: 3.986A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.705A  pdb=" N   GLY B 572 " --> pdb=" O   LEU B 568 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA B 578 " --> pdb=" O   ILE B 574 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER B 584 " --> pdb=" O   VAL B 580 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASN B 585 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 625
      removed outlier: 3.506A  pdb=" N   LEU B 602 " --> pdb=" O   LYS B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 642
    Processing helix  chain 'B' and resid 667 through 685
    Processing helix  chain 'B' and resid 689 through 694
    Processing helix  chain 'B' and resid 701 through 716
      removed outlier: 3.653A  pdb=" N   ILE B 705 " --> pdb=" O   MET B 701 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B 716 " --> pdb=" O   ILE B 712 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268
      removed outlier: 3.784A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268
      removed outlier: 3.784A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)

    694 hydrogen bonds defined for protein.
    2046 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.39

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1722
        1.31 -     1.44: 3226
        1.44 -     1.57: 6564
        1.57 -     1.70: 68
        1.70 -     1.83: 66
  Bond restraints: 11646
  Sorted by residual:
  bond pdb=" C1  PGW A 820 "
       pdb=" O01 PGW A 820 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" C1  PGW A 809 "
       pdb=" O01 PGW A 809 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" C1  PGW B 820 "
       pdb=" O01 PGW B 820 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C1  PGW B 809 "
       pdb=" O01 PGW B 809 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C1  PGW A 817 "
       pdb=" O01 PGW A 817 "
    ideal  model  delta    sigma   weight residual
    1.332  1.427 -0.095 2.00e-02 2.50e+03 2.24e+01
  ... (remaining 11641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.90: 15536
        9.90 -    19.80: 78
       19.80 -    29.70: 2
       29.70 -    39.60: 0
       39.60 -    49.50: 6
  Bond angle restraints: 15622
  Sorted by residual:
  angle pdb=" C2  PGW A 805 "
        pdb=" C1  PGW A 805 "
        pdb=" O01 PGW A 805 "
      ideal   model   delta    sigma   weight residual
     110.92  160.42  -49.50 3.00e+00 1.11e-01 2.72e+02
  angle pdb=" C2  PGW B 805 "
        pdb=" C1  PGW B 805 "
        pdb=" O01 PGW B 805 "
      ideal   model   delta    sigma   weight residual
     110.92  160.38  -49.46 3.00e+00 1.11e-01 2.72e+02
  angle pdb=" C2  PGW B 805 "
        pdb=" C1  PGW B 805 "
        pdb=" O02 PGW B 805 "
      ideal   model   delta    sigma   weight residual
     125.44   80.14   45.30 3.00e+00 1.11e-01 2.28e+02
  angle pdb=" C2  PGW A 805 "
        pdb=" C1  PGW A 805 "
        pdb=" O02 PGW A 805 "
      ideal   model   delta    sigma   weight residual
     125.44   80.21   45.23 3.00e+00 1.11e-01 2.27e+02
  angle pdb=" O01 PGW A 805 "
        pdb=" C1  PGW A 805 "
        pdb=" O02 PGW A 805 "
      ideal   model   delta    sigma   weight residual
     123.63   80.21   43.42 3.00e+00 1.11e-01 2.09e+02
  ... (remaining 15617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.20: 6550
       33.20 -    66.41: 400
       66.41 -    99.61: 58
       99.61 -   132.82: 20
      132.82 -   166.02: 28
  Dihedral angle restraints: 7056
    sinusoidal: 3268
      harmonic: 3788
  Sorted by residual:
  dihedral pdb=" CA  ILE A 101 "
           pdb=" C   ILE A 101 "
           pdb=" N   ALA A 102 "
           pdb=" CA  ALA A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.57  -23.43     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  ILE B 101 "
           pdb=" C   ILE B 101 "
           pdb=" N   ALA B 102 "
           pdb=" CA  ALA B 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.58  -23.42     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" O01 PGW B 815 "
           pdb=" C01 PGW B 815 "
           pdb=" C02 PGW B 815 "
           pdb=" O03 PGW B 815 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.30 -106.72  166.02     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 7053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1242
       0.054 -    0.109: 292
       0.109 -    0.163: 74
       0.163 -    0.217: 20
       0.217 -    0.272: 4
  Chirality restraints: 1632
  Sorted by residual:
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  THR B 340 "
            pdb=" N   THR B 340 "
            pdb=" C   THR B 340 "
            pdb=" CB  THR B 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL B 111 "
            pdb=" CA  VAL B 111 "
            pdb=" CG1 VAL B 111 "
            pdb=" CG2 VAL B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1629 not shown)

  Planarity restraints: 1914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 396 "    0.014 2.00e-02 2.50e+03   1.86e-02 6.03e+00
        pdb=" CG  PHE B 396 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 396 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 396 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 396 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 396 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 396 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 396 "   -0.014 2.00e-02 2.50e+03   1.85e-02 5.98e+00
        pdb=" CG  PHE A 396 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 396 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 396 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 396 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 396 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 396 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 134 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.65e+00
        pdb=" C   VAL B 134 "    0.041 2.00e-02 2.50e+03
        pdb=" O   VAL B 134 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   THR B 135 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1911 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 3412
        2.83 -     3.35: 10087
        3.35 -     3.87: 18858
        3.87 -     4.38: 21109
        4.38 -     4.90: 36789
  Nonbonded interactions: 90255
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 188 "
            pdb=" OD2 ASP A 539 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OH  TYR B 188 "
            pdb=" OD2 ASP B 539 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   TRP B 570 "
            pdb=" OG  SER B 573 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   TRP A 570 "
            pdb=" OG  SER A 573 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OE2 GLU B 358 "
            pdb=" OH  TYR B 360 "
     model   vdw
     2.360 3.040
  ... (remaining 90250 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.580
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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      :  0.010   0.096  11646  Z= 0.575
  Angle     :  1.856  49.496  15622  Z= 0.718
  Chirality :  0.054   0.272   1632
  Planarity :  0.006   0.053   1914
  Dihedral  : 24.382 166.024   4596
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.20), residues: 1274
  helix: -0.55 (0.15), residues: 888
  sheet: -1.94 (0.77), residues: 44
  loop : -1.97 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 141 
 HIS   0.004   0.001   HIS B 366 
 PHE   0.043   0.002   PHE B 396 
 TYR   0.017   0.002   TYR B 457 
 ARG   0.003   0.000   ARG B 537 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.124 
Fit side-chains
REVERT: A  320 TYR cc_start: 0.8068 (t80) cc_final: 0.7754 (t80)
REVERT: B   55 GLU cc_start: 0.7866 (tp30) cc_final: 0.7066 (mm-30)
REVERT: B  320 TYR cc_start: 0.8143 (t80) cc_final: 0.7800 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 1.2902
  time to fit residues: 230.8338
Evaluate side-chains
  131 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 116 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 153 HIS
A 265 HIS
A 310 ASN
A 366 HIS
A 696 GLN
A 698 GLN
B  79 GLN
B 153 HIS
B 265 HIS
B 310 ASN
B 366 HIS
B 696 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11646  Z= 0.197
  Angle     :  1.070  46.300  15622  Z= 0.417
  Chirality :  0.040   0.159   1632
  Planarity :  0.004   0.044   1914
  Dihedral  : 26.313 160.955   2250
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.33 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.23), residues: 1274
  helix:  1.09 (0.17), residues: 892
  sheet: -1.55 (0.81), residues: 44
  loop : -1.65 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 479 
 PHE   0.022   0.001   PHE A 406 
 TYR   0.013   0.001   TYR A 188 
 ARG   0.003   0.000   ARG A 697 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 1.125 
Fit side-chains
  outliers start: 17
  outliers final: 6
  residues processed: 138
  average time/residue: 1.1147
  time to fit residues: 167.9955
Evaluate side-chains
  135 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 129
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  282 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 116 optimal weight:    0.0470
   chunk 125 optimal weight:   20.0000
   chunk 103 optimal weight:    6.9990
   chunk 115 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.8086

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

Flipped N/Q/H residues before XYZ refinement:
A  25 HIS
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
A 510 GLN
A 531 ASN
A 696 GLN
B  25 HIS
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN
B 531 ASN
B 641 GLN
B 696 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  11646  Z= 0.321
  Angle     :  1.078  46.190  15622  Z= 0.425
  Chirality :  0.042   0.162   1632
  Planarity :  0.004   0.036   1914
  Dihedral  : 24.873 163.048   2250
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.66 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.23), residues: 1274
  helix:  1.58 (0.17), residues: 902
  sheet: -1.11 (0.88), residues: 44
  loop : -1.64 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 235 
 HIS   0.005   0.001   HIS A 611 
 PHE   0.012   0.001   PHE A 396 
 TYR   0.018   0.002   TYR B  26 
 ARG   0.006   0.000   ARG B 697 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 1.193 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7449 (tm-30)
REVERT: A  400 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6801 (pp)
REVERT: B   33 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8162 (ttp80)
REVERT: B  400 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6863 (pp)
  outliers start: 33
  outliers final: 5
  residues processed: 154
  average time/residue: 1.1192
  time to fit residues: 187.8379
Evaluate side-chains
  137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  627 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 60 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 116 optimal weight:    0.7980
   chunk 123 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 110 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 641 GLN
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11646  Z= 0.276
  Angle     :  1.063  46.222  15622  Z= 0.416
  Chirality :  0.042   0.158   1632
  Planarity :  0.004   0.038   1914
  Dihedral  : 23.816 165.429   2250
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 12.97 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.24), residues: 1274
  helix:  1.87 (0.17), residues: 892
  sheet: -1.05 (0.88), residues: 44
  loop : -1.58 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 153 
 PHE   0.026   0.001   PHE B 406 
 TYR   0.017   0.002   TYR B  26 
 ARG   0.004   0.000   ARG A 697 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 1.234 
Fit side-chains
REVERT: A  320 TYR cc_start: 0.8076 (t80) cc_final: 0.7873 (t80)
REVERT: B  320 TYR cc_start: 0.8028 (t80) cc_final: 0.7822 (t80)
REVERT: B  325 LYS cc_start: 0.8615 (tppt) cc_final: 0.8374 (tppt)
  outliers start: 33
  outliers final: 6
  residues processed: 146
  average time/residue: 1.1357
  time to fit residues: 181.0520
Evaluate side-chains
  133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain B residue  282 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 0 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 111 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
A 696 GLN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
B 479 HIS
B 696 GLN
B 715 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11646  Z= 0.218
  Angle     :  1.062  46.232  15622  Z= 0.411
  Chirality :  0.041   0.153   1632
  Planarity :  0.004   0.034   1914
  Dihedral  : 22.937 166.359   2250
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.53 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.24), residues: 1274
  helix:  1.94 (0.17), residues: 908
  sheet: -1.05 (0.88), residues: 44
  loop : -1.50 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 141 
 HIS   0.003   0.001   HIS B 366 
 PHE   0.011   0.001   PHE A 406 
 TYR   0.017   0.001   TYR A  26 
 ARG   0.004   0.000   ARG A 697 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 1.176 
Fit side-chains
REVERT: A  320 TYR cc_start: 0.8033 (t80) cc_final: 0.7824 (t80)
REVERT: A  484 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7398 (tm-30)
REVERT: B  320 TYR cc_start: 0.7864 (t80) cc_final: 0.7613 (t80)
REVERT: B  325 LYS cc_start: 0.8604 (tppt) cc_final: 0.8344 (tppt)
  outliers start: 33
  outliers final: 9
  residues processed: 143
  average time/residue: 1.2138
  time to fit residues: 188.4927
Evaluate side-chains
  137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 123 optimal weight:   10.0000
   chunk 102 optimal weight:    0.0370
   chunk 57 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.9460

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 HIS
A 696 GLN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 HIS
B 696 GLN
** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11646  Z= 0.207
  Angle     :  1.062  46.195  15622  Z= 0.410
  Chirality :  0.040   0.153   1632
  Planarity :  0.004   0.036   1914
  Dihedral  : 22.270 166.472   2250
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.30 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1274
  helix:  2.04 (0.17), residues: 910
  sheet: -0.98 (0.88), residues: 44
  loop : -1.35 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A 366 
 PHE   0.030   0.001   PHE B 406 
 TYR   0.016   0.001   TYR A  26 
 ARG   0.004   0.000   ARG B  33 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 1.398 
Fit side-chains
REVERT: A  282 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7817 (tpp)
REVERT: A  320 TYR cc_start: 0.8074 (t80) cc_final: 0.7835 (t80)
REVERT: B  282 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7832 (tpp)
REVERT: B  320 TYR cc_start: 0.8000 (t80) cc_final: 0.7645 (t80)
REVERT: B  325 LYS cc_start: 0.8542 (tppt) cc_final: 0.8280 (tppt)
REVERT: B  701 MET cc_start: 0.7967 (tpp) cc_final: 0.7641 (tpt)
  outliers start: 26
  outliers final: 9
  residues processed: 145
  average time/residue: 1.1285
  time to fit residues: 178.6499
Evaluate side-chains
  142 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  357 MET
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 119 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0020
   chunk 70 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0270
   chunk 104 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 123 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.5448

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 GLN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 GLN
B 698 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11646  Z= 0.169
  Angle     :  1.058  46.278  15622  Z= 0.407
  Chirality :  0.040   0.149   1632
  Planarity :  0.003   0.033   1914
  Dihedral  : 21.574 166.699   2250
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.95 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.24), residues: 1274
  helix:  2.12 (0.17), residues: 910
  sheet: -0.90 (0.87), residues: 48
  loop : -1.25 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 141 
 HIS   0.002   0.000   HIS B 366 
 PHE   0.031   0.001   PHE A 406 
 TYR   0.014   0.001   TYR A 188 
 ARG   0.003   0.000   ARG B  33 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 1.148 
Fit side-chains
REVERT: A  282 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7771 (tpp)
REVERT: A  320 TYR cc_start: 0.7942 (t80) cc_final: 0.7699 (t80)
REVERT: A  437 MET cc_start: 0.8714 (tpt) cc_final: 0.8092 (tpt)
REVERT: A  546 SER cc_start: 0.8639 (t) cc_final: 0.8293 (t)
REVERT: B  282 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7807 (tpp)
REVERT: B  320 TYR cc_start: 0.7983 (t80) cc_final: 0.7566 (t80)
REVERT: B  325 LYS cc_start: 0.8441 (tppt) cc_final: 0.8167 (tppt)
  outliers start: 21
  outliers final: 4
  residues processed: 142
  average time/residue: 1.1380
  time to fit residues: 176.1497
Evaluate side-chains
  134 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0270
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 60 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.8240

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
B 696 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11646  Z= 0.191
  Angle     :  1.060  46.207  15622  Z= 0.409
  Chirality :  0.040   0.152   1632
  Planarity :  0.003   0.034   1914
  Dihedral  : 20.946 165.943   2250
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.07 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.24), residues: 1274
  helix:  2.18 (0.17), residues: 910
  sheet: -0.93 (0.87), residues: 48
  loop : -1.18 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 366 
 PHE   0.033   0.001   PHE B 406 
 TYR   0.014   0.001   TYR A 188 
 ARG   0.003   0.000   ARG B  33 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.201 
Fit side-chains
REVERT: A  320 TYR cc_start: 0.8103 (t80) cc_final: 0.7850 (t80)
REVERT: A  437 MET cc_start: 0.8725 (tpt) cc_final: 0.8084 (tpt)
REVERT: A  546 SER cc_start: 0.8655 (t) cc_final: 0.8311 (t)
REVERT: B  282 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7825 (tpp)
REVERT: B  320 TYR cc_start: 0.8036 (t80) cc_final: 0.7667 (t80)
  outliers start: 19
  outliers final: 4
  residues processed: 138
  average time/residue: 1.1004
  time to fit residues: 166.2852
Evaluate side-chains
  133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 118 optimal weight:    0.0870
   chunk 107 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 108 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 121 optimal weight:    1.9990
   overall best weight:    0.9760

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 GLN
B 317 ASN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11646  Z= 0.215
  Angle     :  1.075  46.178  15622  Z= 0.417
  Chirality :  0.041   0.151   1632
  Planarity :  0.004   0.034   1914
  Dihedral  : 20.532 165.450   2250
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.91 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.24), residues: 1274
  helix:  2.25 (0.17), residues: 898
  sheet: -0.90 (0.86), residues: 48
  loop : -1.28 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.034   0.001   PHE A 406 
 TYR   0.014   0.001   TYR B  26 
 ARG   0.004   0.000   ARG B  33 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 1.219 
Fit side-chains
REVERT: A  282 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7804 (tpp)
REVERT: A  320 TYR cc_start: 0.8150 (t80) cc_final: 0.7854 (t80)
REVERT: A  437 MET cc_start: 0.8735 (tpt) cc_final: 0.8089 (tpt)
REVERT: B  282 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7835 (tpp)
REVERT: B  320 TYR cc_start: 0.8195 (t80) cc_final: 0.7890 (t80)
REVERT: B  701 MET cc_start: 0.7955 (tpp) cc_final: 0.7539 (tpt)
  outliers start: 13
  outliers final: 5
  residues processed: 131
  average time/residue: 1.1269
  time to fit residues: 161.2879
Evaluate side-chains
  136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
B 696 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11646  Z= 0.262
  Angle     :  1.087  46.174  15622  Z= 0.426
  Chirality :  0.042   0.153   1632
  Planarity :  0.004   0.034   1914
  Dihedral  : 20.242 164.531   2250
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.54 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.24), residues: 1274
  helix:  2.21 (0.17), residues: 898
  sheet: -0.87 (0.86), residues: 48
  loop : -1.29 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 141 
 HIS   0.004   0.001   HIS B  25 
 PHE   0.037   0.001   PHE B 406 
 TYR   0.015   0.002   TYR B 457 
 ARG   0.004   0.000   ARG A  33 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.233 
Fit side-chains
REVERT: A  320 TYR cc_start: 0.8225 (t80) cc_final: 0.7861 (t80)
REVERT: A  437 MET cc_start: 0.8742 (tpt) cc_final: 0.8087 (tpt)
REVERT: B  282 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7842 (tpp)
REVERT: B  320 TYR cc_start: 0.8120 (t80) cc_final: 0.7813 (t80)
REVERT: B  701 MET cc_start: 0.8022 (tpp) cc_final: 0.7619 (tpt)
  outliers start: 15
  outliers final: 4
  residues processed: 135
  average time/residue: 1.1746
  time to fit residues: 172.5733
Evaluate side-chains
  134 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 ASN
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 ASN
B 696 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.127782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.091344 restraints weight = 16130.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.98
r_work: 0.3090 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11646  Z= 0.195
  Angle     :  1.074  46.208  15622  Z= 0.418
  Chirality :  0.041   0.150   1632
  Planarity :  0.003   0.035   1914
  Dihedral  : 19.762 164.422   2250
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.82 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.24), residues: 1274
  helix:  2.18 (0.17), residues: 910
  sheet: -0.80 (0.87), residues: 48
  loop : -1.15 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.039   0.001   PHE A 406 
 TYR   0.014   0.001   TYR B 457 
 ARG   0.004   0.000   ARG A  33 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3917.93 seconds
wall clock time: 69 minutes 39.93 seconds (4179.93 seconds total)