Starting phenix.real_space_refine
on Fri Jan 17 14:42:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xng_38503/01_2025/8xng_38503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xng_38503/01_2025/8xng_38503.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xng_38503/01_2025/8xng_38503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xng_38503/01_2025/8xng_38503.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xng_38503/01_2025/8xng_38503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xng_38503/01_2025/8xng_38503.cif"
  }
  resolution = 3.56
  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=   0.012 sd=   0.063
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    7240      2.51       5
     N    1774      2.21       5
     O    1858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10922
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5461
          Classifications: {'peptide': 683}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 36, 'TRANS': 646}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 10.41, per 1000 atoms: 0.95
  Number of scatterers: 10922
  At special positions: 0
  Unit cell: (89.675, 140.315, 108.665, 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      50     16.00
     O    1858      8.00
     N    1774      7.00
     C    7240      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: 2.92
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2624

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 2 sheets defined
      72.5% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
      removed outlier: 3.699A  pdb=" N   ILE A   7 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
      removed outlier: 3.836A  pdb=" N   TYR A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.863A  pdb=" N   GLU A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 92 through 120
      removed outlier: 4.536A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 121 through 124
      removed outlier: 3.721A  pdb=" N   ASN A 124 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 121 through 124'
    Processing helix  chain 'A' and resid 155 through 195
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 314
    Processing helix  chain 'A' and resid 315 through 319
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 389 through 398
      removed outlier: 3.510A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 408 through 413
    Processing helix  chain 'A' and resid 420 through 437
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 440 through 453
    Processing helix  chain 'A' and resid 456 through 475
    Processing helix  chain 'A' and resid 477 through 488
      removed outlier: 3.907A  pdb=" N   GLU A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 494
      removed outlier: 4.406A  pdb=" N   SER A 492 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 494 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 507
    Processing helix  chain 'A' and resid 508 through 523
      removed outlier: 3.651A  pdb=" N   LYS A 512 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 534
    Processing helix  chain 'A' and resid 534 through 547
      removed outlier: 3.611A  pdb=" N   LEU A 538 " --> pdb=" O   MET A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 583
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 587 through 589
      No H-bonds generated for 'chain 'A' and resid 587 through 589'
    Processing helix  chain 'A' and resid 590 through 612
      removed outlier: 3.569A  pdb=" N   ILE A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 647
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 659 through 677
      removed outlier: 4.031A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
      removed outlier: 3.982A  pdb=" N   ALA A 688 " --> pdb=" O   PRO A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 4.162A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 31
      removed outlier: 3.586A  pdb=" N   GLN B  31 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.836A  pdb=" N   TYR B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.861A  pdb=" N   GLU B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 92 through 120
      removed outlier: 4.535A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 121 through 124
      removed outlier: 3.720A  pdb=" N   ASN B 124 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 121 through 124'
    Processing helix  chain 'B' and resid 155 through 195
    Processing helix  chain 'B' and resid 216 through 229
    Processing helix  chain 'B' and resid 242 through 269
    Processing helix  chain 'B' and resid 290 through 314
    Processing helix  chain 'B' and resid 315 through 319
    Processing helix  chain 'B' and resid 329 through 338
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 389
    Processing helix  chain 'B' and resid 389 through 398
      removed outlier: 3.510A  pdb=" N   ILE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 407
      No H-bonds generated for 'chain 'B' and resid 405 through 407'
    Processing helix  chain 'B' and resid 408 through 413
    Processing helix  chain 'B' and resid 420 through 437
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 440 through 453
    Processing helix  chain 'B' and resid 456 through 475
    Processing helix  chain 'B' and resid 477 through 488
      removed outlier: 3.907A  pdb=" N   GLU B 488 " --> pdb=" O   GLY B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 494
      removed outlier: 4.406A  pdb=" N   SER B 492 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU B 494 " --> pdb=" O   LEU B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 507
    Processing helix  chain 'B' and resid 508 through 523
      removed outlier: 3.651A  pdb=" N   LYS B 512 " --> pdb=" O   ALA B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 534
    Processing helix  chain 'B' and resid 534 through 547
      removed outlier: 3.611A  pdb=" N   LEU B 538 " --> pdb=" O   MET B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 565 through 583
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 587 through 589
      No H-bonds generated for 'chain 'B' and resid 587 through 589'
    Processing helix  chain 'B' and resid 590 through 612
      removed outlier: 3.569A  pdb=" N   ILE B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 647
    Processing helix  chain 'B' and resid 654 through 659
    Processing helix  chain 'B' and resid 659 through 677
      removed outlier: 4.031A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 684 through 699
      removed outlier: 3.982A  pdb=" N   ALA B 688 " --> pdb=" O   PRO B 684 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 4.162A  pdb=" N   ASN B 710 " --> pdb=" O   GLY B 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 238
      removed outlier: 3.628A  pdb=" N   ALA A 323 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 238
      removed outlier: 3.629A  pdb=" N   ALA B 323 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL B 206 " --> pdb=" O   ALA B 323 " (cutoff:3.500A)

    682 hydrogen bonds defined for protein.
    2016 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: 3.41

  Time building geometry restraints manager: 3.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3302
        1.34 -     1.45: 1831
        1.45 -     1.57: 6001
        1.57 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 11226
  Sorted by residual:
  bond pdb=" CB  TRP A 348 "
       pdb=" CG  TRP A 348 "
    ideal  model  delta    sigma   weight residual
    1.498  1.424  0.074 3.10e-02 1.04e+03 5.67e+00
  bond pdb=" CB  TRP B 348 "
       pdb=" CG  TRP B 348 "
    ideal  model  delta    sigma   weight residual
    1.498  1.424  0.074 3.10e-02 1.04e+03 5.66e+00
  bond pdb=" CA  GLU B 618 "
       pdb=" CB  GLU B 618 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.028 1.46e-02 4.69e+03 3.79e+00
  bond pdb=" CA  GLU A 618 "
       pdb=" CB  GLU A 618 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.028 1.46e-02 4.69e+03 3.72e+00
  bond pdb=" CG1 ILE A 108 "
       pdb=" CD1 ILE A 108 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.02e+00
  ... (remaining 11221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 14628
        1.96 -     3.92: 528
        3.92 -     5.89: 87
        5.89 -     7.85: 17
        7.85 -     9.81: 6
  Bond angle restraints: 15266
  Sorted by residual:
  angle pdb=" C   ALA B 133 "
        pdb=" N   LYS B 134 "
        pdb=" CA  LYS B 134 "
      ideal   model   delta    sigma   weight residual
     122.23  127.88   -5.65 1.48e+00 4.57e-01 1.46e+01
  angle pdb=" C   ALA A 133 "
        pdb=" N   LYS A 134 "
        pdb=" CA  LYS A 134 "
      ideal   model   delta    sigma   weight residual
     122.23  127.83   -5.60 1.48e+00 4.57e-01 1.43e+01
  angle pdb=" C   ALA A 118 "
        pdb=" N   VAL A 119 "
        pdb=" CA  VAL A 119 "
      ideal   model   delta    sigma   weight residual
     122.66  119.22    3.44 9.70e-01 1.06e+00 1.26e+01
  angle pdb=" C   ALA B 118 "
        pdb=" N   VAL B 119 "
        pdb=" CA  VAL B 119 "
      ideal   model   delta    sigma   weight residual
     122.66  119.27    3.39 9.70e-01 1.06e+00 1.22e+01
  angle pdb=" N   PHE A 420 "
        pdb=" CA  PHE A 420 "
        pdb=" C   PHE A 420 "
      ideal   model   delta    sigma   weight residual
     113.18  108.75    4.43 1.33e+00 5.65e-01 1.11e+01
  ... (remaining 15261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 5915
       17.28 -    34.56: 585
       34.56 -    51.85: 94
       51.85 -    69.13: 10
       69.13 -    86.41: 16
  Dihedral angle restraints: 6620
    sinusoidal: 2584
      harmonic: 4036
  Sorted by residual:
  dihedral pdb=" CA  ILE A 152 "
           pdb=" C   ILE A 152 "
           pdb=" N   PRO A 153 "
           pdb=" CA  PRO A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.32  -38.68     0      5.00e+00 4.00e-02 5.98e+01
  dihedral pdb=" CA  ILE B 152 "
           pdb=" C   ILE B 152 "
           pdb=" N   PRO B 153 "
           pdb=" CA  PRO B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.35  -38.65     0      5.00e+00 4.00e-02 5.97e+01
  dihedral pdb=" CA  ASN A 475 "
           pdb=" C   ASN A 475 "
           pdb=" N   VAL A 476 "
           pdb=" CA  VAL A 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.32  -22.68     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 6617 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1131
       0.046 -    0.092: 447
       0.092 -    0.137: 135
       0.137 -    0.183: 11
       0.183 -    0.229: 6
  Chirality restraints: 1730
  Sorted by residual:
  chirality pdb=" CB  VAL A 476 "
            pdb=" CA  VAL A 476 "
            pdb=" CG1 VAL A 476 "
            pdb=" CG2 VAL A 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  VAL B 476 "
            pdb=" CA  VAL B 476 "
            pdb=" CG1 VAL B 476 "
            pdb=" CG2 VAL B 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CG  LEU A 579 "
            pdb=" CB  LEU A 579 "
            pdb=" CD1 LEU A 579 "
            pdb=" CD2 LEU A 579 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1727 not shown)

  Planarity restraints: 1900
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 348 "   -0.037 2.00e-02 2.50e+03   3.73e-02 3.47e+01
        pdb=" CG  TRP A 348 "    0.095 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 348 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 348 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 348 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 348 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 348 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 348 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 348 "   -0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 348 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 348 "    0.037 2.00e-02 2.50e+03   3.72e-02 3.46e+01
        pdb=" CG  TRP B 348 "   -0.095 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 348 "    0.055 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 348 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 348 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 348 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 348 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 348 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 348 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 348 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  31 "   -0.046 5.00e-02 4.00e+02   6.92e-02 7.66e+00
        pdb=" N   PRO B  32 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1897 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 359
        2.70 -     3.25: 12431
        3.25 -     3.80: 18229
        3.80 -     4.35: 21566
        4.35 -     4.90: 35605
  Nonbonded interactions: 88190
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 303 "
            pdb=" OG  SER B 306 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   LYS A 303 "
            pdb=" OG  SER A 306 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   GLN A 135 "
            pdb=" ND2 ASN A 138 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" O   GLN B 135 "
            pdb=" ND2 ASN B 138 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" O   PHE B 454 "
            pdb=" OG1 THR B 455 "
     model   vdw
     2.194 3.040
  ... (remaining 88185 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: 0.06
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     30.040
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
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      :  0.008   0.074  11226  Z= 0.493
  Angle     :  0.892   9.810  15266  Z= 0.484
  Chirality :  0.052   0.229   1730
  Planarity :  0.006   0.069   1900
  Dihedral  : 14.281  86.411   3996
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -1.58 (0.22), residues: 1350
  helix:  0.08 (0.16), residues: 894
  sheet: -2.64 (0.82), residues: 46
  loop : -3.39 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.095   0.004   TRP A 348 
 HIS   0.005   0.001   HIS B 379 
 PHE   0.037   0.002   PHE B 224 
 TYR   0.030   0.003   TYR B 468 
 ARG   0.011   0.001   ARG B 682 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.6373 (mtt180) cc_final: 0.4964 (mtt90)
REVERT: A  180 GLU cc_start: 0.7247 (tp30) cc_final: 0.6926 (tp30)
REVERT: A  260 ASP cc_start: 0.8798 (m-30) cc_final: 0.8583 (m-30)
REVERT: A  303 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8075 (ptmt)
REVERT: A  448 MET cc_start: 0.7717 (ttm) cc_final: 0.7340 (ttm)
REVERT: A  521 MET cc_start: 0.8320 (tpp) cc_final: 0.8096 (mmm)
REVERT: A  589 MET cc_start: 0.8289 (tmm) cc_final: 0.8062 (tmm)
REVERT: B  253 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8913 (tptt)
REVERT: B  303 LYS cc_start: 0.8414 (ptpp) cc_final: 0.8118 (ptmt)
REVERT: B  589 MET cc_start: 0.8255 (tmm) cc_final: 0.7980 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2294
  time to fit residues: 75.4561
Evaluate side-chains
  184 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0040
   chunk 106 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:   20.0000
   chunk 123 optimal weight:    5.9990
   overall best weight:    0.7996

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A 256 GLN
A 397 GLN
A 475 ASN
B 208 ASN
B 397 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.137128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.110420 restraints weight = 23862.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.113267 restraints weight = 12147.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.115056 restraints weight = 7931.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11226  Z= 0.198
  Angle     :  0.672   6.950  15266  Z= 0.340
  Chirality :  0.044   0.174   1730
  Planarity :  0.005   0.049   1900
  Dihedral  :  4.674  38.606   1464
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.72 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.26 (0.23), residues: 1350
  helix:  1.26 (0.17), residues: 888
  sheet: -2.91 (0.73), residues: 46
  loop : -3.14 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 348 
 HIS   0.004   0.001   HIS B 236 
 PHE   0.019   0.001   PHE B 487 
 TYR   0.014   0.002   TYR B 155 
 ARG   0.005   0.001   ARG A 207 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 218
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.6322 (mtt180) cc_final: 0.4902 (mtt90)
REVERT: A  260 ASP cc_start: 0.8920 (m-30) cc_final: 0.8622 (m-30)
REVERT: A  303 LYS cc_start: 0.8392 (ptpp) cc_final: 0.8127 (pmmt)
REVERT: A  448 MET cc_start: 0.7581 (ttm) cc_final: 0.7248 (ttm)
REVERT: A  589 MET cc_start: 0.8065 (tmm) cc_final: 0.7714 (tmm)
REVERT: B  253 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8878 (tptt)
REVERT: B  263 GLN cc_start: 0.9293 (tp-100) cc_final: 0.8971 (tm-30)
REVERT: B  314 ASN cc_start: 0.9057 (m110) cc_final: 0.8654 (p0)
REVERT: B  589 MET cc_start: 0.7878 (tmm) cc_final: 0.7160 (tmm)
  outliers start: 11
  outliers final: 6
  residues processed: 224
  average time/residue: 0.2082
  time to fit residues: 68.8322
Evaluate side-chains
  191 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 185
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0770
   chunk 49 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 70 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.9342

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 475 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.135165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.108553 restraints weight = 24290.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.111337 restraints weight = 12361.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.113026 restraints weight = 8060.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11226  Z= 0.231
  Angle     :  0.658   6.677  15266  Z= 0.331
  Chirality :  0.045   0.180   1730
  Planarity :  0.005   0.046   1900
  Dihedral  :  4.501  39.181   1464
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.03 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: 1350
  helix:  1.45 (0.17), residues: 886
  sheet: -3.13 (0.70), residues: 46
  loop : -3.02 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 624 
 HIS   0.003   0.001   HIS A 714 
 PHE   0.030   0.001   PHE A  72 
 TYR   0.013   0.001   TYR B 261 
 ARG   0.005   0.000   ARG B 330 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.6289 (mtt180) cc_final: 0.4930 (mtt90)
REVERT: A  157 MET cc_start: 0.5975 (mpp) cc_final: 0.5665 (mpp)
REVERT: A  260 ASP cc_start: 0.8888 (m-30) cc_final: 0.8618 (m-30)
REVERT: A  303 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8099 (pmmt)
REVERT: A  448 MET cc_start: 0.7615 (ttm) cc_final: 0.7211 (ttm)
REVERT: A  589 MET cc_start: 0.8062 (tmm) cc_final: 0.7312 (tmm)
REVERT: B  157 MET cc_start: 0.5055 (mpp) cc_final: 0.4753 (mpp)
REVERT: B  253 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8946 (tptp)
REVERT: B  263 GLN cc_start: 0.9315 (tp-100) cc_final: 0.8972 (tm-30)
REVERT: B  307 LYS cc_start: 0.9236 (mppt) cc_final: 0.8969 (mttt)
REVERT: B  320 MET cc_start: 0.8674 (mmm) cc_final: 0.8313 (mmm)
REVERT: B  589 MET cc_start: 0.7856 (tmm) cc_final: 0.6892 (tmm)
  outliers start: 31
  outliers final: 23
  residues processed: 225
  average time/residue: 0.1999
  time to fit residues: 66.2774
Evaluate side-chains
  209 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   23 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  627 VAL
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0040
   chunk 24 optimal weight:    0.0670
   chunk 73 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8134

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
B 208 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.137885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.110710 restraints weight = 24418.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.113571 restraints weight = 12493.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.115274 restraints weight = 8201.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11226  Z= 0.182
  Angle     :  0.634   6.874  15266  Z= 0.318
  Chirality :  0.044   0.303   1730
  Planarity :  0.005   0.050   1900
  Dihedral  :  4.347  38.452   1464
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.73 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.15 (0.24), residues: 1350
  helix:  1.55 (0.17), residues: 894
  sheet: -3.20 (0.69), residues: 46
  loop : -2.91 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 624 
 HIS   0.002   0.000   HIS B 162 
 PHE   0.023   0.001   PHE B  72 
 TYR   0.023   0.001   TYR A 261 
 ARG   0.004   0.000   ARG B 330 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.6208 (mtt180) cc_final: 0.4861 (mtt90)
REVERT: A  157 MET cc_start: 0.5946 (mpp) cc_final: 0.5602 (mpp)
REVERT: A  184 ILE cc_start: 0.7447 (mm) cc_final: 0.6991 (mm)
REVERT: A  260 ASP cc_start: 0.8921 (m-30) cc_final: 0.8639 (m-30)
REVERT: A  303 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8271 (pmmt)
REVERT: A  448 MET cc_start: 0.7550 (ttm) cc_final: 0.7242 (ttm)
REVERT: A  589 MET cc_start: 0.8008 (tmm) cc_final: 0.7188 (tmm)
REVERT: A  682 ARG cc_start: 0.8922 (ptt90) cc_final: 0.8552 (ptp90)
REVERT: B  157 MET cc_start: 0.5212 (mpp) cc_final: 0.4905 (mpp)
REVERT: B  253 LYS cc_start: 0.9204 (tmtt) cc_final: 0.8932 (tptp)
REVERT: B  263 GLN cc_start: 0.9306 (tp-100) cc_final: 0.8954 (tm-30)
REVERT: B  307 LYS cc_start: 0.9257 (mppt) cc_final: 0.8960 (mttp)
REVERT: B  320 MET cc_start: 0.8614 (mmm) cc_final: 0.8158 (mmm)
REVERT: B  589 MET cc_start: 0.7777 (tmm) cc_final: 0.6763 (tmm)
  outliers start: 27
  outliers final: 15
  residues processed: 229
  average time/residue: 0.2026
  time to fit residues: 67.9572
Evaluate side-chains
  209 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 194
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 102 optimal weight:    3.9990
   chunk 132 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 118 optimal weight:    0.5980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
** B 363 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 = 0.4028 r_free = 0.4028 target = 0.137657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.110636 restraints weight = 24480.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.113431 restraints weight = 12620.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.115212 restraints weight = 8298.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11226  Z= 0.191
  Angle     :  0.631   6.952  15266  Z= 0.315
  Chirality :  0.043   0.199   1730
  Planarity :  0.005   0.051   1900
  Dihedral  :  4.257  38.764   1464
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.95 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.28 (0.24), residues: 1350
  helix:  1.67 (0.17), residues: 886
  sheet: -3.20 (0.67), residues: 46
  loop : -2.84 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 348 
 HIS   0.002   0.000   HIS B 236 
 PHE   0.023   0.001   PHE B  72 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.004   0.000   ARG B 330 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 204
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 MET cc_start: 0.5935 (mpp) cc_final: 0.5588 (mpp)
REVERT: A  260 ASP cc_start: 0.8929 (m-30) cc_final: 0.8617 (m-30)
REVERT: A  303 LYS cc_start: 0.8452 (ptpp) cc_final: 0.8250 (pmmt)
REVERT: A  448 MET cc_start: 0.7591 (ttm) cc_final: 0.7202 (ttm)
REVERT: A  589 MET cc_start: 0.7981 (tmm) cc_final: 0.7114 (tmm)
REVERT: A  682 ARG cc_start: 0.8893 (ptt90) cc_final: 0.8511 (ptp90)
REVERT: B  157 MET cc_start: 0.5152 (mpp) cc_final: 0.4856 (mpp)
REVERT: B  253 LYS cc_start: 0.9206 (tmtt) cc_final: 0.8937 (tptp)
REVERT: B  263 GLN cc_start: 0.9299 (tp-100) cc_final: 0.8983 (tm-30)
REVERT: B  307 LYS cc_start: 0.9267 (mppt) cc_final: 0.8971 (mttp)
REVERT: B  536 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7785 (pttt)
REVERT: B  589 MET cc_start: 0.7759 (tmm) cc_final: 0.6734 (tmm)
  outliers start: 36
  outliers final: 21
  residues processed: 229
  average time/residue: 0.2127
  time to fit residues: 71.6823
Evaluate side-chains
  219 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 197
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  169 PHE
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  536 LYS
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0050
   chunk 114 optimal weight:   30.0000
   chunk 97 optimal weight:    9.9990
   chunk 90 optimal weight:    7.9990
   chunk 121 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 52 optimal weight:    0.6980
   chunk 79 optimal weight:   40.0000
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
A 257 ASN
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.138271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.112005 restraints weight = 23944.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.114800 restraints weight = 12075.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.116436 restraints weight = 7831.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11226  Z= 0.175
  Angle     :  0.643   9.166  15266  Z= 0.314
  Chirality :  0.043   0.193   1730
  Planarity :  0.005   0.053   1900
  Dihedral  :  4.184  38.725   1464
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.56 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.29 (0.24), residues: 1350
  helix:  1.65 (0.17), residues: 900
  sheet: -3.11 (0.66), residues: 46
  loop : -2.93 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 348 
 HIS   0.002   0.000   HIS B 628 
 PHE   0.022   0.001   PHE B 169 
 TYR   0.016   0.001   TYR B 261 
 ARG   0.004   0.000   ARG B 330 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 209
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 MET cc_start: 0.5874 (mpp) cc_final: 0.5505 (mpp)
REVERT: A  260 ASP cc_start: 0.8918 (m-30) cc_final: 0.8605 (m-30)
REVERT: A  448 MET cc_start: 0.7581 (ttm) cc_final: 0.7189 (ttm)
REVERT: A  589 MET cc_start: 0.7974 (tmm) cc_final: 0.7131 (tmm)
REVERT: A  682 ARG cc_start: 0.8855 (ptt90) cc_final: 0.8532 (ptp90)
REVERT: A  690 MET cc_start: 0.7760 (tpp) cc_final: 0.7552 (mtm)
REVERT: B  157 MET cc_start: 0.5067 (mpp) cc_final: 0.4727 (mpp)
REVERT: B  253 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8944 (tptp)
REVERT: B  263 GLN cc_start: 0.9301 (tp-100) cc_final: 0.8987 (tm-30)
REVERT: B  307 LYS cc_start: 0.9265 (mppt) cc_final: 0.8968 (mttp)
REVERT: B  536 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7750 (pttt)
REVERT: B  589 MET cc_start: 0.7700 (tmm) cc_final: 0.6702 (tmm)
  outliers start: 30
  outliers final: 23
  residues processed: 226
  average time/residue: 0.2255
  time to fit residues: 73.9963
Evaluate side-chains
  221 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 197
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  169 PHE
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  536 LYS
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  627 VAL
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 129 optimal weight:    0.0970
   chunk 86 optimal weight:    9.9990
   chunk 36 optimal weight:    0.1980
   chunk 39 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
B 228 ASN
B 256 GLN
** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.138291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.112081 restraints weight = 24462.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.114832 restraints weight = 12359.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.116468 restraints weight = 8063.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11226  Z= 0.181
  Angle     :  0.645   8.609  15266  Z= 0.317
  Chirality :  0.043   0.190   1730
  Planarity :  0.005   0.053   1900
  Dihedral  :  4.166  38.926   1464
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.78 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.31 (0.24), residues: 1350
  helix:  1.68 (0.17), residues: 900
  sheet: -2.97 (0.66), residues: 46
  loop : -2.96 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 348 
 HIS   0.004   0.000   HIS A 229 
 PHE   0.023   0.001   PHE B 224 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.004   0.000   ARG A 207 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 209
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 MET cc_start: 0.5877 (mpp) cc_final: 0.5504 (mpp)
REVERT: A  260 ASP cc_start: 0.8900 (m-30) cc_final: 0.8575 (m-30)
REVERT: A  448 MET cc_start: 0.7571 (ttm) cc_final: 0.7161 (ttm)
REVERT: A  589 MET cc_start: 0.7964 (tmm) cc_final: 0.7188 (tmm)
REVERT: A  682 ARG cc_start: 0.8834 (ptt90) cc_final: 0.8590 (ptp90)
REVERT: A  690 MET cc_start: 0.7747 (tpp) cc_final: 0.7540 (mtm)
REVERT: B  157 MET cc_start: 0.5093 (mpp) cc_final: 0.4753 (mpp)
REVERT: B  165 MET cc_start: 0.8244 (tpp) cc_final: 0.8007 (tpp)
REVERT: B  253 LYS cc_start: 0.9252 (tmtt) cc_final: 0.8979 (tptp)
REVERT: B  263 GLN cc_start: 0.9316 (tp-100) cc_final: 0.9004 (tm-30)
REVERT: B  307 LYS cc_start: 0.9269 (mppt) cc_final: 0.8971 (mttp)
REVERT: B  511 MET cc_start: 0.6410 (pmm) cc_final: 0.6200 (pmm)
REVERT: B  536 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7642 (pttm)
REVERT: B  589 MET cc_start: 0.7691 (tmm) cc_final: 0.6735 (tmm)
  outliers start: 30
  outliers final: 22
  residues processed: 227
  average time/residue: 0.2301
  time to fit residues: 77.2504
Evaluate side-chains
  223 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 200
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  536 LYS
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 114 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0050
   chunk 116 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   overall best weight:    1.2000

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
B 228 ASN
** B 363 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 = 0.4043 r_free = 0.4043 target = 0.138805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.111661 restraints weight = 24405.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.114526 restraints weight = 12383.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.116175 restraints weight = 8082.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11226  Z= 0.187
  Angle     :  0.649   8.377  15266  Z= 0.318
  Chirality :  0.043   0.205   1730
  Planarity :  0.005   0.054   1900
  Dihedral  :  4.159  38.986   1464
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.56 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.32 (0.24), residues: 1350
  helix:  1.67 (0.17), residues: 900
  sheet: -2.91 (0.66), residues: 46
  loop : -2.94 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP B 348 
 HIS   0.002   0.000   HIS B 236 
 PHE   0.037   0.001   PHE A  72 
 TYR   0.019   0.001   TYR B 261 
 ARG   0.004   0.000   ARG B 330 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 206
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 MET cc_start: 0.5816 (mpp) cc_final: 0.5440 (mpp)
REVERT: A  180 GLU cc_start: 0.7839 (tp30) cc_final: 0.7613 (tp30)
REVERT: A  260 ASP cc_start: 0.8918 (m-30) cc_final: 0.8591 (m-30)
REVERT: A  266 TYR cc_start: 0.8121 (t80) cc_final: 0.7786 (t80)
REVERT: A  448 MET cc_start: 0.7562 (ttm) cc_final: 0.7173 (ttm)
REVERT: A  589 MET cc_start: 0.7861 (tmm) cc_final: 0.7117 (tmm)
REVERT: A  682 ARG cc_start: 0.8797 (ptt90) cc_final: 0.8584 (ptp90)
REVERT: B  157 MET cc_start: 0.5097 (mpp) cc_final: 0.4762 (mpp)
REVERT: B  165 MET cc_start: 0.8140 (tpp) cc_final: 0.7650 (mmm)
REVERT: B  253 LYS cc_start: 0.9255 (tmtt) cc_final: 0.8987 (tptp)
REVERT: B  263 GLN cc_start: 0.9317 (tp-100) cc_final: 0.9028 (tm-30)
REVERT: B  303 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8492 (ptmt)
REVERT: B  307 LYS cc_start: 0.9270 (mppt) cc_final: 0.8973 (mttp)
REVERT: B  511 MET cc_start: 0.6401 (pmm) cc_final: 0.6182 (pmm)
REVERT: B  589 MET cc_start: 0.7732 (tmm) cc_final: 0.6749 (tmm)
  outliers start: 32
  outliers final: 27
  residues processed: 223
  average time/residue: 0.2097
  time to fit residues: 69.4746
Evaluate side-chains
  228 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 201
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  627 VAL
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 117 optimal weight:    0.6980
   chunk 131 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 114 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 120 optimal weight:    7.9990
   chunk 73 optimal weight:    0.0570
   chunk 18 optimal weight:    0.2980
   chunk 107 optimal weight:    6.9990
   chunk 118 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.2100

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
B 228 ASN
B 341 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.138814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.111589 restraints weight = 24813.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.114494 restraints weight = 12555.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.116113 restraints weight = 8159.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11226  Z= 0.190
  Angle     :  0.660   8.439  15266  Z= 0.326
  Chirality :  0.043   0.188   1730
  Planarity :  0.005   0.052   1900
  Dihedral  :  4.179  39.038   1464
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 23.61 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.31 (0.24), residues: 1350
  helix:  1.63 (0.17), residues: 908
  sheet: -2.89 (0.65), residues: 46
  loop : -2.94 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP B 348 
 HIS   0.002   0.000   HIS B 236 
 PHE   0.037   0.001   PHE A  72 
 TYR   0.011   0.001   TYR A 155 
 ARG   0.003   0.000   ARG B 330 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 208
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 MET cc_start: 0.5818 (mpp) cc_final: 0.5424 (mpp)
REVERT: A  260 ASP cc_start: 0.8920 (m-30) cc_final: 0.8601 (m-30)
REVERT: A  266 TYR cc_start: 0.8131 (t80) cc_final: 0.7794 (t80)
REVERT: A  448 MET cc_start: 0.7565 (ttm) cc_final: 0.7171 (ttm)
REVERT: B  157 MET cc_start: 0.5296 (mpp) cc_final: 0.4933 (mpp)
REVERT: B  253 LYS cc_start: 0.9260 (tmtt) cc_final: 0.8992 (tptp)
REVERT: B  263 GLN cc_start: 0.9315 (tp-100) cc_final: 0.9030 (tm-30)
REVERT: B  307 LYS cc_start: 0.9269 (mppt) cc_final: 0.8979 (mttp)
REVERT: B  511 MET cc_start: 0.6381 (pmm) cc_final: 0.6154 (pmm)
REVERT: B  536 LYS cc_start: 0.8274 (pttt) cc_final: 0.7844 (pttm)
REVERT: B  589 MET cc_start: 0.7718 (tmm) cc_final: 0.7255 (ttp)
  outliers start: 29
  outliers final: 26
  residues processed: 224
  average time/residue: 0.2117
  time to fit residues: 69.3142
Evaluate side-chains
  227 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 201
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  228 ASN
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  627 VAL
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 123 optimal weight:    0.0270
   chunk 12 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    3.1444

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
B 228 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.134370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.108152 restraints weight = 24458.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.110869 restraints weight = 12475.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.112633 restraints weight = 8170.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11226  Z= 0.310
  Angle     :  0.734   9.290  15266  Z= 0.369
  Chirality :  0.047   0.293   1730
  Planarity :  0.005   0.052   1900
  Dihedral  :  4.382  39.427   1464
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.34 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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 (0.23), residues: 1350
  helix:  1.31 (0.17), residues: 912
  sheet: -2.91 (0.66), residues: 46
  loop : -3.05 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP B 348 
 HIS   0.004   0.001   HIS A 714 
 PHE   0.038   0.002   PHE A  72 
 TYR   0.024   0.002   TYR B 261 
 ARG   0.007   0.000   ARG A 207 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 MET cc_start: 0.5888 (mpp) cc_final: 0.5496 (mpp)
REVERT: A  260 ASP cc_start: 0.8952 (m-30) cc_final: 0.8626 (m-30)
REVERT: A  266 TYR cc_start: 0.8116 (t80) cc_final: 0.7772 (t80)
REVERT: A  448 MET cc_start: 0.7555 (ttm) cc_final: 0.7141 (ttm)
REVERT: B  157 MET cc_start: 0.5312 (mpp) cc_final: 0.4927 (mpp)
REVERT: B  253 LYS cc_start: 0.9285 (tmtt) cc_final: 0.9017 (tptp)
REVERT: B  303 LYS cc_start: 0.8820 (ptmt) cc_final: 0.8564 (ptpp)
REVERT: B  368 TYR cc_start: 0.7698 (t80) cc_final: 0.7341 (t80)
REVERT: B  511 MET cc_start: 0.6473 (pmm) cc_final: 0.6241 (pmm)
REVERT: B  536 LYS cc_start: 0.8305 (pttt) cc_final: 0.7861 (pttm)
REVERT: B  589 MET cc_start: 0.7916 (tmm) cc_final: 0.7460 (ttp)
  outliers start: 32
  outliers final: 26
  residues processed: 215
  average time/residue: 0.2001
  time to fit residues: 64.1389
Evaluate side-chains
  220 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 194
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  228 ASN
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  627 VAL
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 118 optimal weight:    0.0870
   chunk 62 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 94 optimal weight:   10.0000
   chunk 4 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
B 228 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.138775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.112688 restraints weight = 24084.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.115564 restraints weight = 12186.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.117194 restraints weight = 7832.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11226  Z= 0.178
  Angle     :  0.688   9.313  15266  Z= 0.336
  Chirality :  0.043   0.213   1730
  Planarity :  0.005   0.052   1900
  Dihedral  :  4.263  38.807   1464
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 24.30 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.22 (0.24), residues: 1350
  helix:  1.53 (0.18), residues: 902
  sheet: -2.76 (0.66), residues: 46
  loop : -2.85 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP B 348 
 HIS   0.015   0.001   HIS B 229 
 PHE   0.037   0.001   PHE A  72 
 TYR   0.018   0.001   TYR A 368 
 ARG   0.007   0.000   ARG A 207 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3107.11 seconds
wall clock time: 56 minutes 49.07 seconds (3409.07 seconds total)