Starting phenix.real_space_refine
on Mon Jul 28 20:50:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qmb_4594/07_2025/6qmb_4594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qmb_4594/07_2025/6qmb_4594.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qmb_4594/07_2025/6qmb_4594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qmb_4594/07_2025/6qmb_4594.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qmb_4594/07_2025/6qmb_4594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qmb_4594/07_2025/6qmb_4594.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      40      5.16       5
     C    6960      2.51       5
     N    1782      2.21       5
     O    1912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10698
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 661, 5347
          Classifications: {'peptide': 661}
          Link IDs: {'PTRANS': 28, 'TRANS': 632}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.36, per 1000 atoms: 0.87
  Number of scatterers: 10698
  At special positions: 0
  Unit cell: (118.404, 109.296, 108.284, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      40     16.00
     O    1912      8.00
     N    1782      7.00
     C    6960      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: 2.72
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2508

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 4 sheets defined
      75.8% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 32 through 50
      removed outlier: 3.796A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.678A  pdb=" N   HIS A  90 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 4.118A  pdb=" N   ALA A 104 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 126 through 130
    Processing helix  chain 'A' and resid 152 through 166
      removed outlier: 3.704A  pdb=" N   GLU A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.838A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS A 180 " --> pdb=" O   ASN A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 199
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 246
      removed outlier: 3.581A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 254
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.541A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   THR A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 320
      removed outlier: 3.690A  pdb=" N   PHE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 329
    Processing helix  chain 'A' and resid 330 through 358
      Proline residue:  A 341  - end of helix
      removed outlier: 3.724A  pdb=" N   VAL A 346 " --> pdb=" O   THR A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 391
      removed outlier: 6.066A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 416
      removed outlier: 3.917A  pdb=" N   THR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE A 416 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 3.945A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 482 through 494
      removed outlier: 4.041A  pdb=" N   THR A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 518
      removed outlier: 4.516A  pdb=" N   ASP A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET A 507 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 546
      removed outlier: 4.011A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.685A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 560 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE A 574 " --> pdb=" O   TRP A 570 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 626
      removed outlier: 3.561A  pdb=" N   LEU A 602 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 603 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 604 " --> pdb=" O   TRP A 600 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS A 626 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 650
      removed outlier: 3.847A  pdb=" N   GLN A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 684
    Processing helix  chain 'A' and resid 689 through 696
    Processing helix  chain 'A' and resid 700 through 718
    Processing helix  chain 'B' and resid 29 through 31
      No H-bonds generated for 'chain 'B' and resid 29 through 31'
    Processing helix  chain 'B' and resid 32 through 50
      removed outlier: 3.797A  pdb=" N   VAL B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.678A  pdb=" N   HIS B  90 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
      removed outlier: 4.119A  pdb=" N   ALA B 104 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 126 through 130
    Processing helix  chain 'B' and resid 152 through 166
      removed outlier: 3.705A  pdb=" N   GLU B 158 " --> pdb=" O   SER B 154 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS B 166 " --> pdb=" O   LYS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.838A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 180 " --> pdb=" O   ASN B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 199
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 246
      removed outlier: 3.580A  pdb=" N   ALA B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.541A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   THR B 287 " --> pdb=" O   LYS B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 320
      removed outlier: 3.691A  pdb=" N   PHE B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 329
    Processing helix  chain 'B' and resid 330 through 358
      Proline residue:  B 341  - end of helix
      removed outlier: 3.724A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 391
      removed outlier: 6.066A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 399
      No H-bonds generated for 'chain 'B' and resid 397 through 399'
    Processing helix  chain 'B' and resid 400 through 416
      removed outlier: 3.916A  pdb=" N   THR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE B 416 " --> pdb=" O   GLN B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 3.946A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 466
    Processing helix  chain 'B' and resid 482 through 494
      removed outlier: 4.041A  pdb=" N   THR B 494 " --> pdb=" O   ARG B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 518
      removed outlier: 4.515A  pdb=" N   ASP B 503 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET B 507 " --> pdb=" O   ASP B 503 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 546
      removed outlier: 4.010A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.685A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 560 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 574 " --> pdb=" O   TRP B 570 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 626
      removed outlier: 3.561A  pdb=" N   LEU B 602 " --> pdb=" O   LYS B 598 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 603 " --> pdb=" O   ALA B 599 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU B 604 " --> pdb=" O   TRP B 600 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS B 626 " --> pdb=" O   PHE B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 650
      removed outlier: 3.847A  pdb=" N   GLN B 633 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 684
    Processing helix  chain 'B' and resid 689 through 696
    Processing helix  chain 'B' and resid 700 through 718
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 59
      removed outlier: 3.595A  pdb=" N   PHE A  22 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266
      removed outlier: 3.542A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 59
      removed outlier: 3.595A  pdb=" N   PHE B  22 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266
      removed outlier: 3.542A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)

    730 hydrogen bonds defined for protein.
    2142 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: 4.23

  Time building geometry restraints manager: 2.87 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: 3326
        1.34 -     1.45: 1955
        1.45 -     1.57: 5627
        1.57 -     1.69: 0
        1.69 -     1.80: 66
  Bond restraints: 10974
  Sorted by residual:
  bond pdb=" CB  PRO A 202 "
       pdb=" CG  PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.492  1.397  0.095 5.00e-02 4.00e+02 3.58e+00
  bond pdb=" CB  PRO B 202 "
       pdb=" CG  PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.492  1.398  0.094 5.00e-02 4.00e+02 3.52e+00
  bond pdb=" CB  VAL B 229 "
       pdb=" CG2 VAL B 229 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.38e+00
  bond pdb=" CB  VAL A 229 "
       pdb=" CG2 VAL A 229 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.34e+00
  bond pdb=" C   THR B 689 "
       pdb=" N   PRO B 690 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.20e-02 6.94e+03 2.53e+00
  ... (remaining 10969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 14335
        1.99 -     3.99: 474
        3.99 -     5.98: 49
        5.98 -     7.97: 16
        7.97 -     9.97: 12
  Bond angle restraints: 14886
  Sorted by residual:
  angle pdb=" N   THR B 689 "
        pdb=" CA  THR B 689 "
        pdb=" C   THR B 689 "
      ideal   model   delta    sigma   weight residual
     109.81  119.37   -9.56 2.21e+00 2.05e-01 1.87e+01
  angle pdb=" N   THR A 689 "
        pdb=" CA  THR A 689 "
        pdb=" C   THR A 689 "
      ideal   model   delta    sigma   weight residual
     109.81  119.35   -9.54 2.21e+00 2.05e-01 1.86e+01
  angle pdb=" CA  THR A 689 "
        pdb=" C   THR A 689 "
        pdb=" N   PRO A 690 "
      ideal   model   delta    sigma   weight residual
     118.44  124.60   -6.16 1.59e+00 3.96e-01 1.50e+01
  angle pdb=" CA  THR B 689 "
        pdb=" C   THR B 689 "
        pdb=" N   PRO B 690 "
      ideal   model   delta    sigma   weight residual
     118.44  124.57   -6.13 1.59e+00 3.96e-01 1.49e+01
  angle pdb=" C   SER B 584 "
        pdb=" N   ASN B 585 "
        pdb=" CA  ASN B 585 "
      ideal   model   delta    sigma   weight residual
     121.70  128.29   -6.59 1.80e+00 3.09e-01 1.34e+01
  ... (remaining 14881 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 5749
       17.71 -    35.41: 571
       35.41 -    53.12: 94
       53.12 -    70.83: 26
       70.83 -    88.53: 8
  Dihedral angle restraints: 6448
    sinusoidal: 2586
      harmonic: 3862
  Sorted by residual:
  dihedral pdb=" CA  ILE B 271 "
           pdb=" C   ILE B 271 "
           pdb=" N   THR B 272 "
           pdb=" CA  THR B 272 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  LEU A 212 "
           pdb=" C   LEU A 212 "
           pdb=" N   LEU A 213 "
           pdb=" CA  LEU A 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.20  -18.80     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  LEU B 212 "
           pdb=" C   LEU B 212 "
           pdb=" N   LEU B 213 "
           pdb=" CA  LEU B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.21  -18.79     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 6445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1330
       0.066 -    0.133: 249
       0.133 -    0.199: 47
       0.199 -    0.265: 0
       0.265 -    0.331: 4
  Chirality restraints: 1630
  Sorted by residual:
  chirality pdb=" CB  VAL B 248 "
            pdb=" CA  VAL B 248 "
            pdb=" CG1 VAL B 248 "
            pdb=" CG2 VAL B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CB  VAL A 248 "
            pdb=" CA  VAL A 248 "
            pdb=" CG1 VAL A 248 "
            pdb=" CG2 VAL A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  THR A 689 "
            pdb=" N   THR A 689 "
            pdb=" C   THR A 689 "
            pdb=" CB  THR A 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1627 not shown)

  Planarity restraints: 1890
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 401 "   -0.037 5.00e-02 4.00e+02   5.59e-02 5.01e+00
        pdb=" N   PRO B 402 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 402 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 402 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 401 "   -0.037 5.00e-02 4.00e+02   5.58e-02 4.98e+00
        pdb=" N   PRO A 402 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 402 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 402 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 677 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" CD  GLU B 677 "    0.038 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 677 "   -0.014 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 677 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1887 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 3096
        2.81 -     3.33: 10282
        3.33 -     3.85: 18138
        3.85 -     4.38: 19923
        4.38 -     4.90: 34980
  Nonbonded interactions: 86419
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 120 "
            pdb=" OG1 THR A 124 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   TYR B 120 "
            pdb=" OG1 THR B 124 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR A  26 "
            pdb=" O   ALA A  36 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OH  TYR B  26 "
            pdb=" O   ALA B  36 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   MET B 701 "
            pdb=" OG1 THR B 704 "
     model   vdw
     2.325 3.040
  ... (remaining 86414 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: 0.05
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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     30.530
  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:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
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   0.095  10974  Z= 0.323
  Angle     :  0.866   9.968  14886  Z= 0.475
  Chirality :  0.055   0.331   1630
  Planarity :  0.007   0.056   1890
  Dihedral  : 14.676  88.534   3940
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.18), residues: 1298
  helix: -2.02 (0.12), residues: 898
  sheet: -2.70 (0.64), residues: 58
  loop : -2.33 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 235 
 HIS   0.006   0.001   HIS B 611 
 PHE   0.037   0.002   PHE A 396 
 TYR   0.015   0.003   TYR B 279 
 ARG   0.003   0.001   ARG B 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11322 (  730)
  hydrogen bonds       : angle       5.96671 ( 2142)
  covalent geometry    : bond        0.00752 (10974)
  covalent geometry    : angle       0.86648 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 LEU cc_start: 0.8680 (tt) cc_final: 0.7874 (mm)
REVERT: A  282 MET cc_start: 0.8864 (mmt) cc_final: 0.8626 (mpp)
REVERT: A  372 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8675 (tt0)
REVERT: A  457 TYR cc_start: 0.7527 (t80) cc_final: 0.7237 (t80)
REVERT: A  531 ASN cc_start: 0.9234 (t0) cc_final: 0.8572 (t160)
REVERT: A  598 LYS cc_start: 0.7976 (mttt) cc_final: 0.6674 (pttt)
REVERT: B  223 LEU cc_start: 0.8702 (tt) cc_final: 0.7937 (mm)
REVERT: B  320 TYR cc_start: 0.5945 (m-10) cc_final: 0.5732 (m-80)
REVERT: B  335 PHE cc_start: 0.8573 (m-80) cc_final: 0.8276 (t80)
REVERT: B  457 TYR cc_start: 0.7515 (t80) cc_final: 0.7230 (t80)
REVERT: B  531 ASN cc_start: 0.9256 (t0) cc_final: 0.8612 (t160)
REVERT: B  598 LYS cc_start: 0.8047 (mttt) cc_final: 0.6848 (pttt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2717
  time to fit residues: 55.0249
Evaluate side-chains
  93 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 138 ASN
A 355 ASN
A 510 GLN
A 531 ASN
A 633 GLN
A 641 GLN
A 666 HIS
A 715 GLN
B 138 ASN
B 355 ASN
B 372 GLN
B 401 HIS
B 510 GLN
B 531 ASN
B 633 GLN
B 641 GLN
B 715 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.108324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.081331 restraints weight = 23413.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.084012 restraints weight = 11841.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.085713 restraints weight = 8072.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10974  Z= 0.124
  Angle     :  0.531   6.532  14886  Z= 0.278
  Chirality :  0.039   0.149   1630
  Planarity :  0.004   0.039   1890
  Dihedral  :  4.369  16.575   1420
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.71 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.21), residues: 1298
  helix:  0.13 (0.15), residues: 902
  sheet: -2.42 (0.68), residues: 58
  loop : -1.72 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B  58 
 PHE   0.013   0.001   PHE A 396 
 TYR   0.017   0.002   TYR B 393 
 ARG   0.004   0.000   ARG B 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  730)
  hydrogen bonds       : angle       4.24280 ( 2142)
  covalent geometry    : bond        0.00266 (10974)
  covalent geometry    : angle       0.53115 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8704 (tt0)
REVERT: A  400 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7985 (pp)
REVERT: A  403 PHE cc_start: 0.7811 (m-80) cc_final: 0.7381 (m-80)
REVERT: A  463 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6904 (t80)
REVERT: A  598 LYS cc_start: 0.8272 (mttt) cc_final: 0.7461 (pttt)
REVERT: A  680 ARG cc_start: 0.6603 (mmp-170) cc_final: 0.5784 (tmm-80)
REVERT: B  400 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8109 (pp)
REVERT: B  463 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6896 (t80)
REVERT: B  598 LYS cc_start: 0.8363 (mttt) cc_final: 0.7560 (pttt)
  outliers start: 19
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2164
  time to fit residues: 40.6299
Evaluate side-chains
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  357 MET
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 125 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 95 optimal weight:    9.9990
   chunk 105 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
B  99 ASN
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.103296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.075840 restraints weight = 23899.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.078351 restraints weight = 12363.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.079933 restraints weight = 8618.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067  10974  Z= 0.339
  Angle     :  0.676   8.645  14886  Z= 0.358
  Chirality :  0.045   0.147   1630
  Planarity :  0.005   0.034   1890
  Dihedral  :  4.519  20.942   1420
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.46 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.22), residues: 1298
  helix:  0.75 (0.16), residues: 894
  sheet: -2.51 (0.66), residues: 58
  loop : -1.71 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 235 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.028   0.002   PHE A 315 
 TYR   0.017   0.002   TYR A 327 
 ARG   0.004   0.000   ARG B 548 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04686 (  730)
  hydrogen bonds       : angle       4.28787 ( 2142)
  covalent geometry    : bond        0.00774 (10974)
  covalent geometry    : angle       0.67635 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 MET cc_start: 0.9191 (mmt) cc_final: 0.8935 (mmm)
REVERT: A  372 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8717 (tt0)
REVERT: A  384 MET cc_start: 0.8045 (ttp) cc_final: 0.7828 (ttp)
REVERT: A  463 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6985 (t80)
REVERT: B  315 PHE cc_start: 0.8232 (t80) cc_final: 0.7927 (t80)
REVERT: B  463 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7011 (t80)
  outliers start: 28
  outliers final: 19
  residues processed: 119
  average time/residue: 0.2081
  time to fit residues: 36.8742
Evaluate side-chains
  112 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  577 SER
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 104 optimal weight:    0.0980
   chunk 34 optimal weight:   10.0000
   chunk 108 optimal weight:    5.9990
   chunk 110 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.107445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.080430 restraints weight = 23497.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.083114 restraints weight = 11780.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.084816 restraints weight = 8029.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10974  Z= 0.130
  Angle     :  0.531  10.486  14886  Z= 0.271
  Chirality :  0.039   0.150   1630
  Planarity :  0.004   0.031   1890
  Dihedral  :  4.100  15.821   1420
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.99 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.23), residues: 1298
  helix:  1.30 (0.16), residues: 902
  sheet: -2.17 (0.69), residues: 58
  loop : -1.46 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 611 
 PHE   0.030   0.001   PHE A 315 
 TYR   0.016   0.002   TYR A 327 
 ARG   0.005   0.000   ARG B 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  730)
  hydrogen bonds       : angle       3.91907 ( 2142)
  covalent geometry    : bond        0.00289 (10974)
  covalent geometry    : angle       0.53066 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9058 (t) cc_final: 0.8404 (p)
REVERT: A  372 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8689 (tt0)
REVERT: A  463 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6746 (t80)
REVERT: B  203 SER cc_start: 0.9073 (t) cc_final: 0.8470 (p)
REVERT: B  348 MET cc_start: 0.9110 (mmt) cc_final: 0.8884 (mmm)
REVERT: B  463 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6711 (t80)
  outliers start: 31
  outliers final: 17
  residues processed: 136
  average time/residue: 0.1945
  time to fit residues: 40.3429
Evaluate side-chains
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0970
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.2180

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.107972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.081042 restraints weight = 23430.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.083735 restraints weight = 11722.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.085384 restraints weight = 8011.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10974  Z= 0.131
  Angle     :  0.535  10.057  14886  Z= 0.270
  Chirality :  0.039   0.140   1630
  Planarity :  0.003   0.030   1890
  Dihedral  :  3.958  15.584   1420
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.78 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.23), residues: 1298
  helix:  1.53 (0.16), residues: 904
  sheet: -2.05 (0.72), residues: 58
  loop : -1.54 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.031   0.001   PHE A 315 
 TYR   0.015   0.002   TYR B 457 
 ARG   0.004   0.000   ARG A 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  730)
  hydrogen bonds       : angle       3.81552 ( 2142)
  covalent geometry    : bond        0.00295 (10974)
  covalent geometry    : angle       0.53538 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 1.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9086 (t) cc_final: 0.8426 (p)
REVERT: A  372 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8679 (tt0)
REVERT: A  463 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6651 (t80)
REVERT: B  203 SER cc_start: 0.9034 (t) cc_final: 0.8433 (p)
REVERT: B  403 PHE cc_start: 0.7724 (m-80) cc_final: 0.7299 (m-80)
REVERT: B  463 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6696 (t80)
  outliers start: 34
  outliers final: 23
  residues processed: 133
  average time/residue: 0.2134
  time to fit residues: 43.6826
Evaluate side-chains
  126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 67 optimal weight:    7.9990
   chunk 98 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.109950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.082981 restraints weight = 23424.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.085759 restraints weight = 11730.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.087538 restraints weight = 7945.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10974  Z= 0.111
  Angle     :  0.523  10.603  14886  Z= 0.261
  Chirality :  0.038   0.149   1630
  Planarity :  0.003   0.030   1890
  Dihedral  :  3.814  14.844   1420
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.31 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.23), residues: 1298
  helix:  1.73 (0.16), residues: 906
  sheet: -1.78 (0.75), residues: 58
  loop : -1.41 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 265 
 PHE   0.021   0.001   PHE B 315 
 TYR   0.015   0.001   TYR A 457 
 ARG   0.002   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  730)
  hydrogen bonds       : angle       3.75157 ( 2142)
  covalent geometry    : bond        0.00240 (10974)
  covalent geometry    : angle       0.52332 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9021 (t) cc_final: 0.8381 (p)
REVERT: A  372 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8626 (tt0)
REVERT: A  531 ASN cc_start: 0.9091 (t0) cc_final: 0.8612 (t160)
REVERT: B  203 SER cc_start: 0.8991 (t) cc_final: 0.8388 (p)
REVERT: B  463 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6631 (t80)
REVERT: B  531 ASN cc_start: 0.9091 (t0) cc_final: 0.8597 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 131
  average time/residue: 0.2418
  time to fit residues: 48.2147
Evaluate side-chains
  124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 108 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 HIS
A 715 GLN
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 715 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.110033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.083090 restraints weight = 23559.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.085845 restraints weight = 11800.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.087586 restraints weight = 8030.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10974  Z= 0.115
  Angle     :  0.536  10.532  14886  Z= 0.263
  Chirality :  0.038   0.140   1630
  Planarity :  0.003   0.029   1890
  Dihedral  :  3.750  14.311   1420
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.57 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.23), residues: 1298
  helix:  1.78 (0.16), residues: 906
  sheet: -1.67 (0.75), residues: 58
  loop : -1.45 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 235 
 HIS   0.002   0.000   HIS B 611 
 PHE   0.018   0.001   PHE B 315 
 TYR   0.016   0.001   TYR B 457 
 ARG   0.002   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03421 (  730)
  hydrogen bonds       : angle       3.72327 ( 2142)
  covalent geometry    : bond        0.00256 (10974)
  covalent geometry    : angle       0.53589 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 1.705 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9018 (t) cc_final: 0.8377 (p)
REVERT: A  372 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8639 (tt0)
REVERT: A  531 ASN cc_start: 0.9091 (t0) cc_final: 0.8621 (t160)
REVERT: B  203 SER cc_start: 0.9007 (t) cc_final: 0.8410 (p)
REVERT: B  463 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6528 (t80)
REVERT: B  531 ASN cc_start: 0.9091 (t0) cc_final: 0.8597 (t0)
  outliers start: 28
  outliers final: 23
  residues processed: 122
  average time/residue: 0.2560
  time to fit residues: 49.8794
Evaluate side-chains
  125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 2.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  357 MET
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 115 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 HIS
A 715 GLN
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 715 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.108158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.080724 restraints weight = 23300.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.083426 restraints weight = 11859.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.085096 restraints weight = 8160.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10974  Z= 0.162
  Angle     :  0.567  10.194  14886  Z= 0.284
  Chirality :  0.040   0.191   1630
  Planarity :  0.003   0.029   1890
  Dihedral  :  3.855  14.882   1420
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.10 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.23), residues: 1298
  helix:  1.77 (0.16), residues: 898
  sheet: -1.64 (0.73), residues: 58
  loop : -1.19 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 600 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.013   0.001   PHE B 379 
 TYR   0.016   0.002   TYR A 457 
 ARG   0.002   0.000   ARG B 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  730)
  hydrogen bonds       : angle       3.81574 ( 2142)
  covalent geometry    : bond        0.00371 (10974)
  covalent geometry    : angle       0.56745 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 2.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9129 (t) cc_final: 0.8462 (p)
REVERT: A  372 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8682 (tt0)
REVERT: B  203 SER cc_start: 0.9116 (t) cc_final: 0.8481 (p)
REVERT: B  463 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6585 (t80)
  outliers start: 28
  outliers final: 25
  residues processed: 127
  average time/residue: 0.2571
  time to fit residues: 51.8909
Evaluate side-chains
  130 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 109 optimal weight:    0.2980
   chunk 91 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 127 optimal weight:    6.9990
   chunk 116 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 129 optimal weight:    5.9990
   chunk 125 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 HIS
A 715 GLN
** B 326 GLN ** 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 = 0.3584 r_free = 0.3584 target = 0.108735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.081636 restraints weight = 23579.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.084365 restraints weight = 11804.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.086144 restraints weight = 8017.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10974  Z= 0.141
  Angle     :  0.569  10.805  14886  Z= 0.280
  Chirality :  0.040   0.303   1630
  Planarity :  0.003   0.029   1890
  Dihedral  :  3.836  14.763   1420
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.01 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.23), residues: 1298
  helix:  1.77 (0.16), residues: 898
  sheet: -1.66 (0.73), residues: 58
  loop : -1.17 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 600 
 HIS   0.002   0.001   HIS B  58 
 PHE   0.012   0.001   PHE A 379 
 TYR   0.016   0.002   TYR A 457 
 ARG   0.003   0.000   ARG B 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  730)
  hydrogen bonds       : angle       3.80239 ( 2142)
  covalent geometry    : bond        0.00321 (10974)
  covalent geometry    : angle       0.56863 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9113 (t) cc_final: 0.8457 (p)
REVERT: A  372 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8677 (tt0)
REVERT: A  645 ARG cc_start: 0.7736 (mmp80) cc_final: 0.7358 (mmp80)
REVERT: B  203 SER cc_start: 0.9105 (t) cc_final: 0.8475 (p)
REVERT: B  645 ARG cc_start: 0.7686 (mmp80) cc_final: 0.7308 (mmp80)
  outliers start: 30
  outliers final: 25
  residues processed: 124
  average time/residue: 0.2062
  time to fit residues: 40.4570
Evaluate side-chains
  125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 2.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 HIS
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.109788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.082894 restraints weight = 23207.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.085638 restraints weight = 11671.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.087371 restraints weight = 7946.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10974  Z= 0.121
  Angle     :  0.558  11.316  14886  Z= 0.271
  Chirality :  0.039   0.297   1630
  Planarity :  0.003   0.030   1890
  Dihedral  :  3.751  14.745   1420
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.63 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.23), residues: 1298
  helix:  1.87 (0.16), residues: 900
  sheet: -1.52 (0.74), residues: 58
  loop : -1.08 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 600 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.011   0.001   PHE B 379 
 TYR   0.016   0.001   TYR A 457 
 ARG   0.003   0.000   ARG B 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03403 (  730)
  hydrogen bonds       : angle       3.75549 ( 2142)
  covalent geometry    : bond        0.00272 (10974)
  covalent geometry    : angle       0.55831 (14886)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 1.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9124 (t) cc_final: 0.8461 (p)
REVERT: A  372 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8641 (tt0)
REVERT: A  531 ASN cc_start: 0.9124 (t0) cc_final: 0.8626 (t160)
REVERT: A  645 ARG cc_start: 0.7749 (mmp80) cc_final: 0.7370 (mmp80)
REVERT: B  203 SER cc_start: 0.9093 (t) cc_final: 0.8441 (p)
REVERT: B  531 ASN cc_start: 0.9121 (t0) cc_final: 0.8608 (t160)
REVERT: B  645 ARG cc_start: 0.7784 (mmp80) cc_final: 0.7392 (mmp80)
  outliers start: 24
  outliers final: 22
  residues processed: 123
  average time/residue: 0.1744
  time to fit residues: 33.6244
Evaluate side-chains
  121 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 94 optimal weight:    0.6980
   chunk 117 optimal weight:    0.0770
   chunk 100 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 611 HIS
B 326 GLN
B 715 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.111209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.084518 restraints weight = 23080.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.087280 restraints weight = 11640.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.088995 restraints weight = 7953.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10974  Z= 0.103
  Angle     :  0.546  11.560  14886  Z= 0.261
  Chirality :  0.039   0.300   1630
  Planarity :  0.003   0.030   1890
  Dihedral  :  3.656  14.804   1420
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.37 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.23), residues: 1298
  helix:  1.88 (0.16), residues: 920
  sheet: -1.47 (0.76), residues: 58
  loop : -1.28 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 235 
 HIS   0.003   0.000   HIS A 666 
 PHE   0.012   0.001   PHE B 379 
 TYR   0.016   0.001   TYR B 457 
 ARG   0.002   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03188 (  730)
  hydrogen bonds       : angle       3.66507 ( 2142)
  covalent geometry    : bond        0.00222 (10974)
  covalent geometry    : angle       0.54648 (14886)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3506.63 seconds
wall clock time: 65 minutes 29.42 seconds (3929.42 seconds total)