Starting phenix.real_space_refine
on Mon May 12 14:12:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l2e_62773/05_2025/9l2e_62773.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l2e_62773/05_2025/9l2e_62773.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l2e_62773/05_2025/9l2e_62773.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l2e_62773/05_2025/9l2e_62773.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l2e_62773/05_2025/9l2e_62773.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l2e_62773/05_2025/9l2e_62773.cif"
  }
  resolution = 2.46
  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=  -0.002 sd=   0.169
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5680      2.51       5
     N    1624      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9064
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1133
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 2, 'TRANS': 136}
  Restraints were copied for chains:
    C, B, E, D, G, F, H
  Time building chain proxies: 4.09, per 1000 atoms: 0.45
  Number of scatterers: 9064
  At special positions: 0
  Unit cell: (105.848, 105.848, 62.216, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1712      8.00
     N    1624      7.00
     C    5680      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: 2.63
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 0 sheets defined
      83.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 408 through 412
    Processing helix  chain 'A' and resid 413 through 424
    Processing helix  chain 'A' and resid 426 through 437
    Processing helix  chain 'A' and resid 439 through 445
    Processing helix  chain 'A' and resid 447 through 455
    Processing helix  chain 'A' and resid 459 through 476
      removed outlier: 3.507A  pdb=" N   PHE A 476 " --> pdb=" O   GLU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 495
      removed outlier: 3.865A  pdb=" N   TRP A 490 " --> pdb=" O   ASN A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 500
      removed outlier: 3.692A  pdb=" N   ARG A 499 " --> pdb=" O   PRO A 496 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN A 500 " --> pdb=" O   ARG A 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 496 through 500'
    Processing helix  chain 'A' and resid 501 through 508
      removed outlier: 3.742A  pdb=" N   CYS A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 518
      removed outlier: 3.705A  pdb=" N   LEU A 515 " --> pdb=" O   ARG A 512 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS A 516 " --> pdb=" O   SER A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 526
    Processing helix  chain 'A' and resid 531 through 545
    Processing helix  chain 'B' and resid 408 through 412
    Processing helix  chain 'B' and resid 413 through 424
    Processing helix  chain 'B' and resid 426 through 437
    Processing helix  chain 'B' and resid 439 through 445
    Processing helix  chain 'B' and resid 447 through 455
    Processing helix  chain 'B' and resid 459 through 476
      removed outlier: 3.506A  pdb=" N   PHE B 476 " --> pdb=" O   GLU B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 495
      removed outlier: 3.866A  pdb=" N   TRP B 490 " --> pdb=" O   ASN B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 500
      removed outlier: 3.692A  pdb=" N   ARG B 499 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN B 500 " --> pdb=" O   ARG B 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 496 through 500'
    Processing helix  chain 'B' and resid 501 through 508
      removed outlier: 3.742A  pdb=" N   CYS B 508 " --> pdb=" O   GLY B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 518
      removed outlier: 3.704A  pdb=" N   LEU B 515 " --> pdb=" O   ARG B 512 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS B 516 " --> pdb=" O   SER B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 526
    Processing helix  chain 'B' and resid 531 through 545
    Processing helix  chain 'C' and resid 408 through 412
    Processing helix  chain 'C' and resid 413 through 424
    Processing helix  chain 'C' and resid 426 through 437
    Processing helix  chain 'C' and resid 439 through 445
    Processing helix  chain 'C' and resid 447 through 455
    Processing helix  chain 'C' and resid 459 through 476
      removed outlier: 3.506A  pdb=" N   PHE C 476 " --> pdb=" O   GLU C 472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 486 through 495
      removed outlier: 3.866A  pdb=" N   TRP C 490 " --> pdb=" O   ASN C 486 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 500
      removed outlier: 3.693A  pdb=" N   ARG C 499 " --> pdb=" O   PRO C 496 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN C 500 " --> pdb=" O   ARG C 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 496 through 500'
    Processing helix  chain 'C' and resid 501 through 508
      removed outlier: 3.742A  pdb=" N   CYS C 508 " --> pdb=" O   GLY C 504 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 512 through 518
      removed outlier: 3.705A  pdb=" N   LEU C 515 " --> pdb=" O   ARG C 512 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS C 516 " --> pdb=" O   SER C 513 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 519 through 526
    Processing helix  chain 'C' and resid 531 through 545
    Processing helix  chain 'D' and resid 408 through 412
    Processing helix  chain 'D' and resid 413 through 424
    Processing helix  chain 'D' and resid 426 through 437
    Processing helix  chain 'D' and resid 439 through 445
    Processing helix  chain 'D' and resid 447 through 455
    Processing helix  chain 'D' and resid 459 through 476
      removed outlier: 3.507A  pdb=" N   PHE D 476 " --> pdb=" O   GLU D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 486 through 495
      removed outlier: 3.866A  pdb=" N   TRP D 490 " --> pdb=" O   ASN D 486 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 496 through 500
      removed outlier: 3.692A  pdb=" N   ARG D 499 " --> pdb=" O   PRO D 496 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN D 500 " --> pdb=" O   ARG D 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 496 through 500'
    Processing helix  chain 'D' and resid 501 through 508
      removed outlier: 3.741A  pdb=" N   CYS D 508 " --> pdb=" O   GLY D 504 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 512 through 518
      removed outlier: 3.706A  pdb=" N   LEU D 515 " --> pdb=" O   ARG D 512 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   HIS D 516 " --> pdb=" O   SER D 513 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 519 through 526
    Processing helix  chain 'D' and resid 531 through 545
    Processing helix  chain 'E' and resid 408 through 412
    Processing helix  chain 'E' and resid 413 through 424
    Processing helix  chain 'E' and resid 426 through 437
    Processing helix  chain 'E' and resid 439 through 445
    Processing helix  chain 'E' and resid 447 through 455
    Processing helix  chain 'E' and resid 459 through 476
      removed outlier: 3.506A  pdb=" N   PHE E 476 " --> pdb=" O   GLU E 472 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 486 through 495
      removed outlier: 3.866A  pdb=" N   TRP E 490 " --> pdb=" O   ASN E 486 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 496 through 500
      removed outlier: 3.692A  pdb=" N   ARG E 499 " --> pdb=" O   PRO E 496 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN E 500 " --> pdb=" O   ARG E 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 496 through 500'
    Processing helix  chain 'E' and resid 501 through 508
      removed outlier: 3.742A  pdb=" N   CYS E 508 " --> pdb=" O   GLY E 504 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 512 through 518
      removed outlier: 3.705A  pdb=" N   LEU E 515 " --> pdb=" O   ARG E 512 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS E 516 " --> pdb=" O   SER E 513 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 519 through 526
    Processing helix  chain 'E' and resid 531 through 545
    Processing helix  chain 'F' and resid 408 through 412
    Processing helix  chain 'F' and resid 413 through 424
    Processing helix  chain 'F' and resid 426 through 437
    Processing helix  chain 'F' and resid 439 through 445
    Processing helix  chain 'F' and resid 447 through 455
    Processing helix  chain 'F' and resid 459 through 476
      removed outlier: 3.506A  pdb=" N   PHE F 476 " --> pdb=" O   GLU F 472 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 486 through 495
      removed outlier: 3.865A  pdb=" N   TRP F 490 " --> pdb=" O   ASN F 486 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 496 through 500
      removed outlier: 3.693A  pdb=" N   ARG F 499 " --> pdb=" O   PRO F 496 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN F 500 " --> pdb=" O   ARG F 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 496 through 500'
    Processing helix  chain 'F' and resid 501 through 508
      removed outlier: 3.742A  pdb=" N   CYS F 508 " --> pdb=" O   GLY F 504 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 512 through 518
      removed outlier: 3.705A  pdb=" N   LEU F 515 " --> pdb=" O   ARG F 512 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS F 516 " --> pdb=" O   SER F 513 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 519 through 526
    Processing helix  chain 'F' and resid 531 through 545
    Processing helix  chain 'G' and resid 408 through 412
    Processing helix  chain 'G' and resid 413 through 424
    Processing helix  chain 'G' and resid 426 through 437
    Processing helix  chain 'G' and resid 439 through 445
    Processing helix  chain 'G' and resid 447 through 455
    Processing helix  chain 'G' and resid 459 through 476
      removed outlier: 3.506A  pdb=" N   PHE G 476 " --> pdb=" O   GLU G 472 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 486 through 495
      removed outlier: 3.866A  pdb=" N   TRP G 490 " --> pdb=" O   ASN G 486 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 496 through 500
      removed outlier: 3.691A  pdb=" N   ARG G 499 " --> pdb=" O   PRO G 496 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN G 500 " --> pdb=" O   ARG G 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 496 through 500'
    Processing helix  chain 'G' and resid 501 through 508
      removed outlier: 3.741A  pdb=" N   CYS G 508 " --> pdb=" O   GLY G 504 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 512 through 518
      removed outlier: 3.706A  pdb=" N   LEU G 515 " --> pdb=" O   ARG G 512 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS G 516 " --> pdb=" O   SER G 513 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 519 through 526
    Processing helix  chain 'G' and resid 531 through 545
    Processing helix  chain 'H' and resid 408 through 412
    Processing helix  chain 'H' and resid 413 through 424
    Processing helix  chain 'H' and resid 426 through 437
    Processing helix  chain 'H' and resid 439 through 445
    Processing helix  chain 'H' and resid 447 through 455
    Processing helix  chain 'H' and resid 459 through 476
      removed outlier: 3.506A  pdb=" N   PHE H 476 " --> pdb=" O   GLU H 472 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 486 through 495
      removed outlier: 3.866A  pdb=" N   TRP H 490 " --> pdb=" O   ASN H 486 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 496 through 500
      removed outlier: 3.693A  pdb=" N   ARG H 499 " --> pdb=" O   PRO H 496 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN H 500 " --> pdb=" O   ARG H 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 496 through 500'
    Processing helix  chain 'H' and resid 501 through 508
      removed outlier: 3.742A  pdb=" N   CYS H 508 " --> pdb=" O   GLY H 504 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 512 through 518
      removed outlier: 3.706A  pdb=" N   LEU H 515 " --> pdb=" O   ARG H 512 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS H 516 " --> pdb=" O   SER H 513 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 519 through 526
    Processing helix  chain 'H' and resid 531 through 545

    512 hydrogen bonds defined for protein.
    1440 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3072
        1.34 -     1.46: 1596
        1.46 -     1.57: 4500
        1.57 -     1.69: 0
        1.69 -     1.80: 64
  Bond restraints: 9232
  Sorted by residual:
  bond pdb=" N   TYR C 429 "
       pdb=" CA  TYR C 429 "
    ideal  model  delta    sigma   weight residual
    1.457  1.444  0.013 1.35e-02 5.49e+03 9.24e-01
  bond pdb=" N   TYR G 429 "
       pdb=" CA  TYR G 429 "
    ideal  model  delta    sigma   weight residual
    1.457  1.444  0.013 1.35e-02 5.49e+03 9.10e-01
  bond pdb=" N   TYR E 429 "
       pdb=" CA  TYR E 429 "
    ideal  model  delta    sigma   weight residual
    1.457  1.444  0.013 1.35e-02 5.49e+03 9.10e-01
  bond pdb=" N   TYR D 429 "
       pdb=" CA  TYR D 429 "
    ideal  model  delta    sigma   weight residual
    1.457  1.444  0.013 1.35e-02 5.49e+03 8.95e-01
  bond pdb=" N   TYR A 429 "
       pdb=" CA  TYR A 429 "
    ideal  model  delta    sigma   weight residual
    1.457  1.445  0.013 1.35e-02 5.49e+03 8.60e-01
  ... (remaining 9227 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 11836
        1.22 -     2.44: 516
        2.44 -     3.67: 56
        3.67 -     4.89: 8
        4.89 -     6.11: 16
  Bond angle restraints: 12432
  Sorted by residual:
  angle pdb=" C   VAL F 409 "
        pdb=" CA  VAL F 409 "
        pdb=" CB  VAL F 409 "
      ideal   model   delta    sigma   weight residual
     114.35  111.65    2.70 1.06e+00 8.90e-01 6.51e+00
  angle pdb=" C   VAL C 409 "
        pdb=" CA  VAL C 409 "
        pdb=" CB  VAL C 409 "
      ideal   model   delta    sigma   weight residual
     114.35  111.67    2.68 1.06e+00 8.90e-01 6.41e+00
  angle pdb=" C   VAL D 409 "
        pdb=" CA  VAL D 409 "
        pdb=" CB  VAL D 409 "
      ideal   model   delta    sigma   weight residual
     114.35  111.68    2.67 1.06e+00 8.90e-01 6.34e+00
  angle pdb=" C   VAL A 409 "
        pdb=" CA  VAL A 409 "
        pdb=" CB  VAL A 409 "
      ideal   model   delta    sigma   weight residual
     114.35  111.69    2.66 1.06e+00 8.90e-01 6.32e+00
  angle pdb=" C   VAL B 409 "
        pdb=" CA  VAL B 409 "
        pdb=" CB  VAL B 409 "
      ideal   model   delta    sigma   weight residual
     114.35  111.70    2.65 1.06e+00 8.90e-01 6.26e+00
  ... (remaining 12427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 4560
       17.11 -    34.21: 656
       34.21 -    51.32: 224
       51.32 -    68.43: 80
       68.43 -    85.53: 40
  Dihedral angle restraints: 5560
    sinusoidal: 2344
      harmonic: 3216
  Sorted by residual:
  dihedral pdb=" CA  LEU B 514 "
           pdb=" CB  LEU B 514 "
           pdb=" CG  LEU B 514 "
           pdb=" CD1 LEU B 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.34  -59.34     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LEU F 514 "
           pdb=" CB  LEU F 514 "
           pdb=" CG  LEU F 514 "
           pdb=" CD1 LEU F 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.30  -59.30     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LEU A 514 "
           pdb=" CB  LEU A 514 "
           pdb=" CG  LEU A 514 "
           pdb=" CD1 LEU A 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.29  -59.29     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.021: 562
       0.021 -    0.042: 445
       0.042 -    0.062: 208
       0.062 -    0.083: 86
       0.083 -    0.104: 51
  Chirality restraints: 1352
  Sorted by residual:
  chirality pdb=" CA  PRO B 410 "
            pdb=" N   PRO B 410 "
            pdb=" C   PRO B 410 "
            pdb=" CB  PRO B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.10 2.00e-01 2.50e+01 2.70e-01
  chirality pdb=" CA  PRO H 410 "
            pdb=" N   PRO H 410 "
            pdb=" C   PRO H 410 "
            pdb=" CB  PRO H 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.10 2.00e-01 2.50e+01 2.69e-01
  chirality pdb=" CA  ILE H 529 "
            pdb=" N   ILE H 529 "
            pdb=" C   ILE H 529 "
            pdb=" CB  ILE H 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.68e-01
  ... (remaining 1349 not shown)

  Planarity restraints: 1600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 441 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" CG  ASP C 441 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 441 "    0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 441 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP F 441 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.34e+00
        pdb=" CG  ASP F 441 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASP F 441 "    0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP F 441 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 441 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" CG  ASP B 441 "    0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 441 "   -0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 441 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1597 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 96
        2.62 -     3.19: 7746
        3.19 -     3.76: 14900
        3.76 -     4.33: 20786
        4.33 -     4.90: 34392
  Nonbonded interactions: 77920
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 459 "
            pdb=" OD2 ASP H 454 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" OD2 ASP E 454 "
            pdb=" OG  SER F 459 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" OD2 ASP G 454 "
            pdb=" OG  SER H 459 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OD2 ASP F 454 "
            pdb=" OG  SER G 459 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OD2 ASP D 454 "
            pdb=" OG  SER E 459 "
     model   vdw
     2.118 3.040
  ... (remaining 77915 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.040
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9232  Z= 0.157
  Angle     :  0.582   6.110  12432  Z= 0.334
  Chirality :  0.038   0.104   1352
  Planarity :  0.004   0.026   1600
  Dihedral  : 20.563  85.535   3480
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 31.25 %
    Favored  : 66.94 %
  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:  1.27 (0.26), residues: 1096
  helix:  0.88 (0.19), residues: 808
  sheet:  None (None), residues: 0
  loop :  1.16 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 412 
 HIS   0.003   0.001   HIS D 516 
 PHE   0.012   0.002   PHE H 467 
 TYR   0.010   0.002   TYR H 503 
 ARG   0.004   0.000   ARG B 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16882 (  512)
  hydrogen bonds       : angle       5.86197 ( 1440)
  covalent geometry    : bond        0.00334 ( 9232)
  covalent geometry    : angle       0.58162 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 247
  time to evaluate  : 1.132 
Fit side-chains
REVERT: A  486 ASN cc_start: 0.8012 (t0) cc_final: 0.7168 (t0)
REVERT: A  489 ASP cc_start: 0.7241 (m-30) cc_final: 0.6925 (p0)
REVERT: C  520 GLU cc_start: 0.7642 (tp30) cc_final: 0.7414 (tp30)
REVERT: E  486 ASN cc_start: 0.8079 (t0) cc_final: 0.7375 (t0)
REVERT: E  489 ASP cc_start: 0.7201 (m-30) cc_final: 0.6950 (p0)
REVERT: G  486 ASN cc_start: 0.8015 (t0) cc_final: 0.7264 (t0)
REVERT: G  489 ASP cc_start: 0.7195 (m-30) cc_final: 0.6926 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 255
  average time/residue: 1.4331
  time to fit residues: 384.7837
Evaluate side-chains
  247 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 232
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  462 THR
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  462 THR
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  462 THR
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  462 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 42 optimal weight:    0.3980
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 436 GLN
B 436 GLN
C 436 GLN
D 436 GLN
E 436 GLN
F 436 GLN
G 436 GLN
H 436 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.188795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.168712 restraints weight = 9176.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 1.34
r_work: 0.3712 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9232  Z= 0.161
  Angle     :  0.553   6.129  12432  Z= 0.299
  Chirality :  0.039   0.105   1352
  Planarity :  0.004   0.025   1600
  Dihedral  :  6.444  55.404   1263
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.02 %
    Favored  : 68.04 %
  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:  2.05 (0.28), residues: 1096
  helix:  1.11 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  2.48 (0.43), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 412 
 HIS   0.002   0.001   HIS G 516 
 PHE   0.009   0.002   PHE E 433 
 TYR   0.012   0.002   TYR E 503 
 ARG   0.003   0.000   ARG C 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05357 (  512)
  hydrogen bonds       : angle       5.26988 ( 1440)
  covalent geometry    : bond        0.00343 ( 9232)
  covalent geometry    : angle       0.55272 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 251
  time to evaluate  : 1.082 
Fit side-chains
REVERT: A  446 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7400 (tt)
REVERT: A  486 ASN cc_start: 0.8263 (t0) cc_final: 0.7434 (t0)
REVERT: A  489 ASP cc_start: 0.7873 (m-30) cc_final: 0.7263 (p0)
REVERT: A  515 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7499 (mt)
REVERT: B  446 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7649 (tt)
REVERT: B  515 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7484 (mt)
REVERT: C  446 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7436 (tt)
REVERT: C  520 GLU cc_start: 0.7801 (tp30) cc_final: 0.7491 (tp30)
REVERT: D  446 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7660 (tt)
REVERT: D  489 ASP cc_start: 0.7715 (m-30) cc_final: 0.7411 (p0)
REVERT: D  515 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7565 (mt)
REVERT: E  414 GLU cc_start: 0.7410 (mp0) cc_final: 0.7137 (mt-10)
REVERT: E  446 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7381 (tt)
REVERT: E  486 ASN cc_start: 0.8239 (t0) cc_final: 0.7420 (t0)
REVERT: E  489 ASP cc_start: 0.7878 (m-30) cc_final: 0.7280 (p0)
REVERT: E  515 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7478 (mt)
REVERT: F  446 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7654 (tt)
REVERT: F  489 ASP cc_start: 0.7753 (m-30) cc_final: 0.7398 (p0)
REVERT: F  515 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7487 (mt)
REVERT: G  414 GLU cc_start: 0.7473 (mp0) cc_final: 0.7186 (mt-10)
REVERT: G  446 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7341 (tt)
REVERT: G  486 ASN cc_start: 0.8192 (t0) cc_final: 0.7317 (t0)
REVERT: G  489 ASP cc_start: 0.7799 (m-30) cc_final: 0.7229 (p0)
REVERT: G  515 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7495 (mt)
REVERT: H  446 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7672 (tt)
REVERT: H  489 ASP cc_start: 0.7721 (m-30) cc_final: 0.7417 (p0)
REVERT: H  515 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7521 (mt)
  outliers start: 49
  outliers final: 13
  residues processed: 267
  average time/residue: 1.4524
  time to fit residues: 408.8796
Evaluate side-chains
  256 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 228
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  540 THR
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  462 THR
Chi-restraints excluded: chain C residue  540 THR
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  515 LEU
Chi-restraints excluded: chain D residue  540 THR
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain E residue  454 ASP
Chi-restraints excluded: chain E residue  462 THR
Chi-restraints excluded: chain E residue  515 LEU
Chi-restraints excluded: chain E residue  540 THR
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  515 LEU
Chi-restraints excluded: chain F residue  540 THR
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  462 THR
Chi-restraints excluded: chain G residue  515 LEU
Chi-restraints excluded: chain G residue  540 THR
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  515 LEU
Chi-restraints excluded: chain H residue  540 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0470
   chunk 70 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
F 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.194782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.175730 restraints weight = 9598.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 1.31
r_work: 0.3826 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9232  Z= 0.149
  Angle     :  0.541   6.471  12432  Z= 0.285
  Chirality :  0.038   0.106   1352
  Planarity :  0.004   0.027   1600
  Dihedral  :  6.297  56.763   1258
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 27.42 %
    Favored  : 67.44 %
  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:  2.07 (0.27), residues: 1096
  helix:  1.18 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  2.33 (0.42), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 412 
 HIS   0.002   0.001   HIS A 516 
 PHE   0.010   0.002   PHE C 433 
 TYR   0.011   0.002   TYR A 503 
 ARG   0.003   0.000   ARG C 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05096 (  512)
  hydrogen bonds       : angle       5.16829 ( 1440)
  covalent geometry    : bond        0.00311 ( 9232)
  covalent geometry    : angle       0.54066 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 247
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.7434 (mp0) cc_final: 0.7145 (mt-10)
REVERT: A  446 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7364 (tt)
REVERT: A  515 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7540 (mt)
REVERT: B  414 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7391 (mt-10)
REVERT: B  446 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7577 (tt)
REVERT: B  515 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7512 (mt)
REVERT: C  446 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7354 (tt)
REVERT: C  515 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7370 (mt)
REVERT: D  446 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7578 (tt)
REVERT: D  489 ASP cc_start: 0.7877 (m-30) cc_final: 0.7511 (p0)
REVERT: D  515 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7606 (mt)
REVERT: E  414 GLU cc_start: 0.7432 (mp0) cc_final: 0.7179 (mt-10)
REVERT: E  446 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7323 (tt)
REVERT: E  486 ASN cc_start: 0.8335 (t0) cc_final: 0.8123 (t0)
REVERT: E  515 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7542 (mt)
REVERT: F  446 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7571 (tt)
REVERT: F  489 ASP cc_start: 0.7894 (m-30) cc_final: 0.7518 (p0)
REVERT: F  515 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7534 (mt)
REVERT: G  414 GLU cc_start: 0.7364 (mp0) cc_final: 0.7126 (mt-10)
REVERT: G  446 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7274 (tt)
REVERT: G  486 ASN cc_start: 0.8293 (t0) cc_final: 0.8075 (t0)
REVERT: G  515 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7521 (mt)
REVERT: H  446 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7596 (tt)
REVERT: H  489 ASP cc_start: 0.7761 (m-30) cc_final: 0.7504 (p0)
REVERT: H  515 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7562 (mt)
  outliers start: 51
  outliers final: 7
  residues processed: 267
  average time/residue: 1.4104
  time to fit residues: 396.6881
Evaluate side-chains
  258 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 235
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  513 SER
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  513 SER
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  513 SER
Chi-restraints excluded: chain D residue  515 LEU
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain E residue  462 THR
Chi-restraints excluded: chain E residue  515 LEU
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  513 SER
Chi-restraints excluded: chain F residue  515 LEU
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  515 LEU
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  513 SER
Chi-restraints excluded: chain H residue  515 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0000
   chunk 94 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.1188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.192731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.173554 restraints weight = 9472.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 1.30
r_work: 0.3800 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9232  Z= 0.195
  Angle     :  0.607   6.532  12432  Z= 0.318
  Chirality :  0.041   0.109   1352
  Planarity :  0.004   0.028   1600
  Dihedral  :  6.604  59.319   1256
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  6.75 %
    Allowed  : 24.70 %
    Favored  : 68.55 %
  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:  1.83 (0.27), residues: 1096
  helix:  1.08 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  2.00 (0.41), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 412 
 HIS   0.002   0.001   HIS C 516 
 PHE   0.011   0.002   PHE A 433 
 TYR   0.013   0.002   TYR A 503 
 ARG   0.003   0.000   ARG G 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05600 (  512)
  hydrogen bonds       : angle       5.40715 ( 1440)
  covalent geometry    : bond        0.00427 ( 9232)
  covalent geometry    : angle       0.60681 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 232
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A  446 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7379 (tt)
REVERT: A  515 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7509 (mt)
REVERT: B  414 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7346 (mt-10)
REVERT: B  446 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7677 (tt)
REVERT: B  450 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6713 (mp0)
REVERT: B  515 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7549 (mt)
REVERT: C  446 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7383 (tt)
REVERT: C  494 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7544 (mt)
REVERT: C  515 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7408 (mt)
REVERT: D  446 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7687 (tt)
REVERT: D  515 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7623 (mt)
REVERT: E  414 GLU cc_start: 0.7448 (mp0) cc_final: 0.7165 (mt-10)
REVERT: E  446 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7381 (tt)
REVERT: E  515 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7481 (mt)
REVERT: F  446 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7667 (tt)
REVERT: F  450 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6672 (mp0)
REVERT: F  515 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7581 (mt)
REVERT: G  414 GLU cc_start: 0.7443 (mp0) cc_final: 0.7165 (mt-10)
REVERT: G  446 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7360 (tt)
REVERT: G  515 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7493 (mt)
REVERT: H  446 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7692 (tt)
REVERT: H  515 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7587 (mt)
  outliers start: 67
  outliers final: 31
  residues processed: 259
  average time/residue: 1.3290
  time to fit residues: 363.6922
Evaluate side-chains
  279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 228
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  489 ASP
Chi-restraints excluded: chain B residue  513 SER
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  540 THR
Chi-restraints excluded: chain C residue  441 ASP
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  462 THR
Chi-restraints excluded: chain C residue  494 LEU
Chi-restraints excluded: chain C residue  513 SER
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  540 THR
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  454 ASP
Chi-restraints excluded: chain D residue  462 THR
Chi-restraints excluded: chain D residue  487 LEU
Chi-restraints excluded: chain D residue  515 LEU
Chi-restraints excluded: chain D residue  540 THR
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain E residue  462 THR
Chi-restraints excluded: chain E residue  487 LEU
Chi-restraints excluded: chain E residue  515 LEU
Chi-restraints excluded: chain E residue  540 THR
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  450 GLU
Chi-restraints excluded: chain F residue  454 ASP
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  513 SER
Chi-restraints excluded: chain F residue  515 LEU
Chi-restraints excluded: chain F residue  540 THR
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  462 THR
Chi-restraints excluded: chain G residue  487 LEU
Chi-restraints excluded: chain G residue  515 LEU
Chi-restraints excluded: chain G residue  540 THR
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  454 ASP
Chi-restraints excluded: chain H residue  462 THR
Chi-restraints excluded: chain H residue  513 SER
Chi-restraints excluded: chain H residue  515 LEU
Chi-restraints excluded: chain H residue  540 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.194141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.174971 restraints weight = 9416.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 1.29
r_work: 0.3820 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3699 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9232  Z= 0.158
  Angle     :  0.562   6.386  12432  Z= 0.292
  Chirality :  0.038   0.107   1352
  Planarity :  0.004   0.028   1600
  Dihedral  :  6.569  59.928   1256
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 28.02 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.27), residues: 1096
  helix:  1.10 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  1.88 (0.41), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 490 
 HIS   0.002   0.000   HIS C 516 
 PHE   0.010   0.002   PHE E 433 
 TYR   0.012   0.002   TYR G 503 
 ARG   0.002   0.000   ARG G 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05016 (  512)
  hydrogen bonds       : angle       5.22332 ( 1440)
  covalent geometry    : bond        0.00336 ( 9232)
  covalent geometry    : angle       0.56200 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 236
  time to evaluate  : 1.153 
Fit side-chains
REVERT: A  446 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7369 (tt)
REVERT: A  515 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7511 (mt)
REVERT: B  414 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7351 (mt-10)
REVERT: B  446 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7687 (tt)
REVERT: B  450 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6674 (mp0)
REVERT: C  446 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7376 (tt)
REVERT: D  446 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7695 (tt)
REVERT: D  450 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6698 (mp0)
REVERT: D  489 ASP cc_start: 0.7885 (m-30) cc_final: 0.7411 (p0)
REVERT: D  515 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7580 (mt)
REVERT: E  414 GLU cc_start: 0.7416 (mp0) cc_final: 0.7153 (mt-10)
REVERT: E  446 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7380 (tt)
REVERT: E  515 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7491 (mt)
REVERT: F  414 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: F  446 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7686 (tt)
REVERT: F  489 ASP cc_start: 0.7878 (m-30) cc_final: 0.7425 (p0)
REVERT: G  414 GLU cc_start: 0.7432 (mp0) cc_final: 0.7163 (mt-10)
REVERT: G  446 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7315 (tt)
REVERT: G  515 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7491 (mt)
REVERT: H  446 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7682 (tt)
REVERT: H  450 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6704 (mp0)
REVERT: H  515 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7549 (mt)
  outliers start: 38
  outliers final: 8
  residues processed: 253
  average time/residue: 1.4306
  time to fit residues: 381.4663
Evaluate side-chains
  248 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 223
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  513 SER
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  450 GLU
Chi-restraints excluded: chain D residue  462 THR
Chi-restraints excluded: chain D residue  487 LEU
Chi-restraints excluded: chain D residue  515 LEU
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain E residue  487 LEU
Chi-restraints excluded: chain E residue  515 LEU
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  487 LEU
Chi-restraints excluded: chain G residue  515 LEU
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  450 GLU
Chi-restraints excluded: chain H residue  462 THR
Chi-restraints excluded: chain H residue  515 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.193841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.174832 restraints weight = 9389.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 1.28
r_work: 0.3817 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9232  Z= 0.156
  Angle     :  0.534   5.901  12432  Z= 0.286
  Chirality :  0.038   0.107   1352
  Planarity :  0.004   0.029   1600
  Dihedral  :  6.532  59.971   1256
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 25.81 %
    Favored  : 69.66 %
  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:  1.73 (0.27), residues: 1096
  helix:  1.08 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  1.75 (0.41), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 412 
 HIS   0.001   0.000   HIS C 516 
 PHE   0.010   0.002   PHE E 433 
 TYR   0.012   0.002   TYR G 503 
 ARG   0.002   0.000   ARG E 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04958 (  512)
  hydrogen bonds       : angle       5.17915 ( 1440)
  covalent geometry    : bond        0.00331 ( 9232)
  covalent geometry    : angle       0.53383 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 228
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.7325 (mp0) cc_final: 0.7052 (mt-10)
REVERT: A  446 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7369 (tt)
REVERT: A  515 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7544 (mt)
REVERT: B  414 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7352 (mt-10)
REVERT: B  446 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: B  450 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6691 (mp0)
REVERT: B  515 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7603 (mt)
REVERT: C  446 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7351 (tt)
REVERT: D  446 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7692 (tt)
REVERT: D  450 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6735 (mp0)
REVERT: D  515 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7658 (mt)
REVERT: E  414 GLU cc_start: 0.7395 (mp0) cc_final: 0.7130 (mt-10)
REVERT: E  446 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7358 (tt)
REVERT: E  515 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7541 (mt)
REVERT: F  446 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7679 (tt)
REVERT: F  450 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6683 (mp0)
REVERT: F  515 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7598 (mt)
REVERT: G  414 GLU cc_start: 0.7419 (mp0) cc_final: 0.7153 (mt-10)
REVERT: G  446 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7361 (tt)
REVERT: G  515 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7531 (mt)
REVERT: H  446 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7679 (tt)
REVERT: H  450 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6705 (mp0)
REVERT: H  489 ASP cc_start: 0.7785 (m-30) cc_final: 0.7463 (p0)
  outliers start: 45
  outliers final: 20
  residues processed: 248
  average time/residue: 1.3637
  time to fit residues: 357.2194
Evaluate side-chains
  266 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 227
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  540 THR
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  462 THR
Chi-restraints excluded: chain C residue  487 LEU
Chi-restraints excluded: chain C residue  540 THR
Chi-restraints excluded: chain D residue  430 CYS
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  450 GLU
Chi-restraints excluded: chain D residue  462 THR
Chi-restraints excluded: chain D residue  487 LEU
Chi-restraints excluded: chain D residue  515 LEU
Chi-restraints excluded: chain D residue  540 THR
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain E residue  487 LEU
Chi-restraints excluded: chain E residue  515 LEU
Chi-restraints excluded: chain F residue  430 CYS
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  450 GLU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  487 LEU
Chi-restraints excluded: chain F residue  515 LEU
Chi-restraints excluded: chain F residue  540 THR
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  487 LEU
Chi-restraints excluded: chain G residue  515 LEU
Chi-restraints excluded: chain H residue  430 CYS
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  450 GLU
Chi-restraints excluded: chain H residue  462 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 70 optimal weight:    0.3980
   chunk 51 optimal weight:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.194522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.175214 restraints weight = 9506.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 1.30
r_work: 0.3823 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9232  Z= 0.143
  Angle     :  0.517   5.865  12432  Z= 0.276
  Chirality :  0.037   0.107   1352
  Planarity :  0.004   0.029   1600
  Dihedral  :  6.462  59.951   1256
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 26.31 %
    Favored  : 69.96 %
  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:  1.81 (0.27), residues: 1096
  helix:  1.14 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  1.76 (0.41), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 490 
 HIS   0.001   0.000   HIS C 516 
 PHE   0.009   0.002   PHE G 433 
 TYR   0.011   0.002   TYR A 503 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04730 (  512)
  hydrogen bonds       : angle       5.07862 ( 1440)
  covalent geometry    : bond        0.00299 ( 9232)
  covalent geometry    : angle       0.51677 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 237
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.7297 (mp0) cc_final: 0.7034 (mt-10)
REVERT: A  446 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7338 (tt)
REVERT: A  457 MET cc_start: 0.6224 (mmt) cc_final: 0.5706 (mmt)
REVERT: A  489 ASP cc_start: 0.7843 (m-30) cc_final: 0.7407 (p0)
REVERT: A  515 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7524 (mt)
REVERT: B  446 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7670 (tt)
REVERT: B  450 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6659 (mp0)
REVERT: B  515 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7612 (mt)
REVERT: C  446 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7360 (tt)
REVERT: D  446 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7669 (tt)
REVERT: D  450 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6719 (mp0)
REVERT: D  489 ASP cc_start: 0.7725 (m-30) cc_final: 0.7401 (p0)
REVERT: D  515 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7660 (mt)
REVERT: E  414 GLU cc_start: 0.7398 (mp0) cc_final: 0.7134 (mt-10)
REVERT: E  446 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7330 (tt)
REVERT: E  489 ASP cc_start: 0.7848 (m-30) cc_final: 0.7344 (p0)
REVERT: E  515 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7519 (mt)
REVERT: F  446 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7660 (tt)
REVERT: F  450 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6703 (mp0)
REVERT: F  489 ASP cc_start: 0.7689 (m-30) cc_final: 0.7387 (p0)
REVERT: G  414 GLU cc_start: 0.7401 (mp0) cc_final: 0.7139 (mt-10)
REVERT: G  446 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7337 (tt)
REVERT: G  457 MET cc_start: 0.6247 (mmt) cc_final: 0.5725 (mmt)
REVERT: G  489 ASP cc_start: 0.7842 (m-30) cc_final: 0.7351 (p0)
REVERT: G  515 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7499 (mt)
REVERT: H  446 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7677 (tt)
REVERT: H  450 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6682 (mp0)
REVERT: H  489 ASP cc_start: 0.7793 (m-30) cc_final: 0.7527 (p0)
  outliers start: 37
  outliers final: 13
  residues processed: 260
  average time/residue: 1.4138
  time to fit residues: 387.1625
Evaluate side-chains
  258 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 228
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  540 THR
Chi-restraints excluded: chain C residue  430 CYS
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  487 LEU
Chi-restraints excluded: chain C residue  540 THR
Chi-restraints excluded: chain D residue  430 CYS
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  450 GLU
Chi-restraints excluded: chain D residue  515 LEU
Chi-restraints excluded: chain E residue  430 CYS
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain E residue  515 LEU
Chi-restraints excluded: chain F residue  430 CYS
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  450 GLU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  540 THR
Chi-restraints excluded: chain G residue  430 CYS
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  515 LEU
Chi-restraints excluded: chain H residue  430 CYS
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  450 GLU
Chi-restraints excluded: chain H residue  462 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0050
   chunk 63 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.7598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.193984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.174557 restraints weight = 9654.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 1.32
r_work: 0.3809 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9232  Z= 0.151
  Angle     :  0.523   5.596  12432  Z= 0.283
  Chirality :  0.038   0.107   1352
  Planarity :  0.004   0.029   1600
  Dihedral  :  6.479  59.959   1256
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 25.30 %
    Favored  : 70.56 %
  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:  1.76 (0.27), residues: 1096
  helix:  1.11 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  1.73 (0.41), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 490 
 HIS   0.001   0.000   HIS C 516 
 PHE   0.010   0.002   PHE A 433 
 TYR   0.012   0.002   TYR A 503 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04802 (  512)
  hydrogen bonds       : angle       5.11741 ( 1440)
  covalent geometry    : bond        0.00320 ( 9232)
  covalent geometry    : angle       0.52325 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 228
  time to evaluate  : 1.112 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.7361 (mp0) cc_final: 0.7092 (mt-10)
REVERT: A  446 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7341 (tt)
REVERT: A  489 ASP cc_start: 0.7930 (m-30) cc_final: 0.7468 (p0)
REVERT: A  515 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7534 (mt)
REVERT: B  446 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: B  450 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6665 (mp0)
REVERT: B  515 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7632 (mt)
REVERT: C  446 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7352 (tt)
REVERT: C  457 MET cc_start: 0.6188 (mmt) cc_final: 0.5731 (mmt)
REVERT: C  489 ASP cc_start: 0.7815 (m-30) cc_final: 0.7346 (p0)
REVERT: D  446 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7677 (tt)
REVERT: D  450 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6714 (mp0)
REVERT: D  489 ASP cc_start: 0.7807 (m-30) cc_final: 0.7532 (p0)
REVERT: D  515 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7683 (mt)
REVERT: E  414 GLU cc_start: 0.7405 (mp0) cc_final: 0.7140 (mt-10)
REVERT: E  446 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7322 (tt)
REVERT: E  457 MET cc_start: 0.6212 (mmt) cc_final: 0.5735 (mmt)
REVERT: E  489 ASP cc_start: 0.7834 (m-30) cc_final: 0.7416 (p0)
REVERT: E  515 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7517 (mt)
REVERT: F  446 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7677 (tt)
REVERT: F  450 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6704 (mp0)
REVERT: F  515 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7618 (mt)
REVERT: G  414 GLU cc_start: 0.7458 (mp0) cc_final: 0.7188 (mt-10)
REVERT: G  446 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7352 (tt)
REVERT: G  489 ASP cc_start: 0.7827 (m-30) cc_final: 0.7424 (p0)
REVERT: G  515 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7513 (mt)
REVERT: H  446 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7669 (tt)
REVERT: H  450 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6696 (mp0)
REVERT: H  515 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7635 (mt)
  outliers start: 41
  outliers final: 21
  residues processed: 254
  average time/residue: 1.4443
  time to fit residues: 386.8442
Evaluate side-chains
  266 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 226
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  430 CYS
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  540 THR
Chi-restraints excluded: chain C residue  430 CYS
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  487 LEU
Chi-restraints excluded: chain C residue  540 THR
Chi-restraints excluded: chain D residue  430 CYS
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  450 GLU
Chi-restraints excluded: chain D residue  462 THR
Chi-restraints excluded: chain D residue  487 LEU
Chi-restraints excluded: chain D residue  515 LEU
Chi-restraints excluded: chain D residue  540 THR
Chi-restraints excluded: chain E residue  430 CYS
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain E residue  515 LEU
Chi-restraints excluded: chain F residue  414 GLU
Chi-restraints excluded: chain F residue  430 CYS
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  450 GLU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  515 LEU
Chi-restraints excluded: chain F residue  540 THR
Chi-restraints excluded: chain G residue  430 CYS
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain G residue  515 LEU
Chi-restraints excluded: chain G residue  540 THR
Chi-restraints excluded: chain H residue  414 GLU
Chi-restraints excluded: chain H residue  430 CYS
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  450 GLU
Chi-restraints excluded: chain H residue  462 THR
Chi-restraints excluded: chain H residue  515 LEU
Chi-restraints excluded: chain H residue  540 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   chunk 83 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 58 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.195505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.176280 restraints weight = 9426.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 1.31
r_work: 0.3835 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9232  Z= 0.130
  Angle     :  0.503   5.777  12432  Z= 0.270
  Chirality :  0.036   0.108   1352
  Planarity :  0.004   0.030   1600
  Dihedral  :  6.402  59.598   1256
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 26.61 %
    Favored  : 70.36 %
  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:  1.98 (0.27), residues: 1096
  helix:  1.27 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  1.82 (0.40), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 490 
 HIS   0.002   0.000   HIS D 516 
 PHE   0.009   0.002   PHE C 433 
 TYR   0.011   0.001   TYR C 503 
 ARG   0.002   0.000   ARG H 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04418 (  512)
  hydrogen bonds       : angle       5.00125 ( 1440)
  covalent geometry    : bond        0.00268 ( 9232)
  covalent geometry    : angle       0.50269 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 223
  time to evaluate  : 1.176 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.7266 (mp0) cc_final: 0.7001 (mt-10)
REVERT: A  446 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7352 (tt)
REVERT: A  457 MET cc_start: 0.6093 (mmt) cc_final: 0.5765 (mmt)
REVERT: A  489 ASP cc_start: 0.7840 (m-30) cc_final: 0.7381 (p0)
REVERT: A  515 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7551 (mt)
REVERT: B  446 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7648 (tt)
REVERT: C  446 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7363 (tt)
REVERT: C  457 MET cc_start: 0.6148 (mmt) cc_final: 0.5577 (mmt)
REVERT: C  489 ASP cc_start: 0.7796 (m-30) cc_final: 0.7330 (p0)
REVERT: D  446 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7640 (tt)
REVERT: D  450 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6683 (mp0)
REVERT: D  489 ASP cc_start: 0.7735 (m-30) cc_final: 0.7486 (p0)
REVERT: E  414 GLU cc_start: 0.7348 (mp0) cc_final: 0.7083 (mt-10)
REVERT: E  446 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7344 (tt)
REVERT: E  457 MET cc_start: 0.6199 (mmt) cc_final: 0.5602 (mmt)
REVERT: E  489 ASP cc_start: 0.7787 (m-30) cc_final: 0.7366 (p0)
REVERT: F  446 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7643 (tt)
REVERT: F  450 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6651 (mp0)
REVERT: F  489 ASP cc_start: 0.7642 (m-30) cc_final: 0.7371 (p0)
REVERT: F  515 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7607 (mt)
REVERT: G  414 GLU cc_start: 0.7372 (mp0) cc_final: 0.7108 (mt-10)
REVERT: G  446 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7327 (tt)
REVERT: G  457 MET cc_start: 0.6077 (mmt) cc_final: 0.5749 (mmt)
REVERT: G  489 ASP cc_start: 0.7799 (m-30) cc_final: 0.7386 (p0)
REVERT: H  446 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7637 (tt)
REVERT: H  450 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6661 (mp0)
REVERT: H  489 ASP cc_start: 0.7659 (m-30) cc_final: 0.7408 (p0)
REVERT: H  515 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7625 (mt)
  outliers start: 30
  outliers final: 8
  residues processed: 246
  average time/residue: 1.4805
  time to fit residues: 383.1651
Evaluate side-chains
  240 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  430 CYS
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain C residue  430 CYS
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain D residue  430 CYS
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  450 GLU
Chi-restraints excluded: chain E residue  430 CYS
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain F residue  430 CYS
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  450 GLU
Chi-restraints excluded: chain F residue  515 LEU
Chi-restraints excluded: chain G residue  430 CYS
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain H residue  430 CYS
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  450 GLU
Chi-restraints excluded: chain H residue  515 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.194058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.174702 restraints weight = 9551.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 1.31
r_work: 0.3813 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9232  Z= 0.158
  Angle     :  0.539   5.671  12432  Z= 0.291
  Chirality :  0.038   0.107   1352
  Planarity :  0.004   0.030   1600
  Dihedral  :  6.450  59.557   1256
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 26.21 %
    Favored  : 70.36 %
  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:  1.83 (0.27), residues: 1096
  helix:  1.15 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  1.77 (0.41), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 490 
 HIS   0.001   0.000   HIS F 516 
 PHE   0.010   0.002   PHE C 433 
 TYR   0.012   0.002   TYR G 503 
 ARG   0.003   0.000   ARG D 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04838 (  512)
  hydrogen bonds       : angle       5.10689 ( 1440)
  covalent geometry    : bond        0.00338 ( 9232)
  covalent geometry    : angle       0.53892 (12432)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 217
  time to evaluate  : 1.208 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.7286 (mp0) cc_final: 0.7020 (mt-10)
REVERT: A  446 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7383 (tt)
REVERT: A  515 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7587 (mt)
REVERT: B  446 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7667 (tt)
REVERT: B  515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7594 (mt)
REVERT: C  446 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7363 (tt)
REVERT: C  457 MET cc_start: 0.6191 (mmt) cc_final: 0.5734 (mmt)
REVERT: C  489 ASP cc_start: 0.7904 (m-30) cc_final: 0.7401 (p0)
REVERT: D  446 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7676 (tt)
REVERT: D  450 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6693 (mp0)
REVERT: D  489 ASP cc_start: 0.7780 (m-30) cc_final: 0.7519 (p0)
REVERT: E  414 GLU cc_start: 0.7341 (mp0) cc_final: 0.7079 (mt-10)
REVERT: E  446 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7336 (tt)
REVERT: E  489 ASP cc_start: 0.7899 (m-30) cc_final: 0.7434 (p0)
REVERT: F  446 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7670 (tt)
REVERT: F  450 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6659 (mp0)
REVERT: F  489 ASP cc_start: 0.7662 (m-30) cc_final: 0.7370 (p0)
REVERT: F  515 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7638 (mt)
REVERT: G  414 GLU cc_start: 0.7429 (mp0) cc_final: 0.7154 (mt-10)
REVERT: G  446 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7384 (tt)
REVERT: G  489 ASP cc_start: 0.7871 (m-30) cc_final: 0.7428 (p0)
REVERT: H  446 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7655 (tt)
REVERT: H  450 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6692 (mp0)
REVERT: H  489 ASP cc_start: 0.7678 (m-30) cc_final: 0.7421 (p0)
REVERT: H  515 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7644 (mt)
  outliers start: 34
  outliers final: 16
  residues processed: 238
  average time/residue: 1.4892
  time to fit residues: 372.8356
Evaluate side-chains
  247 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 216
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  430 CYS
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain C residue  430 CYS
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain D residue  430 CYS
Chi-restraints excluded: chain D residue  446 LEU
Chi-restraints excluded: chain D residue  450 GLU
Chi-restraints excluded: chain D residue  462 THR
Chi-restraints excluded: chain E residue  430 CYS
Chi-restraints excluded: chain E residue  446 LEU
Chi-restraints excluded: chain F residue  414 GLU
Chi-restraints excluded: chain F residue  430 CYS
Chi-restraints excluded: chain F residue  446 LEU
Chi-restraints excluded: chain F residue  450 GLU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  487 LEU
Chi-restraints excluded: chain F residue  515 LEU
Chi-restraints excluded: chain G residue  430 CYS
Chi-restraints excluded: chain G residue  446 LEU
Chi-restraints excluded: chain H residue  414 GLU
Chi-restraints excluded: chain H residue  430 CYS
Chi-restraints excluded: chain H residue  446 LEU
Chi-restraints excluded: chain H residue  450 GLU
Chi-restraints excluded: chain H residue  515 LEU
Chi-restraints excluded: chain H residue  540 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.194779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.175248 restraints weight = 9462.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 1.32
r_work: 0.3811 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9232  Z= 0.144
  Angle     :  0.520   5.481  12432  Z= 0.281
  Chirality :  0.037   0.108   1352
  Planarity :  0.004   0.029   1600
  Dihedral  :  6.428  59.452   1256
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 26.31 %
    Favored  : 70.87 %
  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:  1.84 (0.27), residues: 1096
  helix:  1.17 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  1.75 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F 490 
 HIS   0.001   0.000   HIS E 516 
 PHE   0.009   0.002   PHE C 433 
 TYR   0.011   0.002   TYR A 503 
 ARG   0.002   0.000   ARG C 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04631 (  512)
  hydrogen bonds       : angle       5.05467 ( 1440)
  covalent geometry    : bond        0.00302 ( 9232)
  covalent geometry    : angle       0.52018 (12432)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8484.56 seconds
wall clock time: 146 minutes 36.26 seconds (8796.26 seconds total)