Starting phenix.real_space_refine
on Wed Sep 17 17:30:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw3_38729/09_2025/8xw3_38729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw3_38729/09_2025/8xw3_38729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw3_38729/09_2025/8xw3_38729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw3_38729/09_2025/8xw3_38729.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw3_38729/09_2025/8xw3_38729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw3_38729/09_2025/8xw3_38729.map"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.006 sd=   0.062
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    6744      2.51       5
     N    1650      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10150
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5075
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.20, per 1000 atoms: 0.41
  Number of scatterers: 10150
  At special positions: 0
  Unit cell: (91.785, 142.425, 99.17, 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    1708      8.00
     N    1650      7.00
     C    6744      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: 0.91
  Conformation dependent library (CDL) restraints added in 369.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 2 sheets defined
      75.8% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
      removed outlier: 3.571A  pdb=" N   GLN A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.880A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 4.088A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 195
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 315
      removed outlier: 3.669A  pdb=" N   ASN A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 360 through 364
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.693A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 4.411A  pdb=" N   ILE A 425 " --> pdb=" O   MET A 421 " (cutoff:3.500A)
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 475
    Processing helix  chain 'A' and resid 477 through 489
    Processing helix  chain 'A' and resid 504 through 512
      Proline residue:  A 510  - end of helix
    Processing helix  chain 'A' and resid 512 through 532
      removed outlier: 3.944A  pdb=" N   ALA A 526 " --> pdb=" O   VAL A 522 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLY A 527 " --> pdb=" O   ASP A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 590 through 612
      removed outlier: 3.615A  pdb=" N   ILE A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 647
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 659 through 677
      removed outlier: 3.978A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 4.466A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 31
      removed outlier: 3.571A  pdb=" N   GLN B  31 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.880A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 92 through 121
      removed outlier: 4.088A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 157 through 195
    Processing helix  chain 'B' and resid 198 through 201
    Processing helix  chain 'B' and resid 216 through 229
    Processing helix  chain 'B' and resid 242 through 269
    Processing helix  chain 'B' and resid 290 through 315
      removed outlier: 3.669A  pdb=" N   ASN B 314 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 338
    Processing helix  chain 'B' and resid 360 through 364
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 389
    Processing helix  chain 'B' and resid 389 through 400
      removed outlier: 3.693A  pdb=" N   ILE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 438
      removed outlier: 4.411A  pdb=" N   ILE B 425 " --> pdb=" O   MET B 421 " (cutoff:3.500A)
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 440 through 452
    Processing helix  chain 'B' and resid 456 through 475
    Processing helix  chain 'B' and resid 477 through 489
    Processing helix  chain 'B' and resid 504 through 512
      Proline residue:  B 510  - end of helix
    Processing helix  chain 'B' and resid 512 through 532
      removed outlier: 3.945A  pdb=" N   ALA B 526 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLY B 527 " --> pdb=" O   ASP B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 548
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 565 through 584
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 590 through 612
      removed outlier: 3.616A  pdb=" N   ILE B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 647
    Processing helix  chain 'B' and resid 654 through 659
    Processing helix  chain 'B' and resid 659 through 677
      removed outlier: 3.979A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 684 through 699
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 4.466A  pdb=" N   ASN B 710 " --> pdb=" O   GLY B 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240
      removed outlier: 5.779A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240
      removed outlier: 5.779A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)

    697 hydrogen bonds defined for protein.
    2067 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: 1.45

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3011
        1.34 -     1.46: 1764
        1.46 -     1.58: 5577
        1.58 -     1.70: 0
        1.70 -     1.81: 88
  Bond restraints: 10440
  Sorted by residual:
  bond pdb=" CB  VAL B 476 "
       pdb=" CG1 VAL B 476 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.52e+00
  bond pdb=" CB  VAL A 476 "
       pdb=" CG1 VAL A 476 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.48e+00
  bond pdb=" CG  LEU B 579 "
       pdb=" CD2 LEU B 579 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.79e+00
  bond pdb=" CG  LEU A 579 "
       pdb=" CD2 LEU A 579 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  bond pdb=" CA  GLU A 452 "
       pdb=" CB  GLU A 452 "
    ideal  model  delta    sigma   weight residual
    1.528  1.510  0.017 1.39e-02 5.18e+03 1.56e+00
  ... (remaining 10435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 13595
        1.51 -     3.01: 459
        3.01 -     4.52: 90
        4.52 -     6.02: 46
        6.02 -     7.53: 10
  Bond angle restraints: 14200
  Sorted by residual:
  angle pdb=" C   PHE B 451 "
        pdb=" N   GLU B 452 "
        pdb=" CA  GLU B 452 "
      ideal   model   delta    sigma   weight residual
     123.11  117.16    5.95 1.42e+00 4.96e-01 1.76e+01
  angle pdb=" C   PHE A 451 "
        pdb=" N   GLU A 452 "
        pdb=" CA  GLU A 452 "
      ideal   model   delta    sigma   weight residual
     123.11  117.19    5.92 1.42e+00 4.96e-01 1.74e+01
  angle pdb=" CA  GLU B 452 "
        pdb=" CB  GLU B 452 "
        pdb=" CG  GLU B 452 "
      ideal   model   delta    sigma   weight residual
     114.10  107.63    6.47 2.00e+00 2.50e-01 1.05e+01
  angle pdb=" CA  GLU A 452 "
        pdb=" CB  GLU A 452 "
        pdb=" CG  GLU A 452 "
      ideal   model   delta    sigma   weight residual
     114.10  107.64    6.46 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" N   TRP A  42 "
        pdb=" CA  TRP A  42 "
        pdb=" C   TRP A  42 "
      ideal   model   delta    sigma   weight residual
     113.72  109.33    4.39 1.52e+00 4.33e-01 8.35e+00
  ... (remaining 14195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 5510
       16.44 -    32.88: 490
       32.88 -    49.33: 102
       49.33 -    65.77: 16
       65.77 -    82.21: 10
  Dihedral angle restraints: 6128
    sinusoidal: 2386
      harmonic: 3742
  Sorted by residual:
  dihedral pdb=" CA  GLU B 452 "
           pdb=" C   GLU B 452 "
           pdb=" N   GLY B 453 "
           pdb=" CA  GLY B 453 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.49  -23.51     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  GLU A 452 "
           pdb=" C   GLU A 452 "
           pdb=" N   GLY A 453 "
           pdb=" CA  GLY A 453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.50  -23.50     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  ASN A 475 "
           pdb=" C   ASN A 475 "
           pdb=" N   VAL A 476 "
           pdb=" CA  VAL A 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.34  -21.66     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 795
       0.026 -    0.052: 470
       0.052 -    0.078: 187
       0.078 -    0.103: 99
       0.103 -    0.129: 53
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CA  THR A 455 "
            pdb=" N   THR A 455 "
            pdb=" C   THR A 455 "
            pdb=" CB  THR A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  PRO B  77 "
            pdb=" N   PRO B  77 "
            pdb=" C   PRO B  77 "
            pdb=" CB  PRO B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  THR B 455 "
            pdb=" N   THR B 455 "
            pdb=" C   THR B 455 "
            pdb=" CB  THR B 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 1601 not shown)

  Planarity restraints: 1762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 677 "    0.033 5.00e-02 4.00e+02   4.88e-02 3.82e+00
        pdb=" N   PRO B 678 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 678 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 678 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 677 "   -0.033 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO A 678 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 678 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 678 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 472 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.01e+00
        pdb=" C   ASN B 472 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASN B 472 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU B 473 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1759 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 101
        2.65 -     3.21: 9992
        3.21 -     3.77: 16258
        3.77 -     4.34: 20568
        4.34 -     4.90: 34305
  Nonbonded interactions: 81224
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 354 "
            pdb=" OH  TYR B 712 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   PRO A 354 "
            pdb=" OH  TYR A 712 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" NH2 ARG A 198 "
            pdb=" OD2 ASP A 200 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NH2 ARG B 198 "
            pdb=" OD2 ASP B 200 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   GLU A 195 "
            pdb=" NZ  LYS A 691 "
     model   vdw
     2.293 3.120
  ... (remaining 81219 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.030
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
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      :  0.005   0.052  10440  Z= 0.226
  Angle     :  0.728   7.529  14200  Z= 0.399
  Chirality :  0.044   0.129   1604
  Planarity :  0.005   0.049   1762
  Dihedral  : 13.288  82.211   3696
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.24), residues: 1248
  helix:  2.11 (0.17), residues: 868
  sheet: -0.96 (0.85), residues: 36
  loop : -1.74 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 375 
 TYR   0.016   0.002   TYR A 468 
 PHE   0.022   0.002   PHE A 420 
 TRP   0.019   0.001   TRP B 525 
 HIS   0.004   0.001   HIS B 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (10440)
  covalent geometry    : angle       0.72755 (14200)
  hydrogen bonds       : bond        0.08028 (  697)
  hydrogen bonds       : angle       4.51165 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7783 (m-30) cc_final: 0.7546 (m-30)
REVERT: A  521 MET cc_start: 0.8796 (tpp) cc_final: 0.8593 (tpp)
REVERT: B  395 PHE cc_start: 0.8530 (t80) cc_final: 0.8217 (t80)
REVERT: B  525 TRP cc_start: 0.8991 (m-10) cc_final: 0.8661 (m-10)
REVERT: B  536 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7352 (mmtt)
REVERT: B  613 TYR cc_start: 0.7954 (m-10) cc_final: 0.7747 (m-10)
REVERT: B  672 CYS cc_start: 0.9031 (m) cc_final: 0.8709 (m)
REVERT: B  689 MET cc_start: 0.9224 (tpt) cc_final: 0.8994 (tpt)
REVERT: B  699 GLU cc_start: 0.8354 (mp0) cc_final: 0.8003 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0738
  time to fit residues: 24.4628
Evaluate side-chains
  171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0670
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 257 ASN
A 338 GLN
A 397 GLN
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.088617 restraints weight = 19863.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.091316 restraints weight = 10601.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.093082 restraints weight = 7258.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.093920 restraints weight = 5797.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.094687 restraints weight = 5150.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10440  Z= 0.133
  Angle     :  0.596   6.822  14200  Z= 0.299
  Chirality :  0.041   0.161   1604
  Planarity :  0.005   0.054   1762
  Dihedral  :  4.250  19.062   1360
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  7.84 %
    Favored  : 90.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.25), residues: 1248
  helix:  2.22 (0.17), residues: 872
  sheet: -0.27 (0.93), residues: 30
  loop : -1.58 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 698 
 TYR   0.014   0.001   TYR A 468 
 PHE   0.021   0.001   PHE A 471 
 TRP   0.011   0.001   TRP A 624 
 HIS   0.002   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10440)
  covalent geometry    : angle       0.59614 (14200)
  hydrogen bonds       : bond        0.03809 (  697)
  hydrogen bonds       : angle       4.22160 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 193
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.7886 (m-30) cc_final: 0.7599 (m-30)
REVERT: A  521 MET cc_start: 0.8849 (tpp) cc_final: 0.8612 (tpp)
REVERT: A  574 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8926 (mm-40)
REVERT: A  689 MET cc_start: 0.9154 (tpt) cc_final: 0.8929 (tpp)
REVERT: B  200 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8020 (p0)
REVERT: B  395 PHE cc_start: 0.8478 (t80) cc_final: 0.8187 (t80)
REVERT: B  511 MET cc_start: 0.6943 (mmm) cc_final: 0.6547 (mmm)
REVERT: B  540 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8081 (tmm)
REVERT: B  661 LEU cc_start: 0.8891 (mt) cc_final: 0.8675 (mt)
REVERT: B  672 CYS cc_start: 0.9032 (m) cc_final: 0.8637 (m)
REVERT: B  677 GLU cc_start: 0.7980 (tt0) cc_final: 0.7735 (tt0)
REVERT: B  689 MET cc_start: 0.9216 (tpt) cc_final: 0.8994 (tpt)
REVERT: B  699 GLU cc_start: 0.8372 (mp0) cc_final: 0.8152 (mp0)
  outliers start: 19
  outliers final: 7
  residues processed: 198
  average time/residue: 0.0820
  time to fit residues: 24.9673
Evaluate side-chains
  180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 171
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 125 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 108 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 100 optimal weight:    0.4980
   chunk 103 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A 574 GLN
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 397 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.114732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.088068 restraints weight = 19972.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.090913 restraints weight = 10322.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.092740 restraints weight = 6944.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.093645 restraints weight = 5503.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.094522 restraints weight = 4858.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10440  Z= 0.129
  Angle     :  0.592  13.070  14200  Z= 0.290
  Chirality :  0.041   0.160   1604
  Planarity :  0.005   0.056   1762
  Dihedral  :  4.083  17.835   1360
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 10.40 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.25), residues: 1248
  helix:  2.23 (0.17), residues: 874
  sheet:  0.37 (0.95), residues: 36
  loop : -1.71 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 467 
 TYR   0.020   0.001   TYR A 368 
 PHE   0.022   0.001   PHE A 471 
 TRP   0.012   0.001   TRP B 624 
 HIS   0.003   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10440)
  covalent geometry    : angle       0.59209 (14200)
  hydrogen bonds       : bond        0.03558 (  697)
  hydrogen bonds       : angle       4.16256 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7916 (m-30) cc_final: 0.7606 (m-30)
REVERT: A  689 MET cc_start: 0.9128 (tpt) cc_final: 0.8882 (tpp)
REVERT: B  383 PHE cc_start: 0.8810 (t80) cc_final: 0.8597 (t80)
REVERT: B  395 PHE cc_start: 0.8448 (t80) cc_final: 0.8159 (t80)
REVERT: B  470 ILE cc_start: 0.8906 (tp) cc_final: 0.8542 (tt)
REVERT: B  511 MET cc_start: 0.7090 (mmm) cc_final: 0.6652 (mmm)
REVERT: B  672 CYS cc_start: 0.9079 (m) cc_final: 0.8559 (m)
REVERT: B  677 GLU cc_start: 0.8054 (tt0) cc_final: 0.7797 (tt0)
REVERT: B  689 MET cc_start: 0.9190 (tpt) cc_final: 0.8982 (tpt)
  outliers start: 26
  outliers final: 16
  residues processed: 187
  average time/residue: 0.0767
  time to fit residues: 22.3521
Evaluate side-chains
  181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 103 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.088328 restraints weight = 19980.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.091181 restraints weight = 10420.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.093032 restraints weight = 7027.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.094026 restraints weight = 5566.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.094795 restraints weight = 4896.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10440  Z= 0.126
  Angle     :  0.572  10.141  14200  Z= 0.283
  Chirality :  0.041   0.164   1604
  Planarity :  0.004   0.056   1762
  Dihedral  :  3.968  17.339   1360
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 10.78 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.25), residues: 1248
  helix:  2.25 (0.17), residues: 874
  sheet:  0.12 (0.89), residues: 46
  loop : -1.82 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 467 
 TYR   0.014   0.001   TYR A 181 
 PHE   0.018   0.001   PHE A 471 
 TRP   0.012   0.001   TRP A 624 
 HIS   0.002   0.000   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10440)
  covalent geometry    : angle       0.57207 (14200)
  hydrogen bonds       : bond        0.03423 (  697)
  hydrogen bonds       : angle       4.12192 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7905 (m-30) cc_final: 0.7593 (m-30)
REVERT: A  448 MET cc_start: 0.7362 (ttm) cc_final: 0.6635 (tpt)
REVERT: A  470 ILE cc_start: 0.8984 (tp) cc_final: 0.8783 (tp)
REVERT: A  677 GLU cc_start: 0.8159 (tt0) cc_final: 0.7853 (mt-10)
REVERT: A  689 MET cc_start: 0.9144 (tpt) cc_final: 0.8899 (tpp)
REVERT: B  164 VAL cc_start: 0.9172 (t) cc_final: 0.8922 (p)
REVERT: B  383 PHE cc_start: 0.8797 (t80) cc_final: 0.8519 (t80)
REVERT: B  387 PHE cc_start: 0.8422 (t80) cc_final: 0.8106 (t80)
REVERT: B  525 TRP cc_start: 0.8871 (m-10) cc_final: 0.8555 (m-10)
REVERT: B  531 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: B  661 LEU cc_start: 0.8898 (mt) cc_final: 0.8692 (mt)
REVERT: B  677 GLU cc_start: 0.8062 (tt0) cc_final: 0.7784 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 190
  average time/residue: 0.0707
  time to fit residues: 21.3025
Evaluate side-chains
  190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 125 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 120 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0770
   chunk 59 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 121 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0060
   overall best weight:    0.5754

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.115465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.088737 restraints weight = 19807.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.091588 restraints weight = 10360.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093399 restraints weight = 6999.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.094426 restraints weight = 5556.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.095136 restraints weight = 4886.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10440  Z= 0.121
  Angle     :  0.582   9.684  14200  Z= 0.284
  Chirality :  0.041   0.173   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  3.917  18.432   1360
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.48 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.25), residues: 1248
  helix:  2.29 (0.17), residues: 874
  sheet:  0.18 (0.87), residues: 46
  loop : -1.81 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 467 
 TYR   0.017   0.001   TYR B 368 
 PHE   0.014   0.001   PHE B 577 
 TRP   0.012   0.001   TRP A 624 
 HIS   0.002   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10440)
  covalent geometry    : angle       0.58162 (14200)
  hydrogen bonds       : bond        0.03302 (  697)
  hydrogen bonds       : angle       4.09797 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7900 (m-30) cc_final: 0.7586 (m-30)
REVERT: A   30 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8635 (mm)
REVERT: A   93 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (tt)
REVERT: A  448 MET cc_start: 0.7346 (ttm) cc_final: 0.6696 (tpt)
REVERT: A  677 GLU cc_start: 0.8136 (tt0) cc_final: 0.7829 (mt-10)
REVERT: A  689 MET cc_start: 0.9144 (tpt) cc_final: 0.8897 (tpp)
REVERT: B  164 VAL cc_start: 0.9170 (t) cc_final: 0.8925 (p)
REVERT: B  383 PHE cc_start: 0.8793 (t80) cc_final: 0.8521 (t80)
REVERT: B  387 PHE cc_start: 0.8436 (t80) cc_final: 0.8085 (t80)
REVERT: B  448 MET cc_start: 0.7665 (ttp) cc_final: 0.6989 (tpt)
REVERT: B  525 TRP cc_start: 0.8802 (m-10) cc_final: 0.8490 (m-10)
REVERT: B  531 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7798 (tm-30)
REVERT: B  540 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8203 (tmm)
REVERT: B  677 GLU cc_start: 0.7983 (tt0) cc_final: 0.7702 (tt0)
  outliers start: 23
  outliers final: 17
  residues processed: 182
  average time/residue: 0.0706
  time to fit residues: 20.5155
Evaluate side-chains
  185 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 80 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 109 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 608 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.115170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.088014 restraints weight = 20166.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.090822 restraints weight = 10622.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.092674 restraints weight = 7227.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.093737 restraints weight = 5746.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.094100 restraints weight = 5047.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10440  Z= 0.124
  Angle     :  0.580   9.412  14200  Z= 0.283
  Chirality :  0.041   0.178   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  3.897  17.641   1360
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.14 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.25), residues: 1248
  helix:  2.30 (0.17), residues: 874
  sheet:  0.06 (0.85), residues: 46
  loop : -1.82 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 467 
 TYR   0.013   0.001   TYR B 181 
 PHE   0.016   0.001   PHE A 395 
 TRP   0.011   0.001   TRP A 624 
 HIS   0.002   0.000   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10440)
  covalent geometry    : angle       0.57975 (14200)
  hydrogen bonds       : bond        0.03278 (  697)
  hydrogen bonds       : angle       4.08470 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7907 (m-30) cc_final: 0.7599 (m-30)
REVERT: A    7 ILE cc_start: 0.9143 (mm) cc_final: 0.8942 (tp)
REVERT: A   30 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8657 (mm)
REVERT: A   93 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8529 (tt)
REVERT: A  448 MET cc_start: 0.7319 (ttm) cc_final: 0.6709 (tpt)
REVERT: A  677 GLU cc_start: 0.8135 (tt0) cc_final: 0.7814 (mt-10)
REVERT: A  689 MET cc_start: 0.9150 (tpt) cc_final: 0.8898 (tpp)
REVERT: B  383 PHE cc_start: 0.8816 (t80) cc_final: 0.8582 (t80)
REVERT: B  387 PHE cc_start: 0.8423 (t80) cc_final: 0.8087 (t80)
REVERT: B  448 MET cc_start: 0.7662 (ttp) cc_final: 0.6972 (tpt)
REVERT: B  525 TRP cc_start: 0.8802 (m-10) cc_final: 0.8461 (m-10)
REVERT: B  531 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: B  534 MET cc_start: 0.8642 (mtp) cc_final: 0.8433 (mtt)
REVERT: B  540 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8197 (tmm)
REVERT: B  677 GLU cc_start: 0.8001 (tt0) cc_final: 0.7703 (tt0)
  outliers start: 25
  outliers final: 18
  residues processed: 179
  average time/residue: 0.0703
  time to fit residues: 19.8813
Evaluate side-chains
  187 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0970
   chunk 7 optimal weight:    0.0980
   chunk 2 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0270
   chunk 79 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
B 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.116532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.090106 restraints weight = 19839.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.092850 restraints weight = 10828.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.094595 restraints weight = 7487.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.095462 restraints weight = 6002.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.096290 restraints weight = 5336.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10440  Z= 0.113
  Angle     :  0.578  10.375  14200  Z= 0.279
  Chirality :  0.041   0.189   1604
  Planarity :  0.004   0.054   1762
  Dihedral  :  3.829  18.306   1360
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.37 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.25), residues: 1248
  helix:  2.32 (0.17), residues: 876
  sheet: -0.07 (0.83), residues: 46
  loop : -1.76 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 467 
 TYR   0.022   0.001   TYR A 368 
 PHE   0.013   0.001   PHE B 597 
 TRP   0.012   0.001   TRP A 624 
 HIS   0.002   0.000   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10440)
  covalent geometry    : angle       0.57753 (14200)
  hydrogen bonds       : bond        0.03127 (  697)
  hydrogen bonds       : angle       4.04607 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7781 (m-30) cc_final: 0.7507 (m-30)
REVERT: A   30 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8630 (mm)
REVERT: A   93 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8476 (tt)
REVERT: A  448 MET cc_start: 0.7279 (ttm) cc_final: 0.6719 (tpt)
REVERT: A  677 GLU cc_start: 0.8040 (tt0) cc_final: 0.7742 (mt-10)
REVERT: A  689 MET cc_start: 0.9166 (tpt) cc_final: 0.8922 (tpp)
REVERT: B    7 ILE cc_start: 0.9118 (mm) cc_final: 0.8822 (mm)
REVERT: B   19 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7585 (m-80)
REVERT: B  164 VAL cc_start: 0.9145 (t) cc_final: 0.8880 (p)
REVERT: B  383 PHE cc_start: 0.8796 (t80) cc_final: 0.8547 (t80)
REVERT: B  387 PHE cc_start: 0.8313 (t80) cc_final: 0.7955 (t80)
REVERT: B  448 MET cc_start: 0.7633 (ttp) cc_final: 0.6587 (tpt)
REVERT: B  525 TRP cc_start: 0.8654 (m-10) cc_final: 0.8450 (m-10)
REVERT: B  531 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: B  534 MET cc_start: 0.8613 (mtp) cc_final: 0.8395 (mtt)
REVERT: B  540 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8186 (tmm)
REVERT: B  677 GLU cc_start: 0.7939 (tt0) cc_final: 0.7603 (tt0)
  outliers start: 23
  outliers final: 16
  residues processed: 182
  average time/residue: 0.0677
  time to fit residues: 19.6600
Evaluate side-chains
  183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 71 optimal weight:    0.1980
   chunk 84 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 112 optimal weight:    0.5980
   chunk 96 optimal weight:    0.0970
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.116371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.089189 restraints weight = 20205.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.092008 restraints weight = 10731.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.093813 restraints weight = 7310.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094712 restraints weight = 5820.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.095537 restraints weight = 5144.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10440  Z= 0.117
  Angle     :  0.608  14.402  14200  Z= 0.289
  Chirality :  0.041   0.195   1604
  Planarity :  0.004   0.054   1762
  Dihedral  :  3.794  18.073   1360
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.97 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.25), residues: 1248
  helix:  2.32 (0.17), residues: 876
  sheet: -0.19 (0.82), residues: 46
  loop : -1.78 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 467 
 TYR   0.026   0.001   TYR B 368 
 PHE   0.013   0.001   PHE B 597 
 TRP   0.011   0.001   TRP A 624 
 HIS   0.002   0.000   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10440)
  covalent geometry    : angle       0.60832 (14200)
  hydrogen bonds       : bond        0.03126 (  697)
  hydrogen bonds       : angle       4.03726 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7724 (m-30) cc_final: 0.7477 (m-30)
REVERT: A   30 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8676 (mm)
REVERT: A   93 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8482 (tt)
REVERT: A  448 MET cc_start: 0.7304 (ttm) cc_final: 0.6642 (tpt)
REVERT: A  521 MET cc_start: 0.8764 (tpp) cc_final: 0.8503 (tpp)
REVERT: A  677 GLU cc_start: 0.8076 (tt0) cc_final: 0.7778 (mt-10)
REVERT: A  689 MET cc_start: 0.9144 (tpt) cc_final: 0.8886 (tpp)
REVERT: B    7 ILE cc_start: 0.9126 (mm) cc_final: 0.8857 (mm)
REVERT: B   19 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7742 (m-80)
REVERT: B  383 PHE cc_start: 0.8853 (t80) cc_final: 0.8611 (t80)
REVERT: B  387 PHE cc_start: 0.8360 (t80) cc_final: 0.8015 (t80)
REVERT: B  525 TRP cc_start: 0.8620 (m-10) cc_final: 0.8410 (m-10)
REVERT: B  531 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: B  534 MET cc_start: 0.8606 (mtp) cc_final: 0.8389 (mtt)
REVERT: B  540 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8251 (tmm)
REVERT: B  649 LYS cc_start: 0.4816 (tptp) cc_final: 0.4602 (mmmt)
REVERT: B  677 GLU cc_start: 0.8039 (tt0) cc_final: 0.7836 (tt0)
  outliers start: 22
  outliers final: 14
  residues processed: 170
  average time/residue: 0.0739
  time to fit residues: 19.9557
Evaluate side-chains
  179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    0.3980
   chunk 116 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0070
   chunk 109 optimal weight:   10.0000
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0670
   chunk 85 optimal weight:   30.0000
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.3536

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.117311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.090631 restraints weight = 19880.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093485 restraints weight = 10381.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.095312 restraints weight = 7030.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.095945 restraints weight = 5574.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.097024 restraints weight = 5037.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10440  Z= 0.113
  Angle     :  0.610  11.738  14200  Z= 0.289
  Chirality :  0.041   0.204   1604
  Planarity :  0.004   0.053   1762
  Dihedral  :  3.755  17.691   1360
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.45 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.25), residues: 1248
  helix:  2.33 (0.17), residues: 876
  sheet: -0.26 (0.82), residues: 46
  loop : -1.75 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 467 
 TYR   0.025   0.001   TYR A 368 
 PHE   0.013   0.001   PHE B 597 
 TRP   0.011   0.001   TRP A 624 
 HIS   0.002   0.000   HIS A 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10440)
  covalent geometry    : angle       0.61041 (14200)
  hydrogen bonds       : bond        0.03039 (  697)
  hydrogen bonds       : angle       4.02553 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.7584 (m-30) cc_final: 0.7373 (m-30)
REVERT: A   30 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8639 (mm)
REVERT: A   93 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8400 (tt)
REVERT: A  521 MET cc_start: 0.8736 (tpp) cc_final: 0.8454 (tpp)
REVERT: A  677 GLU cc_start: 0.8065 (tt0) cc_final: 0.7767 (mt-10)
REVERT: A  689 MET cc_start: 0.9132 (tpt) cc_final: 0.8874 (tpp)
REVERT: B    7 ILE cc_start: 0.9110 (mm) cc_final: 0.8844 (mm)
REVERT: B  164 VAL cc_start: 0.9202 (t) cc_final: 0.8942 (p)
REVERT: B  383 PHE cc_start: 0.8862 (t80) cc_final: 0.8650 (t80)
REVERT: B  387 PHE cc_start: 0.8313 (t80) cc_final: 0.7997 (t80)
REVERT: B  525 TRP cc_start: 0.8699 (m-10) cc_final: 0.8476 (m-10)
REVERT: B  531 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: B  540 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8233 (tmm)
REVERT: B  649 LYS cc_start: 0.4816 (tptp) cc_final: 0.4594 (mmmt)
  outliers start: 20
  outliers final: 12
  residues processed: 169
  average time/residue: 0.0692
  time to fit residues: 18.7094
Evaluate side-chains
  173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 86 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 104 optimal weight:    7.9990
   chunk 29 optimal weight:    0.5980
   chunk 87 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 120 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   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 379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.116106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.089660 restraints weight = 19769.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.092308 restraints weight = 10793.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.094027 restraints weight = 7505.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094873 restraints weight = 6031.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.095631 restraints weight = 5371.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10440  Z= 0.126
  Angle     :  0.628  11.476  14200  Z= 0.296
  Chirality :  0.041   0.199   1604
  Planarity :  0.004   0.053   1762
  Dihedral  :  3.764  18.220   1360
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 16.35 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.25), residues: 1248
  helix:  2.33 (0.17), residues: 876
  sheet: -0.37 (0.81), residues: 46
  loop : -1.74 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 467 
 TYR   0.018   0.001   TYR B 469 
 PHE   0.012   0.001   PHE B 597 
 TRP   0.010   0.001   TRP B  75 
 HIS   0.004   0.000   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10440)
  covalent geometry    : angle       0.62770 (14200)
  hydrogen bonds       : bond        0.03125 (  697)
  hydrogen bonds       : angle       4.01298 ( 2067)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A   30 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8624 (mm)
REVERT: A   93 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8536 (tt)
REVERT: A  677 GLU cc_start: 0.8053 (tt0) cc_final: 0.7774 (mt-10)
REVERT: A  689 MET cc_start: 0.9177 (tpt) cc_final: 0.8935 (tpp)
REVERT: B    7 ILE cc_start: 0.9104 (mm) cc_final: 0.8821 (mm)
REVERT: B   19 PHE cc_start: 0.7880 (m-80) cc_final: 0.7631 (m-10)
REVERT: B  387 PHE cc_start: 0.8446 (t80) cc_final: 0.8110 (t80)
REVERT: B  525 TRP cc_start: 0.8706 (m-10) cc_final: 0.8493 (m-10)
REVERT: B  531 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7697 (tm-30)
REVERT: B  540 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8156 (tmm)
REVERT: B  649 LYS cc_start: 0.4774 (tptp) cc_final: 0.4563 (mmmt)
  outliers start: 16
  outliers final: 12
  residues processed: 163
  average time/residue: 0.0741
  time to fit residues: 18.7863
Evaluate side-chains
  171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    0.0970
   chunk 79 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.9580

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.115229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.088644 restraints weight = 19885.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.091430 restraints weight = 10400.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.093211 restraints weight = 7036.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.094033 restraints weight = 5580.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094691 restraints weight = 4953.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10440  Z= 0.134
  Angle     :  0.624  11.142  14200  Z= 0.300
  Chirality :  0.042   0.227   1604
  Planarity :  0.004   0.053   1762
  Dihedral  :  3.796  18.529   1360
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.07 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.25), residues: 1248
  helix:  2.36 (0.17), residues: 874
  sheet: -0.12 (0.83), residues: 44
  loop : -1.81 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 467 
 TYR   0.025   0.001   TYR A 368 
 PHE   0.013   0.001   PHE B 597 
 TRP   0.011   0.001   TRP B  75 
 HIS   0.003   0.000   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10440)
  covalent geometry    : angle       0.62414 (14200)
  hydrogen bonds       : bond        0.03209 (  697)
  hydrogen bonds       : angle       4.03797 ( 2067)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1573.54 seconds
wall clock time: 28 minutes 2.03 seconds (1682.03 seconds total)