Starting phenix.real_space_refine
on Tue Feb 11 08:39:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1d_36792/02_2025/8k1d_36792.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1d_36792/02_2025/8k1d_36792.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1d_36792/02_2025/8k1d_36792.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1d_36792/02_2025/8k1d_36792.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1d_36792/02_2025/8k1d_36792.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1d_36792/02_2025/8k1d_36792.cif"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.102
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      38      5.16       5
     C    3310      2.51       5
     N     758      2.21       5
     O     796      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4902
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2451
          Classifications: {'peptide': 305}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 7, 'TRANS': 297}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2451
          Classifications: {'peptide': 305}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 7, 'TRANS': 297}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 32
  Time building chain proxies: 3.40, per 1000 atoms: 0.69
  Number of scatterers: 4902
  At special positions: 0
  Unit cell: (93.15, 71.55, 74.25, 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      38     16.00
     O     796      8.00
     N     758      7.00
     C    3310      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 479 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 485 " - pdb=" SG  CYS A 782 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 479 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 485 " - pdb=" SG  CYS B 782 " distance=2.03

  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: 1.34
  Conformation dependent library (CDL) restraints added in 581.3 milliseconds
  

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      83.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 302 through 333
      removed outlier: 3.895A  pdb=" N   TYR A 306 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 474
      Proline residue:  A 458  - end of helix
    Processing helix  chain 'A' and resid 495 through 500
    Processing helix  chain 'A' and resid 501 through 524
      removed outlier: 3.663A  pdb=" N   VAL A 505 " --> pdb=" O   ASN A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 565
      removed outlier: 4.170A  pdb=" N   CYS A 565 " --> pdb=" O   CYS A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 586
      removed outlier: 3.854A  pdb=" N   GLN A 572 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   PHE A 573 " --> pdb=" O   SER A 569 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE A 577 " --> pdb=" O   PHE A 573 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   MET A 578 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   MET A 586 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 644
      removed outlier: 3.615A  pdb=" N   SER A 644 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 705
    Processing helix  chain 'A' and resid 708 through 735
    Processing helix  chain 'A' and resid 744 through 762
      removed outlier: 3.893A  pdb=" N   ALA A 751 " --> pdb=" O   ILE A 747 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL A 752 " --> pdb=" O   VAL A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 778
      removed outlier: 3.862A  pdb=" N   LYS A 778 " --> pdb=" O   GLU A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 809
    Processing helix  chain 'B' and resid 302 through 333
      removed outlier: 3.804A  pdb=" N   TYR B 306 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   PHE B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 474
      Proline residue:  B 458  - end of helix
    Processing helix  chain 'B' and resid 495 through 500
    Processing helix  chain 'B' and resid 501 through 524
      removed outlier: 3.713A  pdb=" N   VAL B 505 " --> pdb=" O   ASN B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 565
      removed outlier: 4.145A  pdb=" N   CYS B 565 " --> pdb=" O   CYS B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 586
      removed outlier: 3.901A  pdb=" N   GLN B 572 " --> pdb=" O   TYR B 568 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE B 573 " --> pdb=" O   SER B 569 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE B 577 " --> pdb=" O   PHE B 573 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   MET B 578 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   MET B 586 " --> pdb=" O   ALA B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 644
      removed outlier: 3.673A  pdb=" N   SER B 644 " --> pdb=" O   SER B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 705
    Processing helix  chain 'B' and resid 708 through 735
      removed outlier: 3.920A  pdb=" N   TYR B 712 " --> pdb=" O   ASP B 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 744 through 762
      removed outlier: 3.755A  pdb=" N   ALA B 751 " --> pdb=" O   ILE B 747 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL B 752 " --> pdb=" O   VAL B 748 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 771 through 776
    Processing helix  chain 'B' and resid 789 through 809

    381 hydrogen bonds defined for protein.
    1143 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: 1.40

  Time building geometry restraints manager: 1.53 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: 1396
        1.34 -     1.46: 1174
        1.46 -     1.58: 2414
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 5042
  Sorted by residual:
  bond pdb=" C   CYS B 565 "
       pdb=" N   PRO B 566 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 8.70e-03 1.32e+04 7.99e+00
  bond pdb=" C   CYS A 565 "
       pdb=" N   PRO A 566 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 1.11e-02 8.12e+03 5.39e+00
  bond pdb=" N   LEU B 512 "
       pdb=" CA  LEU B 512 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.32e+00
  bond pdb=" C   PRO B 566 "
       pdb=" O   PRO B 566 "
    ideal  model  delta    sigma   weight residual
    1.233  1.217  0.016 9.60e-03 1.09e+04 2.76e+00
  bond pdb=" C   PRO A 566 "
       pdb=" O   PRO A 566 "
    ideal  model  delta    sigma   weight residual
    1.233  1.218  0.016 1.06e-02 8.90e+03 2.19e+00
  ... (remaining 5037 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 6685
        1.90 -     3.80: 119
        3.80 -     5.70: 23
        5.70 -     7.60: 14
        7.60 -     9.49: 5
  Bond angle restraints: 6846
  Sorted by residual:
  angle pdb=" C   PRO B 566 "
        pdb=" CA  PRO B 566 "
        pdb=" CB  PRO B 566 "
      ideal   model   delta    sigma   weight residual
     111.40  108.16    3.24 9.10e-01 1.21e+00 1.27e+01
  angle pdb=" CB  MET A 554 "
        pdb=" CG  MET A 554 "
        pdb=" SD  MET A 554 "
      ideal   model   delta    sigma   weight residual
     112.70  121.74   -9.04 3.00e+00 1.11e-01 9.07e+00
  angle pdb=" CA  LEU B 802 "
        pdb=" CB  LEU B 802 "
        pdb=" CG  LEU B 802 "
      ideal   model   delta    sigma   weight residual
     116.30  125.79   -9.49 3.50e+00 8.16e-02 7.36e+00
  angle pdb=" CA  TYR A 712 "
        pdb=" CB  TYR A 712 "
        pdb=" CG  TYR A 712 "
      ideal   model   delta    sigma   weight residual
     113.90  118.70   -4.80 1.80e+00 3.09e-01 7.12e+00
  angle pdb=" CA  LEU B 699 "
        pdb=" CB  LEU B 699 "
        pdb=" CG  LEU B 699 "
      ideal   model   delta    sigma   weight residual
     116.30  125.01   -8.71 3.50e+00 8.16e-02 6.19e+00
  ... (remaining 6841 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.63: 2392
       16.63 -    33.25: 338
       33.25 -    49.88: 115
       49.88 -    66.50: 7
       66.50 -    83.13: 4
  Dihedral angle restraints: 2856
    sinusoidal: 1060
      harmonic: 1796
  Sorted by residual:
  dihedral pdb=" CB  CYS B 485 "
           pdb=" SG  CYS B 485 "
           pdb=" SG  CYS B 782 "
           pdb=" CB  CYS B 782 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.34  -36.34     1      1.00e+01 1.00e-02 1.87e+01
  dihedral pdb=" CB  CYS A 485 "
           pdb=" SG  CYS A 485 "
           pdb=" SG  CYS A 782 "
           pdb=" CB  CYS A 782 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.81  -34.81     1      1.00e+01 1.00e-02 1.72e+01
  dihedral pdb=" CA  ASN A 482 "
           pdb=" C   ASN A 482 "
           pdb=" N   PHE A 483 "
           pdb=" CA  PHE A 483 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.30  -16.70     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 2853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 649
       0.057 -    0.113: 123
       0.113 -    0.170: 15
       0.170 -    0.226: 1
       0.226 -    0.283: 2
  Chirality restraints: 790
  Sorted by residual:
  chirality pdb=" CG  LEU B 797 "
            pdb=" CB  LEU B 797 "
            pdb=" CD1 LEU B 797 "
            pdb=" CD2 LEU B 797 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CG  LEU A 326 "
            pdb=" CB  LEU A 326 "
            pdb=" CD1 LEU A 326 "
            pdb=" CD2 LEU A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CG  LEU A 797 "
            pdb=" CB  LEU A 797 "
            pdb=" CD1 LEU A 797 "
            pdb=" CD2 LEU A 797 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 787 not shown)

  Planarity restraints: 816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 457 "    0.042 5.00e-02 4.00e+02   6.36e-02 6.48e+00
        pdb=" N   PRO A 458 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 458 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 458 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 457 "   -0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO B 458 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 458 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 458 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 794 "    0.011 2.00e-02 2.50e+03   1.15e-02 3.29e+00
        pdb=" CG  TRP A 794 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 794 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 794 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 794 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 794 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 794 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 794 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 794 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 794 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 813 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 947
        2.76 -     3.30: 5064
        3.30 -     3.83: 8108
        3.83 -     4.37: 8859
        4.37 -     4.90: 15037
  Nonbonded interactions: 38015
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 469 "
            pdb=" OG1 THR B 473 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER A 644 "
            pdb=" OH  TYR A 724 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   ILE B 747 "
            pdb=" OG1 THR B 750 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG  SER B 644 "
            pdb=" OH  TYR B 724 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   TRP A 794 "
            pdb=" OG  SER A 798 "
     model   vdw
     2.300 3.040
  ... (remaining 38010 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: 0.03
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:             0.190
  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:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     15.610
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5042  Z= 0.186
  Angle     :  0.714   9.494   6846  Z= 0.370
  Chirality :  0.045   0.283    790
  Planarity :  0.004   0.064    816
  Dihedral  : 16.894  83.125   1680
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 27.59 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.34), residues: 586
  helix:  1.52 (0.22), residues: 478
  sheet:  None (None), residues: 0
  loop : -2.29 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 794 
 HIS   0.003   0.001   HIS B 504 
 PHE   0.020   0.001   PHE A 745 
 TYR   0.025   0.001   TYR B 321 
 ARG   0.003   0.000   ARG B 518 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8445 (tt) cc_final: 0.8109 (mt)
REVERT: B  517 ARG cc_start: 0.8342 (ptt90) cc_final: 0.8136 (ptt-90)
  outliers start: 3
  outliers final: 2
  residues processed: 115
  average time/residue: 0.1325
  time to fit residues: 20.5077
Evaluate side-chains
  105 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  727 PHE
Chi-restraints excluded: chain A residue  794 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   30.0000
   chunk 45 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.4456 r_free = 0.4456 target = 0.167297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.125370 restraints weight = 10757.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.128565 restraints weight = 5423.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.130499 restraints weight = 3727.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5042  Z= 0.215
  Angle     :  0.626  10.410   6846  Z= 0.320
  Chirality :  0.041   0.172    790
  Planarity :  0.004   0.044    816
  Dihedral  :  4.586  32.507    654
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 24.71 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.33), residues: 586
  helix:  1.53 (0.22), residues: 486
  sheet:  None (None), residues: 0
  loop : -2.87 (0.53), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 446 
 HIS   0.004   0.001   HIS A 504 
 PHE   0.018   0.002   PHE B 806 
 TYR   0.017   0.001   TYR B 321 
 ARG   0.010   0.001   ARG A 517 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.7315 (t80) cc_final: 0.6769 (t80)
REVERT: B  517 ARG cc_start: 0.8386 (ptt90) cc_final: 0.8166 (ptt-90)
REVERT: B  580 MET cc_start: 0.8061 (mmt) cc_final: 0.7856 (mmt)
REVERT: B  699 LEU cc_start: 0.8912 (mm) cc_final: 0.8638 (pp)
REVERT: B  753 MET cc_start: 0.7954 (mmp) cc_final: 0.7644 (mmp)
  outliers start: 20
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1316
  time to fit residues: 21.3147
Evaluate side-chains
  109 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  636 HIS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  496 ASN
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  758 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0980
   chunk 19 optimal weight:    6.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.4477 r_free = 0.4477 target = 0.169195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.127837 restraints weight = 10837.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.131121 restraints weight = 5366.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.133077 restraints weight = 3662.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5042  Z= 0.172
  Angle     :  0.626   9.896   6846  Z= 0.312
  Chirality :  0.041   0.285    790
  Planarity :  0.003   0.035    816
  Dihedral  :  3.896  16.840    650
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.10 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.33), residues: 586
  helix:  1.50 (0.22), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.86 (0.55), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 768 
 HIS   0.007   0.001   HIS B 636 
 PHE   0.011   0.001   PHE A 483 
 TYR   0.012   0.001   TYR A 306 
 ARG   0.007   0.001   ARG A 517 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7756 (m-70)
REVERT: A  554 MET cc_start: 0.7642 (mmp) cc_final: 0.7420 (mmp)
REVERT: B  455 TYR cc_start: 0.7065 (t80) cc_final: 0.6655 (t80)
REVERT: B  802 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7792 (tt)
  outliers start: 19
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1333
  time to fit residues: 21.4468
Evaluate side-chains
  118 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  577 PHE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  791 HIS
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  496 ASN
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  802 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0030
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.0992

-------------------------------------------------------------------------------
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 = 0.4499 r_free = 0.4499 target = 0.170657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.129116 restraints weight = 10788.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.132427 restraints weight = 5365.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.134380 restraints weight = 3659.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5042  Z= 0.154
  Angle     :  0.619  11.192   6846  Z= 0.303
  Chirality :  0.041   0.310    790
  Planarity :  0.003   0.033    816
  Dihedral  :  3.824  17.138    650
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 24.71 %
    Favored  : 70.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.33), residues: 586
  helix:  1.60 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.86 (0.57), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 768 
 HIS   0.008   0.001   HIS B 636 
 PHE   0.021   0.001   PHE B 806 
 TYR   0.012   0.001   TYR A 306 
 ARG   0.005   0.000   ARG A 517 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  455 TYR cc_start: 0.7484 (t80) cc_final: 0.7002 (t80)
REVERT: A  511 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7943 (t80)
REVERT: A  806 PHE cc_start: 0.7694 (m-80) cc_final: 0.7336 (m-80)
REVERT: B  466 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8473 (m-80)
REVERT: B  517 ARG cc_start: 0.8399 (ptt90) cc_final: 0.8153 (ttp-110)
REVERT: B  753 MET cc_start: 0.7928 (mmp) cc_final: 0.7612 (mmp)
  outliers start: 25
  outliers final: 18
  residues processed: 126
  average time/residue: 0.1265
  time to fit residues: 21.6009
Evaluate side-chains
  123 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  791 HIS
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  466 TYR
Chi-restraints excluded: chain B residue  496 ASN
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  577 PHE
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  724 TYR
Chi-restraints excluded: chain B residue  750 THR
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  797 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0670
   chunk 30 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    1.1520

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

Flipped N/Q/H residues before XYZ refinement:
B 791 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.171258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.129864 restraints weight = 10970.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.133251 restraints weight = 5401.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.135254 restraints weight = 3643.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5042  Z= 0.150
  Angle     :  0.643  10.735   6846  Z= 0.307
  Chirality :  0.042   0.309    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.754  18.878    650
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 23.95 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.33), residues: 586
  helix:  1.72 (0.22), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.68 (0.58), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 754 
 HIS   0.008   0.001   HIS A 636 
 PHE   0.019   0.001   PHE A 761 
 TYR   0.015   0.001   TYR B 455 
 ARG   0.001   0.000   ARG B 518 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7684 (m-70)
REVERT: A  511 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7749 (t80)
REVERT: A  745 PHE cc_start: 0.8719 (p90) cc_final: 0.7959 (m-10)
REVERT: A  806 PHE cc_start: 0.7472 (m-80) cc_final: 0.7094 (m-10)
REVERT: B  327 VAL cc_start: 0.7174 (t) cc_final: 0.6962 (p)
REVERT: B  466 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8402 (m-80)
REVERT: B  517 ARG cc_start: 0.8552 (ptt90) cc_final: 0.8285 (ttp-110)
  outliers start: 31
  outliers final: 25
  residues processed: 132
  average time/residue: 0.1285
  time to fit residues: 22.9935
Evaluate side-chains
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  466 TYR
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  496 ASN
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  577 PHE
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  724 TYR
Chi-restraints excluded: chain B residue  750 THR
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  797 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 56 optimal weight:    0.1980
   chunk 48 optimal weight:    6.9990
   chunk 49 optimal weight:   20.0000
   chunk 46 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 791 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.166914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.125985 restraints weight = 10919.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.129240 restraints weight = 5412.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.131098 restraints weight = 3673.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5042  Z= 0.248
  Angle     :  0.699  10.498   6846  Z= 0.346
  Chirality :  0.046   0.336    790
  Planarity :  0.003   0.030    816
  Dihedral  :  4.033  20.161    650
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 24.90 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.33), residues: 586
  helix:  1.47 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.52 (0.59), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 446 
 HIS   0.008   0.002   HIS A 636 
 PHE   0.020   0.002   PHE A 717 
 TYR   0.034   0.002   TYR A 321 
 ARG   0.002   0.000   ARG A 780 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8419 (mt)
REVERT: A  455 TYR cc_start: 0.7689 (t80) cc_final: 0.7441 (t80)
REVERT: A  504 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7790 (m-70)
REVERT: A  806 PHE cc_start: 0.7787 (m-80) cc_final: 0.7441 (m-80)
REVERT: B  325 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8490 (mt)
REVERT: B  455 TYR cc_start: 0.7203 (t80) cc_final: 0.6605 (t80)
REVERT: B  504 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.7824 (m-70)
REVERT: B  753 MET cc_start: 0.8059 (mmp) cc_final: 0.7740 (mmp)
  outliers start: 31
  outliers final: 23
  residues processed: 123
  average time/residue: 0.1355
  time to fit residues: 22.4833
Evaluate side-chains
  128 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  321 TYR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  570 ASN
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  496 ASN
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  519 ASP
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  750 THR
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  797 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0980
   chunk 42 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   overall best weight:    3.6188

-------------------------------------------------------------------------------
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 = 0.4424 r_free = 0.4424 target = 0.165103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.124934 restraints weight = 10705.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.128097 restraints weight = 5258.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.129925 restraints weight = 3573.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5042  Z= 0.276
  Angle     :  0.733  10.511   6846  Z= 0.366
  Chirality :  0.047   0.336    790
  Planarity :  0.004   0.031    816
  Dihedral  :  4.195  21.099    650
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 23.56 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.33), residues: 586
  helix:  1.35 (0.22), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.17 (0.60), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 446 
 HIS   0.009   0.002   HIS A 636 
 PHE   0.022   0.002   PHE A 717 
 TYR   0.033   0.002   TYR A 321 
 ARG   0.002   0.000   ARG A 780 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8523 (mt)
REVERT: A  504 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7983 (m-70)
REVERT: A  745 PHE cc_start: 0.8594 (p90) cc_final: 0.7899 (m-10)
REVERT: A  806 PHE cc_start: 0.7880 (m-80) cc_final: 0.7588 (m-80)
REVERT: B  325 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8592 (mt)
REVERT: B  504 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.8105 (m-70)
REVERT: B  745 PHE cc_start: 0.8531 (p90) cc_final: 0.7883 (m-10)
REVERT: B  753 MET cc_start: 0.8134 (mmp) cc_final: 0.7878 (mmp)
  outliers start: 33
  outliers final: 24
  residues processed: 126
  average time/residue: 0.1286
  time to fit residues: 21.9807
Evaluate side-chains
  131 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  321 TYR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  570 ASN
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  496 ASN
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  519 ASP
Chi-restraints excluded: chain B residue  570 ASN
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  724 TYR
Chi-restraints excluded: chain B residue  750 THR
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  758 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0370
   chunk 50 optimal weight:   20.0000
   chunk 36 optimal weight:    0.4980
   chunk 23 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8262

-------------------------------------------------------------------------------
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 = 0.4485 r_free = 0.4485 target = 0.170248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.130258 restraints weight = 10818.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.133620 restraints weight = 5293.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.135646 restraints weight = 3554.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5042  Z= 0.158
  Angle     :  0.721  12.531   6846  Z= 0.336
  Chirality :  0.046   0.373    790
  Planarity :  0.003   0.027    816
  Dihedral  :  3.867  18.961    650
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 26.25 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.33), residues: 586
  helix:  1.66 (0.22), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.35 (0.59), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 629 
 HIS   0.011   0.001   HIS A 636 
 PHE   0.020   0.001   PHE B 761 
 TYR   0.038   0.001   TYR A 321 
 ARG   0.001   0.000   ARG A 518 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8463 (mt)
REVERT: A  745 PHE cc_start: 0.8575 (p90) cc_final: 0.7949 (m-10)
REVERT: A  806 PHE cc_start: 0.7647 (m-80) cc_final: 0.7340 (m-80)
REVERT: B  325 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8558 (mt)
REVERT: B  745 PHE cc_start: 0.8548 (p90) cc_final: 0.7942 (m-10)
REVERT: B  753 MET cc_start: 0.8146 (mmp) cc_final: 0.7888 (mmp)
  outliers start: 25
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1371
  time to fit residues: 22.2909
Evaluate side-chains
  127 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  724 TYR
Chi-restraints excluded: chain B residue  750 THR
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  797 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0050
   chunk 38 optimal weight:    0.0980
   chunk 47 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0970
   chunk 50 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.3994

-------------------------------------------------------------------------------
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 = 0.4512 r_free = 0.4512 target = 0.172420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.132687 restraints weight = 10560.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.136144 restraints weight = 5136.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.138222 restraints weight = 3421.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5042  Z= 0.153
  Angle     :  0.724  13.373   6846  Z= 0.333
  Chirality :  0.046   0.376    790
  Planarity :  0.003   0.026    816
  Dihedral  :  3.728  17.216    650
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 27.78 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.34), residues: 586
  helix:  1.76 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.38 (0.60), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 754 
 HIS   0.012   0.001   HIS A 636 
 PHE   0.020   0.001   PHE B 761 
 TYR   0.046   0.001   TYR A 321 
 ARG   0.001   0.000   ARG A 518 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.591 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8855 (tt) cc_final: 0.8487 (mt)
REVERT: A  713 MET cc_start: 0.7659 (tmm) cc_final: 0.7267 (tmm)
REVERT: A  745 PHE cc_start: 0.8623 (p90) cc_final: 0.7877 (m-10)
REVERT: A  806 PHE cc_start: 0.7468 (m-80) cc_final: 0.7149 (m-10)
REVERT: B  325 LEU cc_start: 0.8926 (tt) cc_final: 0.8605 (mt)
REVERT: B  713 MET cc_start: 0.7479 (tmm) cc_final: 0.7224 (tmm)
REVERT: B  745 PHE cc_start: 0.8578 (p90) cc_final: 0.7913 (m-10)
REVERT: B  753 MET cc_start: 0.8187 (mmp) cc_final: 0.7941 (mmp)
  outliers start: 19
  outliers final: 16
  residues processed: 125
  average time/residue: 0.1236
  time to fit residues: 21.0501
Evaluate side-chains
  123 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  750 THR
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  797 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 28 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0270
   chunk 19 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0970
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.4513 r_free = 0.4513 target = 0.172756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.132481 restraints weight = 10814.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.135951 restraints weight = 5217.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.138002 restraints weight = 3487.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5042  Z= 0.172
  Angle     :  0.751  13.016   6846  Z= 0.347
  Chirality :  0.046   0.367    790
  Planarity :  0.003   0.027    816
  Dihedral  :  3.700  16.909    650
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 29.89 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.34), residues: 586
  helix:  1.80 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.40 (0.60), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 754 
 HIS   0.012   0.001   HIS A 636 
 PHE   0.022   0.001   PHE B 577 
 TYR   0.045   0.001   TYR A 321 
 ARG   0.001   0.000   ARG B 518 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  320 PHE cc_start: 0.5720 (m-80) cc_final: 0.5248 (t80)
REVERT: A  325 LEU cc_start: 0.8897 (tt) cc_final: 0.8516 (mt)
REVERT: A  580 MET cc_start: 0.8398 (mmm) cc_final: 0.8196 (mmt)
REVERT: A  745 PHE cc_start: 0.8637 (p90) cc_final: 0.7930 (m-10)
REVERT: A  806 PHE cc_start: 0.7480 (m-80) cc_final: 0.7183 (m-10)
REVERT: B  325 LEU cc_start: 0.8958 (tt) cc_final: 0.8643 (mt)
REVERT: B  713 MET cc_start: 0.7532 (tmm) cc_final: 0.7084 (tmm)
REVERT: B  745 PHE cc_start: 0.8522 (p90) cc_final: 0.7852 (m-10)
REVERT: B  753 MET cc_start: 0.8133 (mmp) cc_final: 0.7909 (mmp)
  outliers start: 16
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1276
  time to fit residues: 21.7370
Evaluate side-chains
  124 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  750 THR
Chi-restraints excluded: chain B residue  752 VAL
Chi-restraints excluded: chain B residue  797 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 58 optimal weight:    0.1980
   chunk 39 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.4496 r_free = 0.4496 target = 0.170924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.130809 restraints weight = 10842.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.134219 restraints weight = 5270.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.136271 restraints weight = 3525.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5042  Z= 0.195
  Angle     :  0.772  13.411   6846  Z= 0.364
  Chirality :  0.047   0.354    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.754  17.315    650
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 29.50 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.34), residues: 586
  helix:  1.80 (0.22), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.15 (0.60), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 754 
 HIS   0.012   0.001   HIS A 636 
 PHE   0.019   0.001   PHE B 761 
 TYR   0.043   0.001   TYR A 321 
 ARG   0.001   0.000   ARG A 518 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1709.62 seconds
wall clock time: 31 minutes 15.81 seconds (1875.81 seconds total)