Starting phenix.real_space_refine
on Sat May 10 03:39:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1d_36792/05_2025/8k1d_36792.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1d_36792/05_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_36792/05_2025/8k1d_36792.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1d_36792/05_2025/8k1d_36792.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1d_36792/05_2025/8k1d_36792.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1d_36792/05_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-5687/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: 3.33, per 1000 atoms: 0.68
  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: 1.20
  Conformation dependent library (CDL) restraints added in 556.8 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: 0.49
  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: 1.38

  Time building geometry restraints manager: 1.41 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: 0.02
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:             0.190
  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:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.290
  Find NCS groups from input model:        0.150
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.920
-------------------------------------------------------------------------------
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   5046  Z= 0.157
  Angle     :  0.714   9.494   6854  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10580 (  381)
  hydrogen bonds       : angle       5.26945 ( 1143)
  SS BOND              : bond        0.00032 (    4)
  SS BOND              : angle       0.68372 (    8)
  covalent geometry    : bond        0.00292 ( 5042)
  covalent geometry    : angle       0.71398 ( 6846)

*********************** 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  : 0.480 
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: 0.1215
  time to fit residues: 18.9685
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  : 0.489 
-------------------------------------------------------------------------------
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   5046  Z= 0.162
  Angle     :  0.626  10.410   6854  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04722 (  381)
  hydrogen bonds       : angle       4.55661 ( 1143)
  SS BOND              : bond        0.00158 (    4)
  SS BOND              : angle       0.53670 (    8)
  covalent geometry    : bond        0.00341 ( 5042)
  covalent geometry    : angle       0.62584 ( 6846)

*********************** 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  : 0.468 
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: 0.1266
  time to fit residues: 20.6352
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  : 0.476 
-------------------------------------------------------------------------------
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:    4.9990
   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:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0980
   chunk 19 optimal weight:    6.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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 = 0.4473 r_free = 0.4473 target = 0.168716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.127371 restraints weight = 10877.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.130657 restraints weight = 5403.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.132618 restraints weight = 3688.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5046  Z= 0.140
  Angle     :  0.627   9.548   6854  Z= 0.315
  Chirality :  0.041   0.278    790
  Planarity :  0.003   0.036    816
  Dihedral  :  3.938  17.200    650
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.29 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.33), residues: 586
  helix:  1.46 (0.22), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.84 (0.56), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 754 
 HIS   0.007   0.001   HIS B 636 
 PHE   0.012   0.001   PHE A 483 
 TYR   0.013   0.001   TYR A 306 
 ARG   0.007   0.001   ARG A 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04459 (  381)
  hydrogen bonds       : angle       4.46001 ( 1143)
  SS BOND              : bond        0.00130 (    4)
  SS BOND              : angle       0.39866 (    8)
  covalent geometry    : bond        0.00293 ( 5042)
  covalent geometry    : angle       0.62749 ( 6846)

*********************** 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
  125 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7701 (m-70)
REVERT: A  554 MET cc_start: 0.7660 (mmp) cc_final: 0.7444 (mmp)
REVERT: B  802 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7710 (tt)
  outliers start: 19
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1401
  time to fit residues: 22.8221
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  : 0.538 
-------------------------------------------------------------------------------
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 B residue  316 ILE
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:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0870
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    2.3964

-------------------------------------------------------------------------------
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 = 0.4468 r_free = 0.4468 target = 0.167983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.126408 restraints weight = 10921.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.129651 restraints weight = 5463.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.131552 restraints weight = 3727.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5046  Z= 0.154
  Angle     :  0.634  10.501   6854  Z= 0.319
  Chirality :  0.042   0.278    790
  Planarity :  0.003   0.035    816
  Dihedral  :  4.013  19.209    650
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 24.52 %
    Favored  : 69.92 %
  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:  1.21 (0.33), residues: 586
  helix:  1.48 (0.22), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.76 (0.57), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 754 
 HIS   0.008   0.001   HIS B 636 
 PHE   0.021   0.001   PHE B 806 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.005   0.000   ARG A 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  381)
  hydrogen bonds       : angle       4.45944 ( 1143)
  SS BOND              : bond        0.00142 (    4)
  SS BOND              : angle       0.42736 (    8)
  covalent geometry    : bond        0.00328 ( 5042)
  covalent geometry    : angle       0.63457 ( 6846)

*********************** 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
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.7565 (t80) cc_final: 0.7111 (t80)
REVERT: A  504 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7845 (m-70)
REVERT: A  511 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8083 (t80)
REVERT: B  455 TYR cc_start: 0.7155 (t80) cc_final: 0.6731 (t80)
REVERT: B  504 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.7784 (m-70)
REVERT: B  753 MET cc_start: 0.8113 (mmp) cc_final: 0.7834 (mmp)
  outliers start: 29
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1282
  time to fit residues: 21.0421
Evaluate side-chains
  119 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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  504 HIS
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  570 ASN
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  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  570 ASN
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:   30.0000
   chunk 28 optimal weight:    0.3980
   chunk 54 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    3.2386

-------------------------------------------------------------------------------
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 = 0.4436 r_free = 0.4436 target = 0.165999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.125376 restraints weight = 10904.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.128629 restraints weight = 5343.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.130538 restraints weight = 3607.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5046  Z= 0.185
  Angle     :  0.682  10.205   6854  Z= 0.343
  Chirality :  0.044   0.278    790
  Planarity :  0.004   0.038    816
  Dihedral  :  4.125  22.052    650
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 23.18 %
    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:  1.10 (0.33), residues: 586
  helix:  1.35 (0.22), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.39 (0.61), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 754 
 HIS   0.008   0.002   HIS B 636 
 PHE   0.017   0.002   PHE A 761 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.002   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04610 (  381)
  hydrogen bonds       : angle       4.60380 ( 1143)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       0.52838 (    8)
  covalent geometry    : bond        0.00397 ( 5042)
  covalent geometry    : angle       0.68239 ( 6846)

*********************** 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
  141 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.559 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8426 (mt)
REVERT: A  504 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.8070 (m-70)
REVERT: A  806 PHE cc_start: 0.7809 (m-80) cc_final: 0.7401 (m-80)
REVERT: B  325 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8516 (mt)
REVERT: B  504 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8055 (m-70)
REVERT: B  753 MET cc_start: 0.8212 (mmp) cc_final: 0.7936 (mmp)
  outliers start: 35
  outliers final: 24
  residues processed: 128
  average time/residue: 0.1260
  time to fit residues: 21.9149
Evaluate side-chains
  133 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
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  485 CYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 56 optimal weight:    0.0050
   chunk 48 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.3396

-------------------------------------------------------------------------------
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 = 0.4474 r_free = 0.4474 target = 0.169044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.127953 restraints weight = 10765.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.131231 restraints weight = 5322.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.133173 restraints weight = 3604.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5046  Z= 0.128
  Angle     :  0.681  11.619   6854  Z= 0.324
  Chirality :  0.044   0.311    790
  Planarity :  0.003   0.032    816
  Dihedral  :  3.917  19.721    650
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 25.48 %
    Favored  : 69.73 %
  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:  1.37 (0.33), residues: 586
  helix:  1.55 (0.22), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.52 (0.58), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 754 
 HIS   0.009   0.001   HIS A 636 
 PHE   0.018   0.001   PHE A 761 
 TYR   0.037   0.001   TYR A 321 
 ARG   0.001   0.000   ARG B 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04307 (  381)
  hydrogen bonds       : angle       4.33945 ( 1143)
  SS BOND              : bond        0.00095 (    4)
  SS BOND              : angle       0.33175 (    8)
  covalent geometry    : bond        0.00264 ( 5042)
  covalent geometry    : angle       0.68104 ( 6846)

*********************** 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
  133 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8441 (mt)
REVERT: A  580 MET cc_start: 0.8375 (mmt) cc_final: 0.8137 (mmm)
REVERT: A  722 LEU cc_start: 0.8487 (tp) cc_final: 0.7822 (mt)
REVERT: A  745 PHE cc_start: 0.8596 (p90) cc_final: 0.7957 (m-10)
REVERT: A  806 PHE cc_start: 0.7758 (m-80) cc_final: 0.7457 (m-80)
REVERT: B  325 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8507 (mt)
REVERT: B  451 ILE cc_start: 0.7544 (tp) cc_final: 0.7330 (pt)
REVERT: B  745 PHE cc_start: 0.8511 (p90) cc_final: 0.7908 (m-10)
REVERT: B  753 MET cc_start: 0.8227 (mmp) cc_final: 0.7986 (mmp)
REVERT: B  758 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8396 (mm)
  outliers start: 25
  outliers final: 19
  residues processed: 124
  average time/residue: 0.1255
  time to fit residues: 21.2743
Evaluate side-chains
  125 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  519 ASP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 42 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0470
   chunk 58 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.4505 r_free = 0.4505 target = 0.171727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.131272 restraints weight = 10589.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.134680 restraints weight = 5214.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.136677 restraints weight = 3509.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5046  Z= 0.116
  Angle     :  0.666  12.181   6854  Z= 0.316
  Chirality :  0.043   0.362    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.758  18.933    650
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 27.78 %
    Favored  : 68.01 %
  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:  1.60 (0.34), residues: 586
  helix:  1.69 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.49 (0.58), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 754 
 HIS   0.011   0.001   HIS B 636 
 PHE   0.018   0.001   PHE B 700 
 TYR   0.039   0.001   TYR A 321 
 ARG   0.002   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04058 (  381)
  hydrogen bonds       : angle       4.13155 ( 1143)
  SS BOND              : bond        0.00042 (    4)
  SS BOND              : angle       0.37573 (    8)
  covalent geometry    : bond        0.00230 ( 5042)
  covalent geometry    : angle       0.66601 ( 6846)

*********************** 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
  133 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8764 (tt) cc_final: 0.8408 (mt)
REVERT: A  580 MET cc_start: 0.8351 (mmt) cc_final: 0.8088 (mmm)
REVERT: A  722 LEU cc_start: 0.8484 (tp) cc_final: 0.7806 (mt)
REVERT: A  745 PHE cc_start: 0.8612 (p90) cc_final: 0.7944 (m-10)
REVERT: B  325 LEU cc_start: 0.8868 (tt) cc_final: 0.8546 (mt)
REVERT: B  451 ILE cc_start: 0.7311 (tp) cc_final: 0.7104 (pt)
REVERT: B  745 PHE cc_start: 0.8608 (p90) cc_final: 0.7946 (m-10)
REVERT: B  753 MET cc_start: 0.7994 (mmp) cc_final: 0.7778 (mmp)
REVERT: B  758 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8401 (mm)
  outliers start: 22
  outliers final: 18
  residues processed: 127
  average time/residue: 0.1233
  time to fit residues: 21.2606
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  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  454 PHE
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  321 TYR
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  519 ASP
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 18 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0470
   chunk 23 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.7682

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.169028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.128495 restraints weight = 10855.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.131831 restraints weight = 5344.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.133829 restraints weight = 3597.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5046  Z= 0.135
  Angle     :  0.687  11.472   6854  Z= 0.329
  Chirality :  0.045   0.361    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.813  18.746    650
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 27.01 %
    Favored  : 67.82 %
  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:  1.66 (0.34), residues: 586
  helix:  1.73 (0.22), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.27 (0.60), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 754 
 HIS   0.010   0.002   HIS A 636 
 PHE   0.022   0.001   PHE B 761 
 TYR   0.037   0.001   TYR A 321 
 ARG   0.001   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  381)
  hydrogen bonds       : angle       4.26628 ( 1143)
  SS BOND              : bond        0.00116 (    4)
  SS BOND              : angle       0.35875 (    8)
  covalent geometry    : bond        0.00287 ( 5042)
  covalent geometry    : angle       0.68771 ( 6846)

*********************** 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
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8826 (tt) cc_final: 0.8465 (mt)
REVERT: A  722 LEU cc_start: 0.8449 (tp) cc_final: 0.7776 (mt)
REVERT: A  745 PHE cc_start: 0.8622 (p90) cc_final: 0.7904 (m-10)
REVERT: A  806 PHE cc_start: 0.7722 (m-80) cc_final: 0.7350 (m-10)
REVERT: B  325 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8604 (mt)
REVERT: B  745 PHE cc_start: 0.8631 (p90) cc_final: 0.7993 (m-10)
REVERT: B  753 MET cc_start: 0.8171 (mmp) cc_final: 0.7934 (mmp)
REVERT: B  758 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8346 (mm)
  outliers start: 27
  outliers final: 21
  residues processed: 126
  average time/residue: 0.1235
  time to fit residues: 21.1176
Evaluate side-chains
  127 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  445 PHE
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  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  519 ASP
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:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:   20.0000
   chunk 8 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.6086

-------------------------------------------------------------------------------
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 = 0.4471 r_free = 0.4471 target = 0.169188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.128511 restraints weight = 10690.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.131782 restraints weight = 5285.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.133758 restraints weight = 3593.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5046  Z= 0.134
  Angle     :  0.720  13.055   6854  Z= 0.341
  Chirality :  0.046   0.401    790
  Planarity :  0.003   0.029    816
  Dihedral  :  3.817  18.797    650
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 26.44 %
    Favored  : 68.39 %
  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:  1.61 (0.34), residues: 586
  helix:  1.71 (0.22), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.25 (0.59), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 754 
 HIS   0.011   0.001   HIS A 636 
 PHE   0.026   0.001   PHE A 717 
 TYR   0.037   0.001   TYR A 321 
 ARG   0.001   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  381)
  hydrogen bonds       : angle       4.28570 ( 1143)
  SS BOND              : bond        0.00105 (    4)
  SS BOND              : angle       0.35731 (    8)
  covalent geometry    : bond        0.00287 ( 5042)
  covalent geometry    : angle       0.72049 ( 6846)

*********************** 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
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8763 (tt) cc_final: 0.8389 (mt)
REVERT: A  504 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7948 (m-70)
REVERT: A  722 LEU cc_start: 0.8472 (tp) cc_final: 0.7829 (mt)
REVERT: A  745 PHE cc_start: 0.8595 (p90) cc_final: 0.7879 (m-10)
REVERT: A  806 PHE cc_start: 0.7712 (m-80) cc_final: 0.7331 (m-10)
REVERT: B  325 LEU cc_start: 0.8955 (tt) cc_final: 0.8623 (mt)
REVERT: B  745 PHE cc_start: 0.8609 (p90) cc_final: 0.7992 (m-10)
REVERT: B  753 MET cc_start: 0.8186 (mmp) cc_final: 0.7946 (mmp)
REVERT: B  758 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8351 (mm)
  outliers start: 27
  outliers final: 23
  residues processed: 124
  average time/residue: 0.1102
  time to fit residues: 18.7593
Evaluate side-chains
  131 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  445 PHE
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  686 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain B residue  321 TYR
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0870
   chunk 19 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 21 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.4522 r_free = 0.4522 target = 0.173457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.133174 restraints weight = 10898.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.136672 restraints weight = 5225.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.138705 restraints weight = 3497.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5046  Z= 0.119
  Angle     :  0.722  14.077   6854  Z= 0.334
  Chirality :  0.046   0.390    790
  Planarity :  0.003   0.026    816
  Dihedral  :  3.612  17.303    650
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 28.16 %
    Favored  : 68.77 %
  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:  1.79 (0.34), residues: 586
  helix:  1.83 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.48 (0.58), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 754 
 HIS   0.013   0.001   HIS A 636 
 PHE   0.021   0.001   PHE B 761 
 TYR   0.042   0.001   TYR A 321 
 ARG   0.001   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  381)
  hydrogen bonds       : angle       4.09241 ( 1143)
  SS BOND              : bond        0.00033 (    4)
  SS BOND              : angle       0.34975 (    8)
  covalent geometry    : bond        0.00242 ( 5042)
  covalent geometry    : angle       0.72222 ( 6846)

********************** 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
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8796 (tt) cc_final: 0.8418 (mt)
REVERT: A  713 MET cc_start: 0.7625 (tmm) cc_final: 0.7350 (tmm)
REVERT: A  745 PHE cc_start: 0.8569 (p90) cc_final: 0.7896 (m-10)
REVERT: B  325 LEU cc_start: 0.8979 (tt) cc_final: 0.8665 (mt)
REVERT: B  713 MET cc_start: 0.7411 (tmm) cc_final: 0.6981 (tmm)
REVERT: B  722 LEU cc_start: 0.8525 (tt) cc_final: 0.8190 (pp)
REVERT: B  745 PHE cc_start: 0.8554 (p90) cc_final: 0.7954 (m-10)
REVERT: B  753 MET cc_start: 0.8172 (mmp) cc_final: 0.7969 (mmp)
  outliers start: 16
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1259
  time to fit residues: 22.0507
Evaluate side-chains
  125 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  454 PHE
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  321 TYR
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  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:    2.9990
   chunk 58 optimal weight:    0.0670
   chunk 39 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.0126

-------------------------------------------------------------------------------
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 = 0.4476 r_free = 0.4476 target = 0.169498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.128997 restraints weight = 10769.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.132291 restraints weight = 5272.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.134263 restraints weight = 3576.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5046  Z= 0.146
  Angle     :  0.758  13.065   6854  Z= 0.356
  Chirality :  0.047   0.396    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.771  18.375    650
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 27.20 %
    Favored  : 68.39 %
  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:  1.69 (0.34), residues: 586
  helix:  1.75 (0.22), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.22 (0.60), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 754 
 HIS   0.012   0.002   HIS A 636 
 PHE   0.021   0.001   PHE B 761 
 TYR   0.037   0.001   TYR A 321 
 ARG   0.001   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  381)
  hydrogen bonds       : angle       4.28022 ( 1143)
  SS BOND              : bond        0.00131 (    4)
  SS BOND              : angle       0.29976 (    8)
  covalent geometry    : bond        0.00324 ( 5042)
  covalent geometry    : angle       0.75805 ( 6846)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1805.74 seconds
wall clock time: 32 minutes 22.75 seconds (1942.75 seconds total)