Starting phenix.real_space_refine
on Thu Sep 10 22:52:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1d_36792/09_2026/8k1d_36792.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1d_36792/09_2026/8k1d_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1d_36792/09_2026/8k1d_36792.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1d_36792/09_2026/8k1d_36792.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1d_36792/09_2026/8k1d_36792.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1d_36792/09_2026/8k1d_36792.map"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.102
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'TYR:plan': 1, 'ARG: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, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 32
  Time building chain proxies: 1.28, per 1000 atoms: 0.26
  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: 0.37
  Conformation dependent library (CDL) restraints added in 177.4 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: 0.09
  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: 0.64

  Time building geometry restraints manager: 0.51 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:             0.370
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.830
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.000
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6838
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG B 518 
 TYR   0.025   0.001   TYR B 321 
 PHE   0.020   0.001   PHE A 745 
 TRP   0.031   0.002   TRP A 794 
 HIS   0.003   0.001   HIS B 504 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.16 ( 5042)
  covalent geometry    : angle       0.71398 /  0.37 ( 6846)
  SS BOND              : bond        0.00032 /  0.01 (    4)
  SS BOND              : angle       0.68372 /  0.27 (    8)
  hydrogen bonds       : bond        0.10580 /  6.01 (  381)
  hydrogen bonds       : angle       5.26945 /  3.78 ( 1143)

*********************** 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  : 0.178 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8444 (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: 0.0550
  time to fit residues: 8.8066
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  : 0.171 
-------------------------------------------------------------------------------
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 54 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0000
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.5590

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.169502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.127519 restraints weight = 10742.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.130747 restraints weight = 5381.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.132665 restraints weight = 3693.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.133779 restraints weight = 3022.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.134249 restraints weight = 2723.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5046  Z= 0.129
  Angle     :  0.607  11.213   6854  Z= 0.304
  Chirality :  0.039   0.173    790
  Planarity :  0.003   0.042    816
  Dihedral  :  4.466  32.232    654
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 24.71 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.33), residues: 586
  helix:  1.64 (0.22), residues: 486
  sheet:  None (None), residues: 0
  loop : -2.83 (0.53), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 517 
 TYR   0.018   0.001   TYR B 321 
 PHE   0.012   0.001   PHE B 806 
 TRP   0.003   0.001   TRP A 754 
 HIS   0.003   0.001   HIS B 504 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.13 ( 5042)
  covalent geometry    : angle       0.60719 /  0.30 ( 6846)
  SS BOND              : bond        0.00111 /  0.05 (    4)
  SS BOND              : angle       0.49678 /  0.24 (    8)
  hydrogen bonds       : bond        0.04501 /  2.80 (  381)
  hydrogen bonds       : angle       4.38741 /  3.14 ( 1143)

*********************** 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
  125 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.7211 (t80) cc_final: 0.6758 (t80)
REVERT: B  517 ARG cc_start: 0.8355 (ptt90) cc_final: 0.8138 (ptt-90)
REVERT: B  699 LEU cc_start: 0.8894 (mm) cc_final: 0.8635 (pp)
REVERT: B  753 MET cc_start: 0.7716 (mmp) cc_final: 0.7497 (mmp)
  outliers start: 16
  outliers final: 9
  residues processed: 119
  average time/residue: 0.0527
  time to fit residues: 8.7955
Evaluate side-chains
  111 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 38 optimal weight:    5.9990
   chunk 18 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.1494 > 50:)
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0470
   chunk 11 optimal weight:    7.9990
   overall best weight:    3.6086

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 791 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.165552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.124225 restraints weight = 10858.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.127421 restraints weight = 5426.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.129261 restraints weight = 3714.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.130128 restraints weight = 3053.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.130735 restraints weight = 2790.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5046  Z= 0.203
  Angle     :  0.671   8.422   6854  Z= 0.350
  Chirality :  0.042   0.179    790
  Planarity :  0.004   0.039    816
  Dihedral  :  4.160  19.397    650
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 24.52 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.33), residues: 586
  helix:  1.39 (0.22), residues: 482
  sheet:  None (None), residues: 0
  loop : -2.32 (0.60), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 517 
 TYR   0.015   0.002   TYR A 455 
 PHE   0.033   0.002   PHE B 806 
 TRP   0.005   0.001   TRP A 446 
 HIS   0.007   0.002   HIS A 504 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.20 ( 5042)
  covalent geometry    : angle       0.67072 /  0.35 ( 6846)
  SS BOND              : bond        0.00311 /  0.15 (    4)
  SS BOND              : angle       0.60863 /  0.36 (    8)
  hydrogen bonds       : bond        0.04883 /  3.04 (  381)
  hydrogen bonds       : angle       4.69736 /  3.40 ( 1143)

*********************** 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: 26
    poor density    : 98
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  504 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7742 (m-70)
REVERT: B  517 ARG cc_start: 0.8460 (ptt90) cc_final: 0.8220 (ptt-90)
REVERT: B  580 MET cc_start: 0.8147 (mmt) cc_final: 0.7940 (mmt)
REVERT: B  753 MET cc_start: 0.7890 (mmp) cc_final: 0.7674 (mmp)
REVERT: B  802 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8358 (tt)
  outliers start: 26
  outliers final: 19
  residues processed: 117
  average time/residue: 0.0522
  time to fit residues: 8.4427
Evaluate side-chains
  117 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
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  570 ASN
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  325 LEU
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  553 MET
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
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 5 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.9786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.168378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.127347 restraints weight = 10783.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.130587 restraints weight = 5347.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.132544 restraints weight = 3646.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.133602 restraints weight = 2969.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.133968 restraints weight = 2676.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5046  Z= 0.141
  Angle     :  0.618   8.987   6854  Z= 0.312
  Chirality :  0.041   0.282    790
  Planarity :  0.003   0.034    816
  Dihedral  :  3.951  18.600    650
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 23.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.33), residues: 586
  helix:  1.49 (0.21), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.77 (0.56), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 517 
 TYR   0.013   0.001   TYR A 306 
 PHE   0.025   0.001   PHE B 806 
 TRP   0.005   0.001   TRP A 754 
 HIS   0.008   0.001   HIS B 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 5042)
  covalent geometry    : angle       0.61851 /  0.31 ( 6846)
  SS BOND              : bond        0.00151 /  0.07 (    4)
  SS BOND              : angle       0.36518 /  0.21 (    8)
  hydrogen bonds       : bond        0.04418 /  2.77 (  381)
  hydrogen bonds       : angle       4.40703 /  3.19 ( 1143)

*********************** 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
  127 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.7397 (t80) cc_final: 0.6908 (t80)
REVERT: A  511 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7678 (t80)
REVERT: B  455 TYR cc_start: 0.7103 (t80) cc_final: 0.6738 (t80)
REVERT: B  504 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.7926 (m-70)
REVERT: B  517 ARG cc_start: 0.8422 (ptt90) cc_final: 0.8175 (ttp-110)
  outliers start: 26
  outliers final: 18
  residues processed: 119
  average time/residue: 0.0540
  time to fit residues: 8.9337
Evaluate side-chains
  118 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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  511 PHE
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  504 HIS
Chi-restraints excluded: chain B residue  686 LEU
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 22 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 11 optimal weight:   30.0000
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.3186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.167224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.126089 restraints weight = 10943.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.129390 restraints weight = 5367.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.131330 restraints weight = 3628.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.132381 restraints weight = 2946.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.132820 restraints weight = 2648.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.2522

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= 0.152
  Angle     :  0.649  10.273   6854  Z= 0.322
  Chirality :  0.042   0.299    790
  Planarity :  0.003   0.036    816
  Dihedral  :  3.990  19.800    650
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 22.99 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.33), residues: 586
  helix:  1.49 (0.22), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.64 (0.59), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 518 
 TYR   0.013   0.001   TYR A 306 
 PHE   0.013   0.001   PHE A 761 
 TRP   0.011   0.001   TRP B 754 
 HIS   0.008   0.001   HIS B 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 5042)
  covalent geometry    : angle       0.64873 /  0.32 ( 6846)
  SS BOND              : bond        0.00103 /  0.05 (    4)
  SS BOND              : angle       0.46571 /  0.27 (    8)
  hydrogen bonds       : bond        0.04393 /  2.75 (  381)
  hydrogen bonds       : angle       4.38987 /  3.18 ( 1143)

*********************** 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
  137 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8383 (mt)
REVERT: A  504 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.8097 (m-70)
REVERT: A  511 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7611 (t80)
REVERT: A  745 PHE cc_start: 0.8658 (p90) cc_final: 0.7924 (m-10)
REVERT: A  806 PHE cc_start: 0.7776 (m-80) cc_final: 0.7343 (m-80)
REVERT: B  325 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8502 (mt)
REVERT: B  504 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8016 (m-70)
REVERT: B  753 MET cc_start: 0.7909 (mmp) cc_final: 0.7610 (mmp)
REVERT: B  806 PHE cc_start: 0.7798 (m-80) cc_final: 0.7572 (m-80)
  outliers start: 33
  outliers final: 22
  residues processed: 125
  average time/residue: 0.0531
  time to fit residues: 9.2960
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  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 1 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    2.9988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.166416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.125632 restraints weight = 10915.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.128893 restraints weight = 5358.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.130734 restraints weight = 3619.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.131825 restraints weight = 2949.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.132168 restraints weight = 2650.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5046  Z= 0.177
  Angle     :  0.676   9.610   6854  Z= 0.340
  Chirality :  0.044   0.316    790
  Planarity :  0.003   0.035    816
  Dihedral  :  4.058  20.750    650
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.33), residues: 586
  helix:  1.34 (0.21), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.52 (0.59), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 705 
 TYR   0.035   0.002   TYR A 321 
 PHE   0.026   0.002   PHE B 700 
 TRP   0.011   0.001   TRP B 754 
 HIS   0.009   0.002   HIS B 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.18 ( 5042)
  covalent geometry    : angle       0.67638 /  0.34 ( 6846)
  SS BOND              : bond        0.00204 /  0.09 (    4)
  SS BOND              : angle       0.46632 /  0.27 (    8)
  hydrogen bonds       : bond        0.04563 /  2.83 (  381)
  hydrogen bonds       : angle       4.54215 /  3.28 ( 1143)

*********************** 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
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8452 (mt)
REVERT: A  504 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.8134 (m-70)
REVERT: A  511 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7851 (t80)
REVERT: A  745 PHE cc_start: 0.8745 (p90) cc_final: 0.8067 (m-10)
REVERT: A  806 PHE cc_start: 0.7701 (m-80) cc_final: 0.7307 (m-80)
REVERT: B  325 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8525 (mt)
REVERT: B  504 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8084 (m-70)
REVERT: B  745 PHE cc_start: 0.8536 (p90) cc_final: 0.7940 (m-10)
REVERT: B  753 MET cc_start: 0.7905 (mmp) cc_final: 0.7671 (mmp)
REVERT: B  806 PHE cc_start: 0.7883 (m-80) cc_final: 0.7584 (m-80)
  outliers start: 31
  outliers final: 24
  residues processed: 125
  average time/residue: 0.0512
  time to fit residues: 8.9417
Evaluate side-chains
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
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  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
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 48 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 42 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.7986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.168017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.127777 restraints weight = 10842.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.131094 restraints weight = 5270.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.133056 restraints weight = 3539.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.134130 restraints weight = 2876.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.134478 restraints weight = 2578.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5046  Z= 0.134
  Angle     :  0.653  11.092   6854  Z= 0.318
  Chirality :  0.043   0.321    790
  Planarity :  0.003   0.034    816
  Dihedral  :  3.915  19.974    650
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 23.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.33), residues: 586
  helix:  1.60 (0.22), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.52 (0.59), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.038   0.001   TYR A 321 
 PHE   0.023   0.001   PHE B 700 
 TRP   0.016   0.001   TRP B 754 
 HIS   0.010   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 5042)
  covalent geometry    : angle       0.65372 /  0.32 ( 6846)
  SS BOND              : bond        0.00097 /  0.05 (    4)
  SS BOND              : angle       0.36568 /  0.21 (    8)
  hydrogen bonds       : bond        0.04252 /  2.63 (  381)
  hydrogen bonds       : angle       4.33269 /  3.11 ( 1143)

*********************** 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
  141 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 108
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8469 (mt)
REVERT: A  477 ASP cc_start: 0.8651 (p0) cc_final: 0.8442 (p0)
REVERT: A  511 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7987 (t80)
REVERT: A  745 PHE cc_start: 0.8667 (p90) cc_final: 0.8001 (m-10)
REVERT: A  806 PHE cc_start: 0.7745 (m-80) cc_final: 0.7315 (m-80)
REVERT: B  325 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8547 (mt)
REVERT: B  504 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8108 (m-70)
REVERT: B  745 PHE cc_start: 0.8477 (p90) cc_final: 0.7916 (m-10)
REVERT: B  753 MET cc_start: 0.7946 (mmp) cc_final: 0.7634 (mmp)
REVERT: B  758 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8356 (mm)
REVERT: B  806 PHE cc_start: 0.7870 (m-80) cc_final: 0.7560 (m-80)
  outliers start: 33
  outliers final: 25
  residues processed: 130
  average time/residue: 0.0513
  time to fit residues: 9.3466
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
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  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  511 PHE
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  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  504 HIS
Chi-restraints excluded: chain B residue  519 ASP
Chi-restraints excluded: chain B residue  570 ASN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0970
   chunk 49 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 16 optimal weight:   20.0000
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.9382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.170387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.129415 restraints weight = 10805.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.132793 restraints weight = 5328.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.134798 restraints weight = 3601.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.135817 restraints weight = 2928.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.136493 restraints weight = 2641.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5046  Z= 0.121
  Angle     :  0.679  14.105   6854  Z= 0.324
  Chirality :  0.045   0.409    790
  Planarity :  0.003   0.030    816
  Dihedral  :  3.825  19.504    650
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 27.01 %
    Favored  : 67.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.34), residues: 586
  helix:  1.68 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.46 (0.60), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.039   0.001   TYR A 321 
 PHE   0.022   0.001   PHE B 700 
 TRP   0.016   0.001   TRP B 754 
 HIS   0.011   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 5042)
  covalent geometry    : angle       0.67972 /  0.32 ( 6846)
  SS BOND              : bond        0.00058 /  0.03 (    4)
  SS BOND              : angle       0.34064 /  0.18 (    8)
  hydrogen bonds       : bond        0.04191 /  2.60 (  381)
  hydrogen bonds       : angle       4.22863 /  3.03 ( 1143)

*********************** 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: 28
    poor density    : 106
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8731 (tt) cc_final: 0.8361 (mt)
REVERT: A  477 ASP cc_start: 0.8635 (p0) cc_final: 0.8431 (p0)
REVERT: A  511 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8027 (t80)
REVERT: A  745 PHE cc_start: 0.8643 (p90) cc_final: 0.7974 (m-10)
REVERT: A  754 TRP cc_start: 0.7671 (OUTLIER) cc_final: 0.6823 (m100)
REVERT: A  806 PHE cc_start: 0.7646 (m-80) cc_final: 0.7229 (m-80)
REVERT: B  325 LEU cc_start: 0.8898 (tt) cc_final: 0.8577 (mt)
REVERT: B  745 PHE cc_start: 0.8564 (p90) cc_final: 0.7984 (m-10)
REVERT: B  753 MET cc_start: 0.7978 (mmp) cc_final: 0.7682 (mmp)
REVERT: B  758 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8390 (mm)
REVERT: B  806 PHE cc_start: 0.7777 (m-80) cc_final: 0.7457 (m-80)
  outliers start: 28
  outliers final: 23
  residues processed: 125
  average time/residue: 0.0561
  time to fit residues: 9.7501
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
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  445 PHE
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  511 PHE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  754 TRP
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  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  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 45 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0270
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 1 optimal weight:    8.9990
   chunk 17 optimal weight:   30.0000
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.6240

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.172270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.131677 restraints weight = 10769.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.135095 restraints weight = 5218.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.137190 restraints weight = 3499.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.138314 restraints weight = 2827.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.138914 restraints weight = 2538.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5046  Z= 0.117
  Angle     :  0.691  13.687   6854  Z= 0.324
  Chirality :  0.046   0.400    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.709  18.487    650
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 27.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.34), residues: 586
  helix:  1.75 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.37 (0.61), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.039   0.001   TYR A 321 
 PHE   0.020   0.001   PHE B 700 
 TRP   0.013   0.001   TRP B 754 
 HIS   0.013   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.12 ( 5042)
  covalent geometry    : angle       0.69174 /  0.32 ( 6846)
  SS BOND              : bond        0.00048 /  0.02 (    4)
  SS BOND              : angle       0.33892 /  0.17 (    8)
  hydrogen bonds       : bond        0.04047 /  2.52 (  381)
  hydrogen bonds       : angle       4.11726 /  2.94 ( 1143)

*********************** 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
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8766 (tt) cc_final: 0.8409 (mt)
REVERT: A  511 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8038 (t80)
REVERT: A  713 MET cc_start: 0.7679 (tmm) cc_final: 0.7392 (tmm)
REVERT: A  745 PHE cc_start: 0.8665 (p90) cc_final: 0.7950 (m-10)
REVERT: B  325 LEU cc_start: 0.8941 (tt) cc_final: 0.8628 (mt)
REVERT: B  506 LEU cc_start: 0.9233 (mm) cc_final: 0.8988 (tp)
REVERT: B  745 PHE cc_start: 0.8562 (p90) cc_final: 0.7948 (m-10)
REVERT: B  753 MET cc_start: 0.7996 (mmp) cc_final: 0.7691 (mmp)
REVERT: B  758 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8420 (mm)
  outliers start: 26
  outliers final: 21
  residues processed: 127
  average time/residue: 0.0512
  time to fit residues: 9.0831
Evaluate side-chains
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
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  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  445 PHE
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  519 ASP
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 16 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.9784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.171617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.130739 restraints weight = 10930.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.134106 restraints weight = 5326.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.136150 restraints weight = 3595.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.137052 restraints weight = 2918.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.137713 restraints weight = 2657.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5046  Z= 0.123
  Angle     :  0.724  14.101   6854  Z= 0.338
  Chirality :  0.046   0.403    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.705  19.141    650
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 29.31 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.34), residues: 586
  helix:  1.80 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.39 (0.61), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 518 
 TYR   0.040   0.001   TYR A 321 
 PHE   0.024   0.001   PHE B 761 
 TRP   0.009   0.001   TRP B 754 
 HIS   0.012   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 5042)
  covalent geometry    : angle       0.72428 /  0.34 ( 6846)
  SS BOND              : bond        0.00060 /  0.03 (    4)
  SS BOND              : angle       0.26772 /  0.13 (    8)
  hydrogen bonds       : bond        0.04053 /  2.54 (  381)
  hydrogen bonds       : angle       4.12862 /  2.94 ( 1143)

********************** 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
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8778 (tt) cc_final: 0.8423 (mt)
REVERT: A  511 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8067 (t80)
REVERT: A  745 PHE cc_start: 0.8675 (p90) cc_final: 0.7959 (m-10)
REVERT: A  806 PHE cc_start: 0.7657 (m-80) cc_final: 0.7198 (m-10)
REVERT: B  325 LEU cc_start: 0.8980 (tt) cc_final: 0.8645 (mt)
REVERT: B  506 LEU cc_start: 0.9224 (mm) cc_final: 0.9000 (tp)
REVERT: B  745 PHE cc_start: 0.8610 (p90) cc_final: 0.8005 (m-10)
REVERT: B  753 MET cc_start: 0.7926 (mmp) cc_final: 0.7714 (mmp)
REVERT: B  758 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8391 (mm)
  outliers start: 21
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0527
  time to fit residues: 9.0902
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  : 0.105 
-------------------------------------------------------------------------------
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  505 VAL
Chi-restraints excluded: chain A residue  511 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  454 PHE
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  519 ASP
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 58 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0010
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 41 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 55 optimal weight:    0.2980
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.0390

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.171686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.131440 restraints weight = 10977.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.134890 restraints weight = 5252.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.136975 restraints weight = 3507.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.138070 restraints weight = 2837.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.138522 restraints weight = 2551.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5046  Z= 0.124
  Angle     :  0.737  14.603   6854  Z= 0.343
  Chirality :  0.046   0.396    790
  Planarity :  0.003   0.028    816
  Dihedral  :  3.674  19.026    650
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 29.12 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.34), residues: 586
  helix:  1.84 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.42 (0.60), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.040   0.001   TYR A 321 
 PHE   0.023   0.001   PHE B 761 
 TRP   0.008   0.001   TRP B 754 
 HIS   0.012   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 5042)
  covalent geometry    : angle       0.73721 /  0.34 ( 6846)
  SS BOND              : bond        0.00064 /  0.03 (    4)
  SS BOND              : angle       0.24677 /  0.12 (    8)
  hydrogen bonds       : bond        0.04029 /  2.53 (  381)
  hydrogen bonds       : angle       4.12255 /  2.94 ( 1143)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 998.42 seconds
wall clock time: 17 minutes 59.10 seconds (1079.10 seconds total)