Starting phenix.real_space_refine
on Tue Mar 11 18:49:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n8x_24248/03_2025/7n8x_24248.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n8x_24248/03_2025/7n8x_24248.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n8x_24248/03_2025/7n8x_24248.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n8x_24248/03_2025/7n8x_24248.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n8x_24248/03_2025/7n8x_24248.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n8x_24248/03_2025/7n8x_24248.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.023 sd=   0.773
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      23      5.16       5
     C    4202      2.51       5
     N    1073      2.21       5
     O    1319      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6617
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1093
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 13, 'TRANS': 126}
    Chain: "A"
      Number of atoms: 5524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 691, 5524
          Classifications: {'peptide': 691}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 669}
          Chain breaks: 1
  Time building chain proxies: 4.27, per 1000 atoms: 0.65
  Number of scatterers: 6617
  At special positions: 0
  Unit cell: (109.61, 84.75, 91.53, 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      23     16.00
     O    1319      8.00
     N    1073      7.00
     C    4202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B   6 " - pdb=" SG  CYS B 124 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.65
  Conformation dependent library (CDL) restraints added in 926.5 milliseconds
  

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1580

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      29.0% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'B' and resid 13 through 17
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 87 through 92
    Processing helix  chain 'B' and resid 123 through 127
    Processing helix  chain 'A' and resid 398 through 415
    Processing helix  chain 'A' and resid 416 through 420
      removed outlier: 3.708A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 438
      removed outlier: 3.657A  pdb=" N   GLU A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 450
      removed outlier: 4.326A  pdb=" N   GLU A 449 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 456
      removed outlier: 4.616A  pdb=" N   LEU A 454 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL A 456 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 470
      removed outlier: 3.513A  pdb=" N   ASN A 467 " --> pdb=" O   LYS A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 4.334A  pdb=" N   ALA A 476 " --> pdb=" O   GLU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 510
    Processing helix  chain 'A' and resid 511 through 516
    Processing helix  chain 'A' and resid 523 through 539
      removed outlier: 4.483A  pdb=" N   ALA A 529 " --> pdb=" O   ALA A 525 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   GLU A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 569
    Processing helix  chain 'A' and resid 588 through 601
      removed outlier: 4.026A  pdb=" N   THR A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 682
    Processing helix  chain 'A' and resid 710 through 727
      removed outlier: 4.533A  pdb=" N   ASP A 721 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LYS A 722 " --> pdb=" O   LYS A 718 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLU A 725 " --> pdb=" O   ASP A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 775
      removed outlier: 3.741A  pdb=" N   ILE A 768 " --> pdb=" O   LYS A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 809
    Processing helix  chain 'A' and resid 814 through 836
    Processing helix  chain 'A' and resid 1773 through 1778
      removed outlier: 3.690A  pdb=" N   ASN A1778 " --> pdb=" O   LYS A1774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1796
    Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31
      removed outlier: 6.870A  pdb=" N   VAL B  30 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE B 135 " --> pdb=" O   ASP B 107 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL B 110 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ARG B  65 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31
      removed outlier: 6.870A  pdb=" N   VAL B  30 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE B 135 " --> pdb=" O   ASP B 107 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL B 110 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ARG B  65 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 37
    Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 629
      removed outlier: 4.517A  pdb=" N   TYR A 621 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   SER A 605 " --> pdb=" O   TYR A 621 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 649 " --> pdb=" O   TYR A 580 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ILE A 646 " --> pdb=" O   GLU A 692 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   ASN A 694 " --> pdb=" O   ILE A 646 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU A 648 " --> pdb=" O   ASN A 694 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LEU A 696 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   PHE A 650 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1654 through 1657
      removed outlier: 5.879A  pdb=" N   MET A1655 " --> pdb=" O   VAL A1692 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   VAL A1691 " --> pdb=" O   ILE A1718 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE A1765 " --> pdb=" O   LEU A1751 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1701 through 1704
      removed outlier: 6.043A  pdb=" N   ILE A1702 " --> pdb=" O   ASN A1732 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   VAL A1731 " --> pdb=" O   ASN A1783 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1844 through 1845
      removed outlier: 4.631A  pdb=" N   TYR A1844 " --> pdb=" O   ILE A1853 " (cutoff:3.500A)

    190 hydrogen bonds defined for protein.
    504 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.99 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: 2171
        1.34 -     1.46: 927
        1.46 -     1.57: 3604
        1.57 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 6741
  Sorted by residual:
  bond pdb=" C   VAL B  43 "
       pdb=" O   VAL B  43 "
    ideal  model  delta    sigma   weight residual
    1.236  1.220  0.016 1.19e-02 7.06e+03 1.84e+00
  bond pdb=" N   ASP A 614 "
       pdb=" CA  ASP A 614 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.70e+00
  bond pdb=" CB  PRO A 644 "
       pdb=" CG  PRO A 644 "
    ideal  model  delta    sigma   weight residual
    1.492  1.552 -0.060 5.00e-02 4.00e+02 1.45e+00
  bond pdb=" C   PRO A1847 "
       pdb=" N   PRO A1848 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.33e+00
  bond pdb=" CG1 ILE A 578 "
       pdb=" CD1 ILE A 578 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.09e+00
  ... (remaining 6736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 9026
        2.74 -     5.47: 100
        5.47 -     8.21: 9
        8.21 -    10.94: 1
       10.94 -    13.68: 2
  Bond angle restraints: 9138
  Sorted by residual:
  angle pdb=" C   LEU A 519 "
        pdb=" CA  LEU A 519 "
        pdb=" CB  LEU A 519 "
      ideal   model   delta    sigma   weight residual
     116.63  111.22    5.41 1.16e+00 7.43e-01 2.18e+01
  angle pdb=" CA  LEU B  72 "
        pdb=" CB  LEU B  72 "
        pdb=" CG  LEU B  72 "
      ideal   model   delta    sigma   weight residual
     116.30  129.98  -13.68 3.50e+00 8.16e-02 1.53e+01
  angle pdb=" CG1 ILE A 640 "
        pdb=" CB  ILE A 640 "
        pdb=" CG2 ILE A 640 "
      ideal   model   delta    sigma   weight residual
     110.70   99.57   11.13 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" CA  PRO A 644 "
        pdb=" N   PRO A 644 "
        pdb=" CD  PRO A 644 "
      ideal   model   delta    sigma   weight residual
     112.00  107.10    4.90 1.40e+00 5.10e-01 1.23e+01
  angle pdb=" C   GLU A 613 "
        pdb=" N   ASP A 614 "
        pdb=" CA  ASP A 614 "
      ideal   model   delta    sigma   weight residual
     121.54  127.62   -6.08 1.91e+00 2.74e-01 1.01e+01
  ... (remaining 9133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 3728
       17.27 -    34.54: 316
       34.54 -    51.80: 47
       51.80 -    69.07: 6
       69.07 -    86.34: 8
  Dihedral angle restraints: 4105
    sinusoidal: 1658
      harmonic: 2447
  Sorted by residual:
  dihedral pdb=" CA  ARG A 643 "
           pdb=" C   ARG A 643 "
           pdb=" N   PRO A 644 "
           pdb=" CA  PRO A 644 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -147.82  -32.18     0      5.00e+00 4.00e-02 4.14e+01
  dihedral pdb=" CA  LYS A1764 "
           pdb=" C   LYS A1764 "
           pdb=" N   ILE A1765 "
           pdb=" CA  ILE A1765 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.92  -27.08     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  ASP B 104 "
           pdb=" C   ASP B 104 "
           pdb=" N   THR B 105 "
           pdb=" CA  THR B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.24   25.76     0      5.00e+00 4.00e-02 2.65e+01
  ... (remaining 4102 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 734
       0.047 -    0.095: 220
       0.095 -    0.142: 72
       0.142 -    0.189: 2
       0.189 -    0.237: 3
  Chirality restraints: 1031
  Sorted by residual:
  chirality pdb=" CB  ILE A 640 "
            pdb=" CA  ILE A 640 "
            pdb=" CG1 ILE A 640 "
            pdb=" CG2 ILE A 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  THR A 430 "
            pdb=" CA  THR A 430 "
            pdb=" OG1 THR A 430 "
            pdb=" CG2 THR A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  PRO A 644 "
            pdb=" N   PRO A 644 "
            pdb=" C   PRO A 644 "
            pdb=" CB  PRO A 644 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.88e-01
  ... (remaining 1028 not shown)

  Planarity restraints: 1193
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 643 "   -0.092 5.00e-02 4.00e+02   1.39e-01 3.08e+01
        pdb=" N   PRO A 644 "    0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO A 644 "   -0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A 644 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 699 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.55e+00
        pdb=" C   ASN A 699 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ASN A 699 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   MET A 700 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 462 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   VAL A 462 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 462 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LYS A 463 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1190 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 188
        2.70 -     3.25: 6969
        3.25 -     3.80: 9773
        3.80 -     4.35: 12870
        4.35 -     4.90: 21155
  Nonbonded interactions: 50955
  Sorted by model distance:
  nonbonded pdb=" O   ARG A1739 "
            pdb=" NZ  LYS A1764 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" N   GLY A1814 "
            pdb=" O   TYR A1824 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OD2 ASP B  89 "
            pdb=" OH  TYR A1819 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP A 423 "
            pdb=" OG1 THR A 426 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN A 699 "
            pdb=" ND2 ASN A 699 "
     model   vdw
     2.269 3.120
  ... (remaining 50950 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.890
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
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   0.060   6741  Z= 0.226
  Angle     :  0.735  13.681   9138  Z= 0.390
  Chirality :  0.049   0.237   1031
  Planarity :  0.006   0.139   1193
  Dihedral  : 13.271  86.339   2522
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 10.06 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.30), residues: 825
  helix:  0.74 (0.38), residues: 209
  sheet: -1.64 (0.44), residues: 141
  loop : -1.52 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  40 
 HIS   0.009   0.002   HIS B  69 
 PHE   0.030   0.002   PHE A1676 
 TYR   0.014   0.001   TYR A1661 
 ARG   0.002   0.000   ARG A 643 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.682 
Fit side-chains
REVERT: B  108 GLN cc_start: 0.7970 (pm20) cc_final: 0.7311 (pp30)
REVERT: A  375 ILE cc_start: 0.6364 (tp) cc_final: 0.5961 (tp)
REVERT: A  384 ASN cc_start: 0.5695 (t0) cc_final: 0.5350 (t0)
REVERT: A  466 ILE cc_start: 0.8196 (tp) cc_final: 0.7912 (tp)
REVERT: A  705 ILE cc_start: 0.7805 (tp) cc_final: 0.7566 (tp)
REVERT: A  742 TYR cc_start: 0.7319 (m-80) cc_final: 0.7054 (m-10)
REVERT: A 1705 THR cc_start: 0.7932 (m) cc_final: 0.7684 (m)
REVERT: A 1727 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6572 (pt0)
REVERT: A 1752 MET cc_start: 0.5166 (ttp) cc_final: 0.4879 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2019
  time to fit residues: 38.7050
Evaluate side-chains
  128 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 706 ASN
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.205845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.192884 restraints weight = 8705.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.4350 rms_B_bonded: 1.83
r_work: 0.4265 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4140 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.4140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6741  Z= 0.214
  Angle     :  0.691  12.679   9138  Z= 0.350
  Chirality :  0.049   0.216   1031
  Planarity :  0.005   0.134   1193
  Dihedral  :  6.168  34.514    894
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.12 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.70 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.30), residues: 825
  helix:  0.74 (0.37), residues: 213
  sheet: -1.88 (0.43), residues: 140
  loop : -1.56 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.021   0.002   PHE A 780 
 TYR   0.021   0.002   TYR A1819 
 ARG   0.002   0.000   ARG B 118 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 144
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  375 ILE cc_start: 0.6711 (tp) cc_final: 0.6268 (tp)
REVERT: A  384 ASN cc_start: 0.6038 (t0) cc_final: 0.5518 (t0)
REVERT: A  394 TYR cc_start: 0.5898 (m-80) cc_final: 0.4009 (m-10)
REVERT: A  410 LEU cc_start: 0.7995 (tp) cc_final: 0.7396 (mp)
REVERT: A  466 ILE cc_start: 0.8068 (tp) cc_final: 0.7805 (tp)
REVERT: A  569 LEU cc_start: 0.6466 (tp) cc_final: 0.6147 (pp)
REVERT: A  705 ILE cc_start: 0.8076 (tp) cc_final: 0.7751 (tp)
REVERT: A  709 GLU cc_start: 0.7472 (mp0) cc_final: 0.7220 (tm-30)
REVERT: A  766 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7653 (tt0)
REVERT: A  818 LYS cc_start: 0.8389 (tptt) cc_final: 0.7839 (tptt)
REVERT: A 1681 LEU cc_start: 0.7425 (tt) cc_final: 0.7211 (tt)
REVERT: A 1705 THR cc_start: 0.7736 (m) cc_final: 0.7520 (m)
REVERT: A 1727 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6450 (tp30)
REVERT: A 1734 ASN cc_start: 0.7998 (m110) cc_final: 0.7470 (p0)
REVERT: A 1735 ASP cc_start: 0.7399 (m-30) cc_final: 0.7084 (m-30)
REVERT: A 1752 MET cc_start: 0.5297 (ttp) cc_final: 0.5032 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 146
  average time/residue: 0.1873
  time to fit residues: 36.4288
Evaluate side-chains
  134 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain A residue 1679 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.204605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.191560 restraints weight = 8748.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.4303 rms_B_bonded: 1.83
r_work: 0.4222 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4093 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6741  Z= 0.222
  Angle     :  0.672  11.974   9138  Z= 0.340
  Chirality :  0.049   0.198   1031
  Planarity :  0.006   0.132   1193
  Dihedral  :  6.103  35.193    894
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.33 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.22 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.30), residues: 825
  helix:  0.66 (0.37), residues: 214
  sheet: -2.04 (0.43), residues: 141
  loop : -1.49 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.013   0.001   PHE A 459 
 TYR   0.016   0.002   TYR A1819 
 ARG   0.002   0.000   ARG A 571 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 LEU cc_start: 0.8361 (mt) cc_final: 0.7975 (tp)
REVERT: A  375 ILE cc_start: 0.6804 (tp) cc_final: 0.6402 (tp)
REVERT: A  384 ASN cc_start: 0.6069 (t0) cc_final: 0.5505 (t0)
REVERT: A  394 TYR cc_start: 0.6179 (m-80) cc_final: 0.4058 (m-80)
REVERT: A  401 LYS cc_start: 0.6840 (mtmt) cc_final: 0.5800 (mtmt)
REVERT: A  410 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7406 (mp)
REVERT: A  436 MET cc_start: 0.5771 (ptp) cc_final: 0.5508 (ptm)
REVERT: A  466 ILE cc_start: 0.8093 (tp) cc_final: 0.7843 (tp)
REVERT: A  569 LEU cc_start: 0.6534 (tp) cc_final: 0.6127 (pp)
REVERT: A  705 ILE cc_start: 0.8057 (tp) cc_final: 0.7716 (tp)
REVERT: A  709 GLU cc_start: 0.7541 (mp0) cc_final: 0.7300 (tm-30)
REVERT: A  766 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7599 (tt0)
REVERT: A  781 ASN cc_start: 0.7964 (t0) cc_final: 0.7699 (t0)
REVERT: A 1681 LEU cc_start: 0.7636 (tt) cc_final: 0.7272 (tt)
REVERT: A 1705 THR cc_start: 0.7771 (m) cc_final: 0.7547 (m)
REVERT: A 1727 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6487 (tp30)
REVERT: A 1752 MET cc_start: 0.5304 (ttp) cc_final: 0.5076 (ttp)
  outliers start: 11
  outliers final: 9
  residues processed: 144
  average time/residue: 0.1982
  time to fit residues: 37.7008
Evaluate side-chains
  139 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue 1849 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0020
   chunk 39 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.211337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.198518 restraints weight = 8786.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.4339 rms_B_bonded: 1.79
r_work: 0.4261 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4136 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6741  Z= 0.171
  Angle     :  0.640  10.901   9138  Z= 0.322
  Chirality :  0.047   0.197   1031
  Planarity :  0.005   0.130   1193
  Dihedral  :  5.807  34.819    894
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.24 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.94 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.30), residues: 825
  helix:  0.88 (0.38), residues: 208
  sheet: -1.99 (0.43), residues: 139
  loop : -1.37 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  37 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.022   0.001   PHE A 780 
 TYR   0.015   0.001   TYR A1819 
 ARG   0.001   0.000   ARG A 499 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.773 
Fit side-chains
REVERT: B   54 LEU cc_start: 0.8176 (mt) cc_final: 0.7757 (tp)
REVERT: B   56 LYS cc_start: 0.8233 (tttt) cc_final: 0.8002 (mttt)
REVERT: A  375 ILE cc_start: 0.6757 (tp) cc_final: 0.6253 (mm)
REVERT: A  384 ASN cc_start: 0.5937 (t0) cc_final: 0.5494 (t0)
REVERT: A  394 TYR cc_start: 0.5936 (m-80) cc_final: 0.3286 (m-80)
REVERT: A  404 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6289 (mp0)
REVERT: A  410 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7403 (mp)
REVERT: A  436 MET cc_start: 0.5726 (ptp) cc_final: 0.5500 (ptm)
REVERT: A  466 ILE cc_start: 0.8022 (tp) cc_final: 0.7789 (tp)
REVERT: A  569 LEU cc_start: 0.6527 (tp) cc_final: 0.6124 (pp)
REVERT: A  583 GLN cc_start: 0.8290 (tt0) cc_final: 0.7997 (tt0)
REVERT: A  705 ILE cc_start: 0.8119 (tp) cc_final: 0.7754 (tp)
REVERT: A  766 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7609 (tt0)
REVERT: A  818 LYS cc_start: 0.8345 (tptt) cc_final: 0.7803 (tptt)
REVERT: A 1681 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7211 (tt)
REVERT: A 1727 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6571 (tp30)
REVERT: A 1735 ASP cc_start: 0.7576 (m-30) cc_final: 0.7298 (m-30)
REVERT: A 1752 MET cc_start: 0.5141 (ttp) cc_final: 0.4900 (ttp)
  outliers start: 16
  outliers final: 9
  residues processed: 153
  average time/residue: 0.1941
  time to fit residues: 40.0908
Evaluate side-chains
  144 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1681 LEU
Chi-restraints excluded: chain A residue 1763 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0170
   chunk 51 optimal weight:    0.7980
   chunk 68 optimal weight:    0.4980
   chunk 64 optimal weight:    0.0970
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.210393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.197458 restraints weight = 8728.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 1.82
r_work: 0.4277 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4152 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6741  Z= 0.158
  Angle     :  0.629  10.504   9138  Z= 0.317
  Chirality :  0.047   0.197   1031
  Planarity :  0.005   0.128   1193
  Dihedral  :  5.541  34.158    894
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.88 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.48 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.30), residues: 825
  helix:  0.73 (0.38), residues: 214
  sheet: -1.91 (0.43), residues: 141
  loop : -1.29 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  37 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.008   0.001   PHE A 446 
 TYR   0.013   0.001   TYR A1819 
 ARG   0.001   0.000   ARG A1739 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: B   54 LEU cc_start: 0.8196 (mt) cc_final: 0.7735 (tp)
REVERT: B   56 LYS cc_start: 0.8277 (tttt) cc_final: 0.8035 (mttt)
REVERT: B  108 GLN cc_start: 0.8281 (pm20) cc_final: 0.7730 (pp30)
REVERT: A  375 ILE cc_start: 0.6714 (tp) cc_final: 0.6168 (mm)
REVERT: A  384 ASN cc_start: 0.6004 (t0) cc_final: 0.5572 (t0)
REVERT: A  394 TYR cc_start: 0.5772 (m-80) cc_final: 0.3459 (m-80)
REVERT: A  401 LYS cc_start: 0.6403 (mtmt) cc_final: 0.6149 (mtmt)
REVERT: A  404 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6197 (mp0)
REVERT: A  410 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7382 (mp)
REVERT: A  411 ASN cc_start: 0.5614 (t0) cc_final: 0.5402 (t0)
REVERT: A  436 MET cc_start: 0.5672 (ptp) cc_final: 0.5447 (ptm)
REVERT: A  466 ILE cc_start: 0.7974 (tp) cc_final: 0.7745 (tp)
REVERT: A  489 MET cc_start: 0.7075 (ttm) cc_final: 0.6833 (ttm)
REVERT: A  583 GLN cc_start: 0.8241 (tt0) cc_final: 0.7985 (tt0)
REVERT: A  705 ILE cc_start: 0.8065 (tp) cc_final: 0.7804 (tp)
REVERT: A  766 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7624 (tt0)
REVERT: A  776 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6855 (tt0)
REVERT: A  818 LYS cc_start: 0.8452 (tptt) cc_final: 0.7857 (tptt)
REVERT: A 1708 TYR cc_start: 0.8168 (p90) cc_final: 0.7939 (p90)
REVERT: A 1727 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6334 (tp30)
REVERT: A 1752 MET cc_start: 0.5110 (ttp) cc_final: 0.4863 (ttp)
  outliers start: 21
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1794
  time to fit residues: 36.6788
Evaluate side-chains
  155 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  121 MET
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 47 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 33 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.204925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.191646 restraints weight = 8827.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.4302 rms_B_bonded: 1.92
r_work: 0.4216 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.4085 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   6741  Z= 0.157
  Angle     :  0.615  10.515   9138  Z= 0.309
  Chirality :  0.047   0.217   1031
  Planarity :  0.005   0.127   1193
  Dihedral  :  5.447  33.829    894
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.76 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.67 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.31), residues: 825
  helix:  0.82 (0.38), residues: 214
  sheet: -1.94 (0.42), residues: 142
  loop : -1.24 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.023   0.001   PHE A 780 
 TYR   0.023   0.001   TYR A 742 
 ARG   0.001   0.000   ARG A1739 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 LEU cc_start: 0.8264 (mt) cc_final: 0.7764 (tp)
REVERT: B   56 LYS cc_start: 0.8269 (tttt) cc_final: 0.8001 (mttt)
REVERT: B  108 GLN cc_start: 0.8213 (pm20) cc_final: 0.7676 (pp30)
REVERT: A  375 ILE cc_start: 0.6658 (tp) cc_final: 0.6061 (mm)
REVERT: A  384 ASN cc_start: 0.5990 (t0) cc_final: 0.5550 (t0)
REVERT: A  394 TYR cc_start: 0.5816 (m-80) cc_final: 0.3374 (m-80)
REVERT: A  401 LYS cc_start: 0.6426 (mtmt) cc_final: 0.6142 (mtmt)
REVERT: A  410 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7364 (mp)
REVERT: A  411 ASN cc_start: 0.5743 (t0) cc_final: 0.5507 (t0)
REVERT: A  436 MET cc_start: 0.5528 (ptp) cc_final: 0.5297 (ptm)
REVERT: A  448 MET cc_start: 0.7373 (ptp) cc_final: 0.7169 (ptp)
REVERT: A  466 ILE cc_start: 0.7892 (tp) cc_final: 0.7675 (tp)
REVERT: A  583 GLN cc_start: 0.8222 (tt0) cc_final: 0.7935 (tt0)
REVERT: A  709 GLU cc_start: 0.7117 (tt0) cc_final: 0.6689 (tm-30)
REVERT: A  766 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7671 (tt0)
REVERT: A  776 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6839 (tt0)
REVERT: A  818 LYS cc_start: 0.8482 (tptt) cc_final: 0.7868 (tptt)
REVERT: A 1681 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6944 (tt)
REVERT: A 1752 MET cc_start: 0.5385 (ttp) cc_final: 0.5160 (ttp)
  outliers start: 22
  outliers final: 15
  residues processed: 157
  average time/residue: 0.1747
  time to fit residues: 37.0330
Evaluate side-chains
  160 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1681 LEU
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 827 ASN
A1744 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.205016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.192278 restraints weight = 8728.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.4314 rms_B_bonded: 1.84
r_work: 0.4236 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.4113 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6741  Z= 0.218
  Angle     :  0.647  10.632   9138  Z= 0.329
  Chirality :  0.048   0.214   1031
  Planarity :  0.006   0.127   1193
  Dihedral  :  5.722  33.747    894
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.73 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.73 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.30), residues: 825
  helix:  0.74 (0.38), residues: 214
  sheet: -2.05 (0.41), residues: 142
  loop : -1.28 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1742 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.013   0.001   PHE A 531 
 TYR   0.013   0.002   TYR A1819 
 ARG   0.002   0.000   ARG A 643 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7246 (mt-10)
REVERT: B   54 LEU cc_start: 0.8397 (mt) cc_final: 0.7903 (tp)
REVERT: B   62 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8286 (p)
REVERT: B  112 GLU cc_start: 0.8214 (mp0) cc_final: 0.7904 (mp0)
REVERT: A  375 ILE cc_start: 0.6885 (tp) cc_final: 0.6484 (tp)
REVERT: A  384 ASN cc_start: 0.6005 (t0) cc_final: 0.5633 (t0)
REVERT: A  394 TYR cc_start: 0.5950 (OUTLIER) cc_final: 0.2375 (m-10)
REVERT: A  401 LYS cc_start: 0.6528 (mtmt) cc_final: 0.6307 (mtmt)
REVERT: A  404 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6473 (mp0)
REVERT: A  410 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7426 (mp)
REVERT: A  411 ASN cc_start: 0.5726 (t0) cc_final: 0.5506 (t0)
REVERT: A  436 MET cc_start: 0.5714 (ptp) cc_final: 0.5491 (ptm)
REVERT: A  466 ILE cc_start: 0.8003 (tp) cc_final: 0.7772 (tp)
REVERT: A  601 THR cc_start: 0.8152 (p) cc_final: 0.7797 (p)
REVERT: A  766 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7597 (tt0)
REVERT: A  776 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6926 (tt0)
REVERT: A  818 LYS cc_start: 0.8463 (tptt) cc_final: 0.7853 (tptt)
REVERT: A 1681 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7063 (tt)
REVERT: A 1727 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6554 (tp30)
REVERT: A 1752 MET cc_start: 0.5367 (ttp) cc_final: 0.5114 (ttp)
REVERT: A 1846 LYS cc_start: 0.7282 (mtpt) cc_final: 0.7040 (mmtp)
  outliers start: 24
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1826
  time to fit residues: 37.1221
Evaluate side-chains
  155 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  636 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1681 LEU
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.207612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.194963 restraints weight = 8820.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 1.81
r_work: 0.4256 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4130 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6741  Z= 0.185
  Angle     :  0.638  10.615   9138  Z= 0.324
  Chirality :  0.047   0.214   1031
  Planarity :  0.005   0.126   1193
  Dihedral  :  5.612  33.140    894
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.48 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.66 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.30), residues: 825
  helix:  0.70 (0.38), residues: 214
  sheet: -2.05 (0.41), residues: 142
  loop : -1.27 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.024   0.001   PHE A 780 
 TYR   0.024   0.001   TYR A 742 
 ARG   0.001   0.000   ARG A1739 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7212 (mt-10)
REVERT: B   54 LEU cc_start: 0.7973 (mt) cc_final: 0.7509 (tp)
REVERT: B   62 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8358 (p)
REVERT: A  375 ILE cc_start: 0.6824 (tp) cc_final: 0.6389 (tp)
REVERT: A  384 ASN cc_start: 0.5950 (t0) cc_final: 0.5616 (t0)
REVERT: A  394 TYR cc_start: 0.5860 (OUTLIER) cc_final: 0.2857 (m-80)
REVERT: A  401 LYS cc_start: 0.6579 (mtmt) cc_final: 0.6116 (mtmt)
REVERT: A  410 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7402 (mp)
REVERT: A  411 ASN cc_start: 0.5724 (t0) cc_final: 0.5509 (t0)
REVERT: A  436 MET cc_start: 0.5677 (ptp) cc_final: 0.5413 (ptm)
REVERT: A  448 MET cc_start: 0.7163 (ptp) cc_final: 0.6834 (mpp)
REVERT: A  466 ILE cc_start: 0.7988 (tp) cc_final: 0.7765 (tp)
REVERT: A  766 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7602 (tt0)
REVERT: A  776 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6836 (tt0)
REVERT: A  818 LYS cc_start: 0.8483 (tptt) cc_final: 0.7858 (tptt)
REVERT: A 1681 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7057 (tt)
REVERT: A 1727 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6534 (tp30)
  outliers start: 22
  outliers final: 12
  residues processed: 148
  average time/residue: 0.1801
  time to fit residues: 35.7480
Evaluate side-chains
  153 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  636 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1681 LEU
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.207275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.194648 restraints weight = 8874.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.4327 rms_B_bonded: 1.82
r_work: 0.4251 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4126 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6741  Z= 0.184
  Angle     :  0.643  10.606   9138  Z= 0.328
  Chirality :  0.047   0.213   1031
  Planarity :  0.005   0.125   1193
  Dihedral  :  5.596  33.016    894
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.73 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.40 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.31), residues: 825
  helix:  0.70 (0.38), residues: 214
  sheet: -2.05 (0.42), residues: 142
  loop : -1.27 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.008   0.001   PHE A1845 
 TYR   0.012   0.001   TYR A1819 
 ARG   0.001   0.000   ARG B 127 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7266 (mt-10)
REVERT: B   54 LEU cc_start: 0.8151 (mt) cc_final: 0.7680 (tp)
REVERT: B   62 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8371 (p)
REVERT: A  375 ILE cc_start: 0.6857 (tp) cc_final: 0.6419 (tp)
REVERT: A  384 ASN cc_start: 0.5992 (t0) cc_final: 0.5651 (t0)
REVERT: A  394 TYR cc_start: 0.5855 (OUTLIER) cc_final: 0.3100 (m-80)
REVERT: A  410 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7399 (mp)
REVERT: A  411 ASN cc_start: 0.5729 (t0) cc_final: 0.5505 (t0)
REVERT: A  436 MET cc_start: 0.5707 (ptp) cc_final: 0.5491 (ptm)
REVERT: A  448 MET cc_start: 0.7155 (ptp) cc_final: 0.6827 (mpp)
REVERT: A  466 ILE cc_start: 0.7978 (tp) cc_final: 0.7755 (tp)
REVERT: A  766 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7624 (tt0)
REVERT: A  776 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6787 (tt0)
REVERT: A  818 LYS cc_start: 0.8492 (tptt) cc_final: 0.8146 (tptt)
REVERT: A 1681 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7046 (tt)
REVERT: A 1727 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6526 (tp30)
  outliers start: 23
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1811
  time to fit residues: 36.3340
Evaluate side-chains
  152 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  636 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1681 LEU
Chi-restraints excluded: chain A residue 1738 ILE
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0370
   chunk 64 optimal weight:    0.3980
   chunk 23 optimal weight:    0.4980
   chunk 80 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0370
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.206141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.192638 restraints weight = 9115.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.4311 rms_B_bonded: 1.96
r_work: 0.4224 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.4094 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058   6741  Z= 0.155
  Angle     :  0.631  10.422   9138  Z= 0.322
  Chirality :  0.047   0.193   1031
  Planarity :  0.005   0.123   1193
  Dihedral  :  5.291  32.186    894
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.36 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.86 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.31), residues: 825
  helix:  0.82 (0.38), residues: 214
  sheet: -1.83 (0.43), residues: 142
  loop : -1.17 (0.31), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1742 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.025   0.001   PHE A 780 
 TYR   0.014   0.001   TYR A 742 
 ARG   0.002   0.000   ARG A1739 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.8383 (tttt) cc_final: 0.8119 (mttm)
REVERT: B  108 GLN cc_start: 0.8172 (pm20) cc_final: 0.7653 (pp30)
REVERT: A  375 ILE cc_start: 0.6644 (tp) cc_final: 0.6024 (mm)
REVERT: A  384 ASN cc_start: 0.5847 (t0) cc_final: 0.5471 (t0)
REVERT: A  394 TYR cc_start: 0.5742 (m-80) cc_final: 0.3352 (m-80)
REVERT: A  410 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7361 (mp)
REVERT: A  411 ASN cc_start: 0.5568 (t0) cc_final: 0.5350 (t0)
REVERT: A  436 MET cc_start: 0.5576 (ptp) cc_final: 0.5374 (ptm)
REVERT: A  448 MET cc_start: 0.7258 (ptp) cc_final: 0.6911 (mpp)
REVERT: A  466 ILE cc_start: 0.7834 (tp) cc_final: 0.7543 (tp)
REVERT: A  583 GLN cc_start: 0.8227 (tt0) cc_final: 0.7967 (tt0)
REVERT: A  766 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7655 (tt0)
REVERT: A  776 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6796 (tt0)
REVERT: A  818 LYS cc_start: 0.8499 (tptt) cc_final: 0.7871 (tptt)
REVERT: A 1676 PHE cc_start: 0.1577 (OUTLIER) cc_final: -0.0293 (t80)
REVERT: A 1681 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6936 (tt)
  outliers start: 17
  outliers final: 9
  residues processed: 149
  average time/residue: 0.1737
  time to fit residues: 35.5704
Evaluate side-chains
  146 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1681 LEU
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 65 optimal weight:    0.0040
   chunk 66 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   chunk 14 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0370
   overall best weight:    0.4470

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

Flipped N/Q/H residues before XYZ refinement:
A 699 ASN
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 802 GLN
A1744 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.205729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.192235 restraints weight = 9044.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.4310 rms_B_bonded: 1.96
r_work: 0.4222 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.4093 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6741  Z= 0.157
  Angle     :  0.622  10.453   9138  Z= 0.318
  Chirality :  0.046   0.184   1031
  Planarity :  0.005   0.122   1193
  Dihedral  :  5.225  32.192    894
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.48 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.79 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.31), residues: 825
  helix:  0.87 (0.38), residues: 214
  sheet: -1.82 (0.44), residues: 142
  loop : -1.12 (0.31), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.006   0.001   PHE A 658 
 TYR   0.012   0.001   TYR A1708 
 ARG   0.001   0.000   ARG A1739 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3482.43 seconds
wall clock time: 60 minutes 23.36 seconds (3623.36 seconds total)