Starting phenix.real_space_refine
on Tue Mar  3 11:34:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swp_25478/03_2026/7swp_25478_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swp_25478/03_2026/7swp_25478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swp_25478/03_2026/7swp_25478_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swp_25478/03_2026/7swp_25478_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swp_25478/03_2026/7swp_25478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swp_25478/03_2026/7swp_25478.map"
  }
  resolution = 3.8
  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=   0.000 sd=   0.002
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      14      5.16       5
     C    2137      2.51       5
     N     573      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3372
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1545
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "H"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 1017
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "L"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 810
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 104}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 0.89, per 1000 atoms: 0.26
  Number of scatterers: 3372
  At special positions: 0
  Unit cell: (84.15, 59.4, 89.1, 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      14     16.00
     O     648      8.00
     N     573      7.00
     C    2137      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.04

  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: 0.25
  Conformation dependent library (CDL) restraints added in 118.5 milliseconds
  

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  782

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 8 sheets defined
      15.1% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.584A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.236A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 409
      removed outlier: 3.828A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 105 through 109
      removed outlier: 3.876A  pdb=" N   TYR H 109 " --> pdb=" O   SER H 106 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 85
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356
      removed outlier: 3.782A  pdb=" N   ALA A 435 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR A 376 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.547A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.687A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.623A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12
    Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 23

    119 hydrogen bonds defined for protein.
    273 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: 0.48

  Time building geometry restraints manager: 0.36 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: 1087
        1.34 -     1.46: 924
        1.46 -     1.58: 1434
        1.58 -     1.71: 0
        1.71 -     1.83: 16
  Bond restraints: 3461
  Sorted by residual:
  bond pdb=" C   TYR A 421 "
       pdb=" N   ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.332  1.282  0.050 1.40e-02 5.10e+03 1.27e+01
  bond pdb=" C   LYS A 424 "
       pdb=" N   LEU A 425 "
    ideal  model  delta    sigma   weight residual
    1.331  1.233  0.098 2.83e-02 1.25e+03 1.19e+01
  bond pdb=" N   VAL L 100 "
       pdb=" CA  VAL L 100 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.036 1.21e-02 6.83e+03 8.88e+00
  bond pdb=" N   VAL L 101 "
       pdb=" CA  VAL L 101 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.036 1.24e-02 6.50e+03 8.21e+00
  bond pdb=" N   THR L 106 "
       pdb=" CA  THR L 106 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.96e+00
  ... (remaining 3456 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 4371
        1.61 -     3.21: 276
        3.21 -     4.82: 43
        4.82 -     6.42: 12
        6.42 -     8.03: 5
  Bond angle restraints: 4707
  Sorted by residual:
  angle pdb=" C   HIS L  36 "
        pdb=" N   TRP L  37 "
        pdb=" CA  TRP L  37 "
      ideal   model   delta    sigma   weight residual
     122.94  115.73    7.21 1.50e+00 4.44e-01 2.31e+01
  angle pdb=" C   TYR A 421 "
        pdb=" N   ASN A 422 "
        pdb=" CA  ASN A 422 "
      ideal   model   delta    sigma   weight residual
     121.54  113.51    8.03 1.91e+00 2.74e-01 1.77e+01
  angle pdb=" C   PRO A 527 "
        pdb=" N   LYS A 528 "
        pdb=" CA  LYS A 528 "
      ideal   model   delta    sigma   weight residual
     121.70  127.24   -5.54 1.80e+00 3.09e-01 9.48e+00
  angle pdb=" N   GLY A 526 "
        pdb=" CA  GLY A 526 "
        pdb=" C   GLY A 526 "
      ideal   model   delta    sigma   weight residual
     112.34  118.59   -6.25 2.04e+00 2.40e-01 9.38e+00
  angle pdb=" CA  GLY L 103 "
        pdb=" C   GLY L 103 "
        pdb=" O   GLY L 103 "
      ideal   model   delta    sigma   weight residual
     122.24  118.32    3.92 1.30e+00 5.92e-01 9.10e+00
  ... (remaining 4702 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 1840
       17.57 -    35.15: 163
       35.15 -    52.72: 15
       52.72 -    70.29: 4
       70.29 -    87.87: 2
  Dihedral angle restraints: 2024
    sinusoidal: 776
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CA  CYS A 391 "
           pdb=" C   CYS A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.49  -28.51     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.90   46.10     1      1.00e+01 1.00e-02 2.94e+01
  dihedral pdb=" CA  SER A 477 "
           pdb=" C   SER A 477 "
           pdb=" N   THR A 478 "
           pdb=" CA  THR A 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.35  -22.65     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 2021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 354
       0.048 -    0.096: 103
       0.096 -    0.145: 33
       0.145 -    0.193: 3
       0.193 -    0.241: 2
  Chirality restraints: 495
  Sorted by residual:
  chirality pdb=" CB  ILE L  50 "
            pdb=" CA  ILE L  50 "
            pdb=" CG1 ILE L  50 "
            pdb=" CG2 ILE L  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CG  LEU H  81 "
            pdb=" CB  LEU H  81 "
            pdb=" CD1 LEU H  81 "
            pdb=" CD2 LEU H  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  VAL L 101 "
            pdb=" N   VAL L 101 "
            pdb=" C   VAL L 101 "
            pdb=" CB  VAL L 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.86e-01
  ... (remaining 492 not shown)

  Planarity restraints: 617
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  37 "   -0.035 2.00e-02 2.50e+03   4.40e-02 4.85e+01
        pdb=" CG  TRP L  37 "    0.109 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  37 "   -0.074 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  37 "    0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  37 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  37 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  37 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  37 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  37 "   -0.023 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  37 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 526 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO A 527 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 527 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 527 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 453 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.16e+00
        pdb=" C   TYR A 453 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   TYR A 453 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ARG A 454 "    0.009 2.00e-02 2.50e+03
  ... (remaining 614 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 569
        2.74 -     3.28: 3775
        3.28 -     3.82: 6048
        3.82 -     4.36: 7001
        4.36 -     4.90: 11348
  Nonbonded interactions: 28741
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP L  94 "
            pdb=" OG  SER L  96 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" NE2 GLN H  13 "
            pdb=" O   SER H 128 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   TYR H  53 "
            pdb=" NH2 ARG H  72 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OG1 THR A 415 "
            pdb=" OG  SER L  58 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LYS A 444 "
            pdb=" NE2 GLN A 498 "
     model   vdw
     2.224 3.120
  ... (remaining 28736 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 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:             1.210
  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:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.980
  Find NCS groups from input model:        0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
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      :  0.008   0.098   3467  Z= 0.412
  Angle     :  0.927   8.029   4719  Z= 0.526
  Chirality :  0.051   0.241    495
  Planarity :  0.006   0.056    617
  Dihedral  : 12.869  87.868   1224
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 40.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.09 %
    Favored  : 87.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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: -2.17 (0.38), residues: 430
  helix: -3.11 (0.87), residues: 21
  sheet: -1.11 (0.44), residues: 122
  loop : -1.50 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 408 
 TYR   0.021   0.003   TYR L  51 
 PHE   0.023   0.002   PHE A 490 
 TRP   0.109   0.006   TRP L  37 
 HIS   0.007   0.003   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00831 ( 3461)
  covalent geometry    : angle       0.92452 ( 4707)
  SS BOND              : bond        0.00744 (    6)
  SS BOND              : angle       1.60220 (   12)
  hydrogen bonds       : bond        0.17133 (  107)
  hydrogen bonds       : angle       9.87188 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8298 (tm-30)
REVERT: A  356 LYS cc_start: 0.8283 (tppt) cc_final: 0.7661 (tptt)
REVERT: A  398 ASP cc_start: 0.7717 (m-30) cc_final: 0.7370 (m-30)
REVERT: A  403 ARG cc_start: 0.6932 (ptt90) cc_final: 0.6645 (ptt90)
REVERT: A  501 ASN cc_start: 0.7846 (t0) cc_final: 0.7430 (t0)
REVERT: A  517 LEU cc_start: 0.8767 (mt) cc_final: 0.8271 (tt)
REVERT: H    2 VAL cc_start: 0.7845 (m) cc_final: 0.7345 (m)
REVERT: H   16 ARG cc_start: 0.5406 (ptt-90) cc_final: 0.5174 (ptp-110)
REVERT: H   34 MET cc_start: 0.8260 (mmp) cc_final: 0.8041 (mmm)
REVERT: H   35 GLN cc_start: 0.8219 (mp10) cc_final: 0.7931 (mp10)
REVERT: H   95 TYR cc_start: 0.7581 (m-80) cc_final: 0.7351 (m-80)
REVERT: H  105 ASP cc_start: 0.8435 (t70) cc_final: 0.7970 (t70)
REVERT: H  111 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7824 (mp10)
REVERT: H  112 THR cc_start: 0.8451 (p) cc_final: 0.8148 (m)
REVERT: L   34 ASP cc_start: 0.7295 (p0) cc_final: 0.6964 (p0)
REVERT: L   87 ASP cc_start: 0.7942 (p0) cc_final: 0.7573 (t70)
REVERT: L  101 VAL cc_start: 0.8381 (t) cc_final: 0.8080 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0756
  time to fit residues: 14.2863
Evaluate side-chains
  98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    3.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 117 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.117697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.100283 restraints weight = 9262.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.105163 restraints weight = 6034.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.108295 restraints weight = 3114.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.109313 restraints weight = 2006.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.110305 restraints weight = 1612.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3467  Z= 0.255
  Angle     :  0.818   9.091   4719  Z= 0.429
  Chirality :  0.050   0.144    495
  Planarity :  0.006   0.040    617
  Dihedral  :  6.051  27.453    487
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 21.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 11.81 %
    Favored  : 82.42 %
  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: -1.96 (0.38), residues: 430
  helix: -3.93 (0.65), residues: 22
  sheet: -0.85 (0.43), residues: 132
  loop : -1.32 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 403 
 TYR   0.022   0.002   TYR A 369 
 PHE   0.017   0.003   PHE H  27 
 TRP   0.055   0.004   TRP L  37 
 HIS   0.004   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 3461)
  covalent geometry    : angle       0.81648 ( 4707)
  SS BOND              : bond        0.00749 (    6)
  SS BOND              : angle       1.37713 (   12)
  hydrogen bonds       : bond        0.04466 (  107)
  hydrogen bonds       : angle       7.69563 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8413 (tppt) cc_final: 0.7864 (tptt)
REVERT: A  365 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7765 (m-80)
REVERT: A  385 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9309 (t)
REVERT: A  398 ASP cc_start: 0.8436 (m-30) cc_final: 0.7859 (m-30)
REVERT: A  403 ARG cc_start: 0.7699 (ptt90) cc_final: 0.6784 (ptt90)
REVERT: A  406 GLU cc_start: 0.9071 (pm20) cc_final: 0.8345 (pm20)
REVERT: A  487 ASN cc_start: 0.6353 (t0) cc_final: 0.6054 (t0)
REVERT: A  493 GLN cc_start: 0.8091 (tp40) cc_final: 0.7841 (tp40)
REVERT: H   35 GLN cc_start: 0.8350 (mp10) cc_final: 0.7871 (mp10)
REVERT: H   59 TYR cc_start: 0.8305 (m-80) cc_final: 0.8020 (m-80)
REVERT: H  105 ASP cc_start: 0.8768 (t70) cc_final: 0.8342 (t70)
REVERT: H  111 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7805 (mp10)
REVERT: L   29 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8120 (tt)
REVERT: L   34 ASP cc_start: 0.7452 (p0) cc_final: 0.7246 (p0)
REVERT: L   38 TYR cc_start: 0.7415 (m-80) cc_final: 0.6957 (m-80)
REVERT: L   51 TYR cc_start: 0.8595 (p90) cc_final: 0.8222 (p90)
REVERT: L  101 VAL cc_start: 0.8738 (t) cc_final: 0.8535 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 135
  average time/residue: 0.0619
  time to fit residues: 10.0925
Evaluate side-chains
  120 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   74 SER
Chi-restraints excluded: chain L residue   80 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
L  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.120487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.103387 restraints weight = 9027.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.106853 restraints weight = 4845.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.109183 restraints weight = 3155.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.110666 restraints weight = 2286.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.111824 restraints weight = 1808.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3467  Z= 0.158
  Angle     :  0.738   9.489   4719  Z= 0.377
  Chirality :  0.048   0.145    495
  Planarity :  0.005   0.042    617
  Dihedral  :  5.545  26.230    487
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 17.58 %
    Favored  : 75.55 %
  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: -1.52 (0.39), residues: 430
  helix: -3.24 (0.80), residues: 22
  sheet: -0.49 (0.43), residues: 133
  loop : -1.09 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  98 
 TYR   0.024   0.002   TYR A 365 
 PHE   0.020   0.002   PHE A 392 
 TRP   0.047   0.003   TRP L  37 
 HIS   0.006   0.003   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3461)
  covalent geometry    : angle       0.73535 ( 4707)
  SS BOND              : bond        0.00587 (    6)
  SS BOND              : angle       1.33753 (   12)
  hydrogen bonds       : bond        0.04046 (  107)
  hydrogen bonds       : angle       7.08368 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8483 (tppt) cc_final: 0.7970 (tptt)
REVERT: A  378 LYS cc_start: 0.7575 (mmmt) cc_final: 0.7275 (mmtt)
REVERT: A  389 ASP cc_start: 0.8970 (t0) cc_final: 0.8761 (t0)
REVERT: A  398 ASP cc_start: 0.8214 (m-30) cc_final: 0.7895 (m-30)
REVERT: A  406 GLU cc_start: 0.9007 (pm20) cc_final: 0.8414 (pm20)
REVERT: A  493 GLN cc_start: 0.7957 (tp40) cc_final: 0.7736 (tp40)
REVERT: H    2 VAL cc_start: 0.8058 (m) cc_final: 0.7613 (p)
REVERT: H   34 MET cc_start: 0.7972 (mmm) cc_final: 0.7682 (mmt)
REVERT: H   35 GLN cc_start: 0.8155 (mp10) cc_final: 0.7891 (mp10)
REVERT: H  105 ASP cc_start: 0.8841 (t70) cc_final: 0.8570 (t70)
REVERT: L   20 ILE cc_start: 0.8834 (mp) cc_final: 0.8620 (mt)
REVERT: L   87 ASP cc_start: 0.7663 (p0) cc_final: 0.7377 (p0)
REVERT: L  101 VAL cc_start: 0.8781 (t) cc_final: 0.8467 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0586
  time to fit residues: 9.5950
Evaluate side-chains
  123 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue  117 GLN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.0870
   chunk 25 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.0162

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.122387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.105479 restraints weight = 8868.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.109004 restraints weight = 4790.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.111298 restraints weight = 3075.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.112907 restraints weight = 2212.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.114011 restraints weight = 1718.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.5446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3467  Z= 0.133
  Angle     :  0.728   9.900   4719  Z= 0.371
  Chirality :  0.047   0.172    495
  Planarity :  0.005   0.041    617
  Dihedral  :  5.201  23.638    487
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 20.88 %
    Favored  : 73.08 %
  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 (0.40), residues: 430
  helix: -3.10 (0.82), residues: 22
  sheet: -0.31 (0.43), residues: 142
  loop : -0.91 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 466 
 TYR   0.020   0.002   TYR A 365 
 PHE   0.020   0.002   PHE A 338 
 TRP   0.048   0.003   TRP L  37 
 HIS   0.007   0.003   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3461)
  covalent geometry    : angle       0.72504 ( 4707)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.54769 (   12)
  hydrogen bonds       : bond        0.03779 (  107)
  hydrogen bonds       : angle       6.78264 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8545 (tppt) cc_final: 0.8066 (tptt)
REVERT: A  389 ASP cc_start: 0.8933 (t0) cc_final: 0.8658 (t0)
REVERT: A  398 ASP cc_start: 0.8189 (m-30) cc_final: 0.7718 (m-30)
REVERT: A  406 GLU cc_start: 0.9013 (pm20) cc_final: 0.8414 (pm20)
REVERT: A  515 PHE cc_start: 0.8127 (m-80) cc_final: 0.7705 (m-10)
REVERT: H    2 VAL cc_start: 0.7762 (m) cc_final: 0.7474 (p)
REVERT: H  117 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7587 (mt0)
REVERT: L   87 ASP cc_start: 0.7719 (p0) cc_final: 0.7388 (p0)
REVERT: L  101 VAL cc_start: 0.8728 (t) cc_final: 0.8446 (p)
REVERT: L  107 LYS cc_start: 0.8713 (tppp) cc_final: 0.8059 (tmtt)
  outliers start: 22
  outliers final: 19
  residues processed: 125
  average time/residue: 0.0474
  time to fit residues: 7.4676
Evaluate side-chains
  117 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  117 GLN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   74 SER
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 12 optimal weight:    9.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
H  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.120694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.103775 restraints weight = 9035.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.107148 restraints weight = 4954.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.109421 restraints weight = 3237.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.110957 restraints weight = 2351.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.111997 restraints weight = 1846.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.5861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3467  Z= 0.150
  Angle     :  0.729  10.731   4719  Z= 0.369
  Chirality :  0.047   0.160    495
  Planarity :  0.005   0.070    617
  Dihedral  :  5.092  22.001    487
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 22.25 %
    Favored  : 70.05 %
  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: -1.15 (0.40), residues: 430
  helix: -2.84 (0.84), residues: 22
  sheet: -0.26 (0.43), residues: 142
  loop : -0.84 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 408 
 TYR   0.020   0.002   TYR A 369 
 PHE   0.016   0.002   PHE L 102 
 TRP   0.034   0.002   TRP L  37 
 HIS   0.005   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3461)
  covalent geometry    : angle       0.72655 ( 4707)
  SS BOND              : bond        0.00702 (    6)
  SS BOND              : angle       1.28900 (   12)
  hydrogen bonds       : bond        0.03767 (  107)
  hydrogen bonds       : angle       6.60091 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8547 (tppt) cc_final: 0.8053 (tptt)
REVERT: A  389 ASP cc_start: 0.9020 (t0) cc_final: 0.8711 (t0)
REVERT: A  398 ASP cc_start: 0.8263 (m-30) cc_final: 0.7822 (m-30)
REVERT: A  414 GLN cc_start: 0.8453 (mp-120) cc_final: 0.8060 (mp10)
REVERT: A  493 GLN cc_start: 0.8032 (tp40) cc_final: 0.7606 (tp40)
REVERT: H    2 VAL cc_start: 0.7728 (m) cc_final: 0.7436 (p)
REVERT: H    3 GLN cc_start: 0.7408 (pm20) cc_final: 0.7116 (pm20)
REVERT: H   47 TRP cc_start: 0.8027 (t60) cc_final: 0.7444 (t60)
REVERT: H  117 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7502 (mt0)
REVERT: L   34 ASP cc_start: 0.6551 (p0) cc_final: 0.6284 (p0)
REVERT: L   36 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8170 (m-70)
REVERT: L   51 TYR cc_start: 0.8185 (p90) cc_final: 0.7863 (p90)
REVERT: L   81 GLN cc_start: 0.7893 (tm-30) cc_final: 0.6661 (tt0)
REVERT: L  101 VAL cc_start: 0.8737 (t) cc_final: 0.8405 (p)
  outliers start: 28
  outliers final: 24
  residues processed: 124
  average time/residue: 0.0528
  time to fit residues: 8.2160
Evaluate side-chains
  125 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain H residue  117 GLN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   36 HIS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   74 SER
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.114196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.096305 restraints weight = 9261.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.100717 restraints weight = 6224.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.103966 restraints weight = 3407.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.104729 restraints weight = 2229.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.105174 restraints weight = 1853.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.6444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   3467  Z= 0.331
  Angle     :  0.870  12.729   4719  Z= 0.452
  Chirality :  0.050   0.174    495
  Planarity :  0.007   0.079    617
  Dihedral  :  6.012  21.331    487
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 23.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers : 10.16 %
    Allowed  : 21.70 %
    Favored  : 68.13 %
  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: -1.31 (0.41), residues: 430
  helix: -2.40 (0.88), residues: 28
  sheet: -0.09 (0.47), residues: 129
  loop : -1.10 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  19 
 TYR   0.026   0.003   TYR A 369 
 PHE   0.024   0.003   PHE A 392 
 TRP   0.039   0.003   TRP L  37 
 HIS   0.004   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00744 ( 3461)
  covalent geometry    : angle       0.86929 ( 4707)
  SS BOND              : bond        0.00776 (    6)
  SS BOND              : angle       1.17352 (   12)
  hydrogen bonds       : bond        0.04696 (  107)
  hydrogen bonds       : angle       7.05222 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 ASP cc_start: 0.8506 (m-30) cc_final: 0.7977 (m-30)
REVERT: A  403 ARG cc_start: 0.7646 (ptt90) cc_final: 0.7311 (ptt90)
REVERT: A  406 GLU cc_start: 0.9264 (pm20) cc_final: 0.8640 (pm20)
REVERT: A  461 LEU cc_start: 0.8772 (tp) cc_final: 0.8502 (tp)
REVERT: H    2 VAL cc_start: 0.8186 (m) cc_final: 0.7951 (p)
REVERT: H    3 GLN cc_start: 0.7420 (pm20) cc_final: 0.7117 (pm20)
REVERT: H   47 TRP cc_start: 0.8199 (OUTLIER) cc_final: 0.7723 (t60)
REVERT: L   34 ASP cc_start: 0.6808 (p0) cc_final: 0.6562 (p0)
REVERT: L   36 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8449 (m-70)
REVERT: L   51 TYR cc_start: 0.8449 (p90) cc_final: 0.8164 (p90)
REVERT: L   81 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7409 (tt0)
REVERT: L  101 VAL cc_start: 0.8779 (t) cc_final: 0.8523 (p)
  outliers start: 37
  outliers final: 29
  residues processed: 121
  average time/residue: 0.0509
  time to fit residues: 7.8274
Evaluate side-chains
  134 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   36 HIS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   74 SER
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  100 VAL
Chi-restraints excluded: chain L residue  109 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 36 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 117 GLN ** 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 = 0.3816 r_free = 0.3816 target = 0.118517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.100602 restraints weight = 9148.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.105074 restraints weight = 6000.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.108374 restraints weight = 3267.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.109285 restraints weight = 2089.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.110202 restraints weight = 1723.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.6686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3467  Z= 0.149
  Angle     :  0.768  14.230   4719  Z= 0.384
  Chirality :  0.047   0.173    495
  Planarity :  0.005   0.061    617
  Dihedral  :  5.323  21.342    487
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  7.97 %
    Allowed  : 24.73 %
    Favored  : 67.31 %
  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: -1.28 (0.40), residues: 430
  helix: -2.52 (0.80), residues: 28
  sheet: -0.42 (0.45), residues: 133
  loop : -0.86 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  31 
 TYR   0.029   0.002   TYR A 365 
 PHE   0.020   0.002   PHE A 392 
 TRP   0.019   0.002   TRP L  37 
 HIS   0.004   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3461)
  covalent geometry    : angle       0.76705 ( 4707)
  SS BOND              : bond        0.00452 (    6)
  SS BOND              : angle       0.99186 (   12)
  hydrogen bonds       : bond        0.03917 (  107)
  hydrogen bonds       : angle       6.61532 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8743 (tppp) cc_final: 0.8084 (tptt)
REVERT: A  398 ASP cc_start: 0.8283 (m-30) cc_final: 0.7870 (m-30)
REVERT: H    3 GLN cc_start: 0.7304 (pm20) cc_final: 0.6982 (pm20)
REVERT: H   47 TRP cc_start: 0.8027 (t60) cc_final: 0.7778 (t60)
REVERT: H   95 TYR cc_start: 0.7358 (m-80) cc_final: 0.7096 (m-80)
REVERT: H  117 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7794 (mt0)
REVERT: L   36 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8099 (m-70)
REVERT: L   81 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7375 (tt0)
REVERT: L  101 VAL cc_start: 0.8682 (t) cc_final: 0.8286 (p)
  outliers start: 29
  outliers final: 26
  residues processed: 124
  average time/residue: 0.0465
  time to fit residues: 7.4044
Evaluate side-chains
  131 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  484 GLU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain H residue  117 GLN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   36 HIS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0670
   chunk 15 optimal weight:    9.9990
   overall best weight:    3.6126

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.114968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.097350 restraints weight = 9361.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.100615 restraints weight = 5131.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.102840 restraints weight = 3396.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.104312 restraints weight = 2509.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.105378 restraints weight = 2016.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.6999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3467  Z= 0.235
  Angle     :  0.848  17.278   4719  Z= 0.422
  Chirality :  0.048   0.163    495
  Planarity :  0.006   0.066    617
  Dihedral  :  5.616  25.264    487
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 21.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  9.34 %
    Allowed  : 26.37 %
    Favored  : 64.29 %
  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 (0.40), residues: 430
  helix: -2.51 (0.85), residues: 27
  sheet: -0.37 (0.46), residues: 132
  loop : -1.01 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 355 
 TYR   0.029   0.002   TYR A 365 
 PHE   0.022   0.002   PHE A 392 
 TRP   0.016   0.002   TRP L  37 
 HIS   0.007   0.003   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 3461)
  covalent geometry    : angle       0.84743 ( 4707)
  SS BOND              : bond        0.00560 (    6)
  SS BOND              : angle       1.05554 (   12)
  hydrogen bonds       : bond        0.04288 (  107)
  hydrogen bonds       : angle       6.66599 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8794 (tppp) cc_final: 0.8106 (tptt)
REVERT: A  398 ASP cc_start: 0.8355 (m-30) cc_final: 0.7791 (m-30)
REVERT: A  406 GLU cc_start: 0.9181 (pm20) cc_final: 0.8731 (pm20)
REVERT: A  465 GLU cc_start: 0.8018 (pm20) cc_final: 0.7715 (pm20)
REVERT: H   28 THR cc_start: 0.8874 (m) cc_final: 0.8578 (p)
REVERT: H   47 TRP cc_start: 0.8118 (t60) cc_final: 0.7818 (t60)
REVERT: H   95 TYR cc_start: 0.7422 (m-80) cc_final: 0.7145 (m-80)
REVERT: H  117 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7994 (mt0)
REVERT: L   34 ASP cc_start: 0.6746 (p0) cc_final: 0.6533 (p0)
REVERT: L   36 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8136 (m-70)
REVERT: L   51 TYR cc_start: 0.8344 (p90) cc_final: 0.7984 (p90)
REVERT: L   81 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7428 (tt0)
REVERT: L   91 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8088 (pt0)
REVERT: L  101 VAL cc_start: 0.8712 (t) cc_final: 0.8374 (p)
  outliers start: 34
  outliers final: 29
  residues processed: 125
  average time/residue: 0.0454
  time to fit residues: 7.2414
Evaluate side-chains
  133 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  484 GLU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain H residue  117 GLN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   36 HIS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   74 SER
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  108 LEU
Chi-restraints excluded: chain L residue  109 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 37 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.118945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.101097 restraints weight = 9210.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.105748 restraints weight = 5939.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.107545 restraints weight = 3286.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108268 restraints weight = 2756.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.109638 restraints weight = 2157.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.7209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3467  Z= 0.149
  Angle     :  0.846  17.965   4719  Z= 0.407
  Chirality :  0.049   0.206    495
  Planarity :  0.005   0.053    617
  Dihedral  :  5.228  23.602    487
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 27.75 %
    Favored  : 64.84 %
  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: -1.19 (0.40), residues: 430
  helix: -2.55 (0.86), residues: 27
  sheet: -0.14 (0.47), residues: 127
  loop : -0.93 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  72 
 TYR   0.026   0.002   TYR A 365 
 PHE   0.020   0.002   PHE A 392 
 TRP   0.015   0.002   TRP L  37 
 HIS   0.006   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3461)
  covalent geometry    : angle       0.84561 ( 4707)
  SS BOND              : bond        0.00400 (    6)
  SS BOND              : angle       0.95828 (   12)
  hydrogen bonds       : bond        0.03809 (  107)
  hydrogen bonds       : angle       6.48111 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8276 (m-40) cc_final: 0.7711 (m-40)
REVERT: A  356 LYS cc_start: 0.8761 (tppp) cc_final: 0.8101 (tptt)
REVERT: A  398 ASP cc_start: 0.8340 (m-30) cc_final: 0.7873 (m-30)
REVERT: A  508 TYR cc_start: 0.8925 (m-80) cc_final: 0.8643 (m-80)
REVERT: H   47 TRP cc_start: 0.8110 (t60) cc_final: 0.7784 (t60)
REVERT: H   95 TYR cc_start: 0.7395 (m-80) cc_final: 0.7085 (m-80)
REVERT: H  117 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7942 (mt0)
REVERT: L   85 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6838 (mm-30)
REVERT: L   91 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8024 (pt0)
REVERT: L  101 VAL cc_start: 0.8619 (t) cc_final: 0.8301 (p)
  outliers start: 27
  outliers final: 24
  residues processed: 127
  average time/residue: 0.0544
  time to fit residues: 8.6252
Evaluate side-chains
  132 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  484 GLU
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain H residue  117 GLN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   74 SER
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 28 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0770
   chunk 29 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    3.3344

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

Flipped N/Q/H residues before XYZ refinement:
** H 117 GLN ** 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 = 0.3774 r_free = 0.3774 target = 0.115816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.097649 restraints weight = 9278.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.102460 restraints weight = 6075.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.105762 restraints weight = 3240.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.106632 restraints weight = 2088.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.107276 restraints weight = 1699.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.7437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3467  Z= 0.227
  Angle     :  0.879  18.337   4719  Z= 0.433
  Chirality :  0.050   0.198    495
  Planarity :  0.006   0.063    617
  Dihedral  :  5.425  22.186    487
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 22.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  7.97 %
    Allowed  : 27.75 %
    Favored  : 64.29 %
  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: -1.46 (0.39), residues: 430
  helix: -2.62 (0.76), residues: 33
  sheet: -0.51 (0.45), residues: 137
  loop : -0.97 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 403 
 TYR   0.026   0.002   TYR A 365 
 PHE   0.022   0.002   PHE A 392 
 TRP   0.016   0.002   TRP L  37 
 HIS   0.007   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 3461)
  covalent geometry    : angle       0.87844 ( 4707)
  SS BOND              : bond        0.00552 (    6)
  SS BOND              : angle       1.02092 (   12)
  hydrogen bonds       : bond        0.04188 (  107)
  hydrogen bonds       : angle       6.85098 (  273)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8779 (tppp) cc_final: 0.8103 (tptt)
REVERT: A  398 ASP cc_start: 0.8322 (m-30) cc_final: 0.7775 (m-30)
REVERT: A  465 GLU cc_start: 0.8164 (pm20) cc_final: 0.7907 (pm20)
REVERT: H   47 TRP cc_start: 0.8142 (t60) cc_final: 0.7883 (t60)
REVERT: H  117 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7823 (mt0)
REVERT: L   85 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6872 (mm-30)
REVERT: L   91 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7994 (pt0)
REVERT: L  101 VAL cc_start: 0.8725 (t) cc_final: 0.8398 (p)
  outliers start: 29
  outliers final: 27
  residues processed: 121
  average time/residue: 0.0518
  time to fit residues: 7.9730
Evaluate side-chains
  132 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  484 GLU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain H residue  117 GLN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   74 SER
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  108 LEU
Chi-restraints excluded: chain L residue  109 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
H 117 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.120401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.102449 restraints weight = 9296.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.107387 restraints weight = 6047.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.110360 restraints weight = 3146.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.111253 restraints weight = 2104.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.112310 restraints weight = 1730.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.7581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3467  Z= 0.143
  Angle     :  0.854  17.309   4719  Z= 0.411
  Chirality :  0.047   0.175    495
  Planarity :  0.006   0.047    617
  Dihedral  :  5.022  21.979    487
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 28.30 %
    Favored  : 64.84 %
  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: -1.33 (0.40), residues: 430
  helix: -2.76 (0.74), residues: 33
  sheet: -0.39 (0.46), residues: 134
  loop : -0.86 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 403 
 TYR   0.026   0.001   TYR A 365 
 PHE   0.021   0.002   PHE A 392 
 TRP   0.012   0.002   TRP L  37 
 HIS   0.005   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3461)
  covalent geometry    : angle       0.85355 ( 4707)
  SS BOND              : bond        0.00332 (    6)
  SS BOND              : angle       0.93298 (   12)
  hydrogen bonds       : bond        0.03654 (  107)
  hydrogen bonds       : angle       6.66492 (  273)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 726.02 seconds
wall clock time: 13 minutes 15.23 seconds (795.23 seconds total)