Starting phenix.real_space_refine
on Wed Jun  4 15:24:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swp_25478/06_2025/7swp_25478_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swp_25478/06_2025/7swp_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swp_25478/06_2025/7swp_25478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swp_25478/06_2025/7swp_25478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swp_25478/06_2025/7swp_25478_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swp_25478/06_2025/7swp_25478_neut.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 2.80, per 1000 atoms: 0.83
  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: 0.88
  Conformation dependent library (CDL) restraints added in 419.7 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: 0.50
  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: 1.12

  Time building geometry restraints manager: 1.04 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:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.770
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.050
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.109   0.006   TRP L  37 
 HIS   0.007   0.003   HIS L  36 
 PHE   0.023   0.002   PHE A 490 
 TYR   0.021   0.003   TYR L  51 
 ARG   0.011   0.001   ARG A 408 

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

*********************** 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  : 0.363 
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: 0.6642 (ptt90)
REVERT: A  501 ASN cc_start: 0.7847 (t0) cc_final: 0.7428 (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: 0.5405 (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: 0.7352 (m-80)
REVERT: H  105 ASP cc_start: 0.8435 (t70) cc_final: 0.7971 (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: 0.8147 (m)
REVERT: L   34 ASP cc_start: 0.7296 (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: 0.8380 (t) cc_final: 0.8081 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1931
  time to fit residues: 35.9646
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  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.122735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.105997 restraints weight = 9013.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.109543 restraints weight = 4793.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.111958 restraints weight = 3087.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3467  Z= 0.161
  Angle     :  0.780   8.530   4719  Z= 0.401
  Chirality :  0.049   0.143    495
  Planarity :  0.005   0.040    617
  Dihedral  :  5.701  24.667    487
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 13.46 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.38), residues: 430
  helix: -3.48 (0.68), residues: 22
  sheet: -0.70 (0.44), residues: 132
  loop : -1.20 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP L  37 
 HIS   0.006   0.003   HIS A 519 
 PHE   0.017   0.002   PHE H  27 
 TYR   0.019   0.002   TYR A 369 
 ARG   0.007   0.001   ARG L  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04256 (  107)
  hydrogen bonds       : angle       7.63188 (  273)
  SS BOND              : bond        0.00557 (    6)
  SS BOND              : angle       1.41241 (   12)
  covalent geometry    : bond        0.00354 ( 3461)
  covalent geometry    : angle       0.77760 ( 4707)

*********************** 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
  151 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8457 (tppt) cc_final: 0.7862 (tptt)
REVERT: A  398 ASP cc_start: 0.8150 (m-30) cc_final: 0.7808 (m-30)
REVERT: A  403 ARG cc_start: 0.7441 (ptt90) cc_final: 0.6505 (ptt90)
REVERT: A  406 GLU cc_start: 0.8596 (pm20) cc_final: 0.8136 (pm20)
REVERT: A  465 GLU cc_start: 0.7973 (pm20) cc_final: 0.7765 (pm20)
REVERT: A  467 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.6783 (p0)
REVERT: A  493 GLN cc_start: 0.8008 (tp40) cc_final: 0.7780 (tp40)
REVERT: H   35 GLN cc_start: 0.8130 (mp10) cc_final: 0.7748 (mp10)
REVERT: H   95 TYR cc_start: 0.7154 (m-80) cc_final: 0.6940 (m-80)
REVERT: H  105 ASP cc_start: 0.8383 (t70) cc_final: 0.8106 (t70)
REVERT: L   38 TYR cc_start: 0.7450 (m-80) cc_final: 0.7056 (m-80)
REVERT: L   89 TYR cc_start: 0.7746 (m-80) cc_final: 0.7383 (m-10)
REVERT: L  101 VAL cc_start: 0.8711 (t) cc_final: 0.8491 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 142
  average time/residue: 0.1668
  time to fit residues: 28.4403
Evaluate side-chains
  118 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  467 ASP
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   45 VAL
Chi-restraints excluded: chain L residue   65 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 23 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 33 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.121435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.104726 restraints weight = 8951.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.108115 restraints weight = 4854.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.110426 restraints weight = 3160.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3467  Z= 0.156
  Angle     :  0.754   9.491   4719  Z= 0.381
  Chirality :  0.048   0.163    495
  Planarity :  0.005   0.042    617
  Dihedral  :  5.412  25.634    487
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 17.03 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.38), residues: 430
  helix: -3.14 (0.86), residues: 22
  sheet: -0.58 (0.44), residues: 123
  loop : -1.13 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP L  37 
 HIS   0.006   0.003   HIS A 519 
 PHE   0.019   0.002   PHE A 400 
 TYR   0.029   0.002   TYR A 351 
 ARG   0.007   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  107)
  hydrogen bonds       : angle       7.17924 (  273)
  SS BOND              : bond        0.00490 (    6)
  SS BOND              : angle       1.07863 (   12)
  covalent geometry    : bond        0.00353 ( 3461)
  covalent geometry    : angle       0.75304 ( 4707)

*********************** 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
  136 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8493 (tppt) cc_final: 0.7935 (tptt)
REVERT: A  389 ASP cc_start: 0.8872 (t0) cc_final: 0.8491 (t0)
REVERT: A  398 ASP cc_start: 0.8289 (m-30) cc_final: 0.7656 (m-30)
REVERT: A  401 VAL cc_start: 0.8907 (t) cc_final: 0.8684 (t)
REVERT: A  406 GLU cc_start: 0.8816 (pm20) cc_final: 0.8258 (pm20)
REVERT: A  493 GLN cc_start: 0.8001 (tp40) cc_final: 0.7767 (tp40)
REVERT: H    2 VAL cc_start: 0.7963 (m) cc_final: 0.7651 (p)
REVERT: H   34 MET cc_start: 0.8004 (mmm) cc_final: 0.7750 (mmt)
REVERT: H   35 GLN cc_start: 0.8176 (mp10) cc_final: 0.7922 (mp10)
REVERT: H  111 GLN cc_start: 0.8056 (mp10) cc_final: 0.7793 (mp10)
REVERT: H  112 THR cc_start: 0.9112 (p) cc_final: 0.8446 (t)
REVERT: H  114 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8422 (mp0)
REVERT: L   51 TYR cc_start: 0.8129 (p90) cc_final: 0.7888 (p90)
REVERT: L  101 VAL cc_start: 0.8802 (t) cc_final: 0.8568 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 127
  average time/residue: 0.1298
  time to fit residues: 20.5315
Evaluate side-chains
  119 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  494 SER
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   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   91 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  91 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 = 0.3860 r_free = 0.3860 target = 0.119941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.103359 restraints weight = 9252.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.106636 restraints weight = 5149.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.108903 restraints weight = 3380.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.5143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3467  Z= 0.168
  Angle     :  0.737   9.941   4719  Z= 0.379
  Chirality :  0.047   0.158    495
  Planarity :  0.005   0.044    617
  Dihedral  :  5.229  23.778    487
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 18.68 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.39), residues: 430
  helix: -3.08 (0.76), residues: 22
  sheet: -0.30 (0.42), residues: 141
  loop : -1.04 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP L  37 
 HIS   0.006   0.003   HIS L  36 
 PHE   0.019   0.002   PHE A 392 
 TYR   0.030   0.002   TYR A 351 
 ARG   0.005   0.001   ARG A 408 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  107)
  hydrogen bonds       : angle       6.79637 (  273)
  SS BOND              : bond        0.00492 (    6)
  SS BOND              : angle       0.87504 (   12)
  covalent geometry    : bond        0.00384 ( 3461)
  covalent geometry    : angle       0.73661 ( 4707)

*********************** 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
  140 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8512 (tppt) cc_final: 0.7970 (tptt)
REVERT: A  385 THR cc_start: 0.9518 (t) cc_final: 0.9317 (t)
REVERT: A  389 ASP cc_start: 0.9061 (t0) cc_final: 0.8653 (t0)
REVERT: A  398 ASP cc_start: 0.8183 (m-30) cc_final: 0.7834 (m-30)
REVERT: A  401 VAL cc_start: 0.8960 (t) cc_final: 0.8727 (t)
REVERT: A  487 ASN cc_start: 0.6980 (t0) cc_final: 0.6709 (t0)
REVERT: H    2 VAL cc_start: 0.7960 (m) cc_final: 0.7640 (p)
REVERT: H   35 GLN cc_start: 0.8204 (mp10) cc_final: 0.7930 (mp10)
REVERT: H  112 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8877 (t)
REVERT: L   36 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8131 (m-70)
REVERT: L   38 TYR cc_start: 0.7861 (m-80) cc_final: 0.7485 (m-80)
REVERT: L   51 TYR cc_start: 0.8249 (p90) cc_final: 0.7991 (p90)
REVERT: L   81 GLN cc_start: 0.7661 (tm-30) cc_final: 0.6352 (tt0)
REVERT: L   87 ASP cc_start: 0.8060 (p0) cc_final: 0.7656 (p0)
REVERT: L   89 TYR cc_start: 0.8158 (m-80) cc_final: 0.7613 (m-80)
REVERT: L  101 VAL cc_start: 0.8760 (t) cc_final: 0.8449 (p)
REVERT: L  107 LYS cc_start: 0.8671 (tppp) cc_final: 0.8010 (tmtt)
  outliers start: 20
  outliers final: 15
  residues processed: 132
  average time/residue: 0.1434
  time to fit residues: 23.2063
Evaluate side-chains
  127 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 H residue   74 ASN
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   23 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
L   6 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.118397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.102005 restraints weight = 9196.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.105260 restraints weight = 5016.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.107368 restraints weight = 3272.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.5746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3467  Z= 0.189
  Angle     :  0.758  11.790   4719  Z= 0.384
  Chirality :  0.048   0.161    495
  Planarity :  0.005   0.045    617
  Dihedral  :  5.257  22.284    487
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 18.41 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.39), residues: 430
  helix: -2.87 (0.82), residues: 22
  sheet: -0.31 (0.42), residues: 143
  loop : -1.07 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP L  37 
 HIS   0.006   0.003   HIS L  36 
 PHE   0.019   0.002   PHE A 392 
 TYR   0.027   0.002   TYR A 351 
 ARG   0.004   0.001   ARG A 408 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  107)
  hydrogen bonds       : angle       6.74967 (  273)
  SS BOND              : bond        0.00533 (    6)
  SS BOND              : angle       0.88635 (   12)
  covalent geometry    : bond        0.00432 ( 3461)
  covalent geometry    : angle       0.75738 ( 4707)

*********************** 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
  140 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.8576 (tppt) cc_final: 0.8053 (tptt)
REVERT: A  389 ASP cc_start: 0.9204 (t0) cc_final: 0.8793 (t0)
REVERT: A  398 ASP cc_start: 0.8222 (m-30) cc_final: 0.7735 (m-30)
REVERT: A  401 VAL cc_start: 0.8987 (t) cc_final: 0.8758 (t)
REVERT: A  414 GLN cc_start: 0.8527 (mp-120) cc_final: 0.8110 (mp10)
REVERT: A  487 ASN cc_start: 0.7093 (t0) cc_final: 0.6685 (t0)
REVERT: A  493 GLN cc_start: 0.8045 (tp40) cc_final: 0.7591 (tp40)
REVERT: H    2 VAL cc_start: 0.8065 (m) cc_final: 0.7790 (p)
REVERT: L   36 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8308 (m-70)
REVERT: L   51 TYR cc_start: 0.8336 (p90) cc_final: 0.8004 (p90)
REVERT: L   81 GLN cc_start: 0.7854 (tm-30) cc_final: 0.6877 (tt0)
REVERT: L   87 ASP cc_start: 0.8051 (p0) cc_final: 0.7673 (p0)
REVERT: L   89 TYR cc_start: 0.8207 (m-80) cc_final: 0.7560 (m-80)
REVERT: L  101 VAL cc_start: 0.8741 (t) cc_final: 0.8513 (p)
  outliers start: 26
  outliers final: 16
  residues processed: 130
  average time/residue: 0.1291
  time to fit residues: 21.0829
Evaluate side-chains
  128 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  494 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain L residue    3 VAL
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 17 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0000
   chunk 27 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.6584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.123022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.105148 restraints weight = 9147.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.108589 restraints weight = 5075.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.110878 restraints weight = 3363.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.6128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3467  Z= 0.128
  Angle     :  0.754  12.226   4719  Z= 0.370
  Chirality :  0.047   0.172    495
  Planarity :  0.005   0.040    617
  Dihedral  :  4.952  23.813    487
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 20.88 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.39), residues: 430
  helix: -3.12 (0.76), residues: 22
  sheet:  0.17 (0.46), residues: 125
  loop : -1.05 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP L  37 
 HIS   0.004   0.002   HIS L  36 
 PHE   0.018   0.002   PHE A 392 
 TYR   0.028   0.002   TYR A 351 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (  107)
  hydrogen bonds       : angle       6.51220 (  273)
  SS BOND              : bond        0.00421 (    6)
  SS BOND              : angle       1.11670 (   12)
  covalent geometry    : bond        0.00286 ( 3461)
  covalent geometry    : angle       0.75288 ( 4707)

*********************** 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
  148 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8165 (m-40) cc_final: 0.7604 (m-40)
REVERT: A  356 LYS cc_start: 0.8532 (tppt) cc_final: 0.8060 (tptt)
REVERT: A  389 ASP cc_start: 0.9183 (t0) cc_final: 0.8890 (t0)
REVERT: A  398 ASP cc_start: 0.8095 (m-30) cc_final: 0.7769 (m-30)
REVERT: A  401 VAL cc_start: 0.8872 (t) cc_final: 0.8636 (t)
REVERT: A  414 GLN cc_start: 0.8436 (mp-120) cc_final: 0.7980 (mp10)
REVERT: A  472 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5271 (mt)
REVERT: A  484 GLU cc_start: 0.5550 (OUTLIER) cc_final: 0.3416 (pm20)
REVERT: A  493 GLN cc_start: 0.7983 (tp40) cc_final: 0.7510 (tp40)
REVERT: H    2 VAL cc_start: 0.8090 (m) cc_final: 0.7754 (p)
REVERT: H    5 VAL cc_start: 0.7751 (t) cc_final: 0.7234 (m)
REVERT: H  117 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7741 (mt0)
REVERT: L   81 GLN cc_start: 0.7793 (tm-30) cc_final: 0.6992 (tt0)
REVERT: L   87 ASP cc_start: 0.8059 (p0) cc_final: 0.7757 (p0)
REVERT: L   89 TYR cc_start: 0.8178 (m-80) cc_final: 0.7876 (m-80)
REVERT: L  100 VAL cc_start: 0.8085 (p) cc_final: 0.7732 (p)
REVERT: L  101 VAL cc_start: 0.8592 (t) cc_final: 0.8268 (p)
  outliers start: 23
  outliers final: 19
  residues processed: 139
  average time/residue: 0.1233
  time to fit residues: 21.4393
Evaluate side-chains
  134 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  449 TYR
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  472 ILE
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   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    2.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.118223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100367 restraints weight = 9292.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.104836 restraints weight = 6185.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.106710 restraints weight = 3468.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.6580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3467  Z= 0.184
  Angle     :  0.789  13.968   4719  Z= 0.391
  Chirality :  0.048   0.171    495
  Planarity :  0.006   0.078    617
  Dihedral  :  5.105  21.866    487
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 20.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  7.97 %
    Allowed  : 22.80 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.40), residues: 430
  helix: -3.00 (0.79), residues: 28
  sheet:  0.23 (0.46), residues: 131
  loop : -1.01 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H  47 
 HIS   0.005   0.002   HIS L  36 
 PHE   0.023   0.002   PHE L 102 
 TYR   0.023   0.002   TYR L  93 
 ARG   0.004   0.001   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03954 (  107)
  hydrogen bonds       : angle       6.58347 (  273)
  SS BOND              : bond        0.00558 (    6)
  SS BOND              : angle       0.82887 (   12)
  covalent geometry    : bond        0.00422 ( 3461)
  covalent geometry    : angle       0.78885 ( 4707)

*********************** 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
  141 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8200 (m-40) cc_final: 0.7595 (m-40)
REVERT: A  356 LYS cc_start: 0.8583 (tppt) cc_final: 0.8064 (tptt)
REVERT: A  389 ASP cc_start: 0.9260 (t0) cc_final: 0.8976 (t0)
REVERT: A  398 ASP cc_start: 0.8375 (m-30) cc_final: 0.7858 (m-30)
REVERT: A  401 VAL cc_start: 0.8973 (t) cc_final: 0.8743 (t)
REVERT: A  465 GLU cc_start: 0.8066 (pm20) cc_final: 0.7628 (pm20)
REVERT: A  493 GLN cc_start: 0.8019 (tp40) cc_final: 0.7770 (tp40)
REVERT: H    2 VAL cc_start: 0.8255 (m) cc_final: 0.7890 (p)
REVERT: H    3 GLN cc_start: 0.7493 (pm20) cc_final: 0.7102 (pm20)
REVERT: H   47 TRP cc_start: 0.8042 (t60) cc_final: 0.7821 (t60)
REVERT: H  114 GLU cc_start: 0.8792 (mp0) cc_final: 0.8538 (mp0)
REVERT: H  117 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8062 (mt0)
REVERT: L   36 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.7968 (m-70)
REVERT: L   51 TYR cc_start: 0.8126 (p90) cc_final: 0.7818 (p90)
REVERT: L   81 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7499 (tt0)
REVERT: L   87 ASP cc_start: 0.8096 (p0) cc_final: 0.7806 (p0)
REVERT: L   89 TYR cc_start: 0.8038 (m-80) cc_final: 0.7726 (m-80)
REVERT: L  101 VAL cc_start: 0.8566 (t) cc_final: 0.8305 (p)
  outliers start: 29
  outliers final: 25
  residues processed: 132
  average time/residue: 0.1319
  time to fit residues: 21.7885
Evaluate side-chains
  132 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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   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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    0.2980
   chunk 20 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.121419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.103945 restraints weight = 9167.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.107293 restraints weight = 5058.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.109537 restraints weight = 3329.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.6794

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= 0.132
  Angle     :  0.772  13.993   4719  Z= 0.376
  Chirality :  0.047   0.170    495
  Planarity :  0.005   0.058    617
  Dihedral  :  4.856  21.050    487
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  8.24 %
    Allowed  : 22.53 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.40), residues: 430
  helix: -3.21 (0.76), residues: 28
  sheet:  0.08 (0.45), residues: 138
  loop : -0.90 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  37 
 HIS   0.004   0.002   HIS L  36 
 PHE   0.023   0.002   PHE A 392 
 TYR   0.024   0.002   TYR A 351 
 ARG   0.004   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  107)
  hydrogen bonds       : angle       6.52063 (  273)
  SS BOND              : bond        0.00379 (    6)
  SS BOND              : angle       0.86381 (   12)
  covalent geometry    : bond        0.00301 ( 3461)
  covalent geometry    : angle       0.77171 ( 4707)

*********************** 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
  141 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8136 (m-40) cc_final: 0.7570 (m-40)
REVERT: A  356 LYS cc_start: 0.8576 (tppt) cc_final: 0.8104 (tptt)
REVERT: A  389 ASP cc_start: 0.9173 (t0) cc_final: 0.8955 (t0)
REVERT: A  398 ASP cc_start: 0.8231 (m-30) cc_final: 0.7716 (m-30)
REVERT: A  401 VAL cc_start: 0.8926 (t) cc_final: 0.8700 (t)
REVERT: A  406 GLU cc_start: 0.9035 (pm20) cc_final: 0.8648 (pm20)
REVERT: A  472 ILE cc_start: 0.5610 (OUTLIER) cc_final: 0.5270 (mt)
REVERT: A  493 GLN cc_start: 0.8040 (tp40) cc_final: 0.7803 (tp40)
REVERT: H    2 VAL cc_start: 0.8210 (m) cc_final: 0.7892 (p)
REVERT: H    3 GLN cc_start: 0.7416 (pm20) cc_final: 0.7127 (pm20)
REVERT: H  117 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8124 (mt0)
REVERT: L   36 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8143 (m-70)
REVERT: L   81 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7523 (tt0)
REVERT: L   87 ASP cc_start: 0.8091 (p0) cc_final: 0.7857 (p0)
REVERT: L   89 TYR cc_start: 0.8157 (m-80) cc_final: 0.7895 (m-80)
REVERT: L   91 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7482 (pt0)
REVERT: L  101 VAL cc_start: 0.8517 (t) cc_final: 0.8160 (p)
  outliers start: 30
  outliers final: 25
  residues processed: 128
  average time/residue: 0.1278
  time to fit residues: 20.6382
Evaluate side-chains
  137 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  472 ILE
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   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  116 PHE
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   18 VAL
Chi-restraints excluded: chain L residue   36 HIS
Chi-restraints excluded: chain L residue   45 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.4584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.121360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.103995 restraints weight = 9142.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.107361 restraints weight = 5036.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.109588 restraints weight = 3301.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.7022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3467  Z= 0.148
  Angle     :  0.820  16.346   4719  Z= 0.394
  Chirality :  0.048   0.199    495
  Planarity :  0.005   0.053    617
  Dihedral  :  4.858  25.722    487
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 24.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.40), residues: 430
  helix: -3.24 (0.74), residues: 28
  sheet:  0.19 (0.45), residues: 131
  loop : -0.97 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  47 
 HIS   0.003   0.002   HIS L  36 
 PHE   0.022   0.002   PHE A 392 
 TYR   0.024   0.002   TYR A 351 
 ARG   0.003   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  107)
  hydrogen bonds       : angle       6.48829 (  273)
  SS BOND              : bond        0.00417 (    6)
  SS BOND              : angle       0.83935 (   12)
  covalent geometry    : bond        0.00344 ( 3461)
  covalent geometry    : angle       0.82031 ( 4707)

*********************** 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
  139 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8180 (m-40) cc_final: 0.7647 (m-40)
REVERT: A  356 LYS cc_start: 0.8598 (tppt) cc_final: 0.8121 (tptt)
REVERT: A  398 ASP cc_start: 0.8258 (m-30) cc_final: 0.7711 (m-30)
REVERT: A  401 VAL cc_start: 0.8970 (t) cc_final: 0.8756 (t)
REVERT: A  406 GLU cc_start: 0.9017 (pm20) cc_final: 0.8668 (pm20)
REVERT: A  493 GLN cc_start: 0.8057 (tp40) cc_final: 0.7805 (tp40)
REVERT: H    2 VAL cc_start: 0.8209 (m) cc_final: 0.7883 (p)
REVERT: H    3 GLN cc_start: 0.7413 (pm20) cc_final: 0.7116 (pm20)
REVERT: H  114 GLU cc_start: 0.8541 (mp0) cc_final: 0.8120 (mp0)
REVERT: H  117 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8079 (mt0)
REVERT: L   81 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7630 (tt0)
REVERT: L   87 ASP cc_start: 0.7991 (p0) cc_final: 0.7752 (p0)
REVERT: L   89 TYR cc_start: 0.8085 (m-80) cc_final: 0.7808 (m-80)
REVERT: L  101 VAL cc_start: 0.8327 (t) cc_final: 0.8102 (p)
REVERT: L  102 PHE cc_start: 0.6901 (m-10) cc_final: 0.6595 (m-10)
  outliers start: 26
  outliers final: 24
  residues processed: 128
  average time/residue: 0.1284
  time to fit residues: 20.5609
Evaluate side-chains
  136 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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   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   18 VAL
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  100 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0970
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    1.1782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.122705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.105326 restraints weight = 9136.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.108727 restraints weight = 5031.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.110939 restraints weight = 3277.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.7189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3467  Z= 0.137
  Angle     :  0.806  14.837   4719  Z= 0.389
  Chirality :  0.049   0.231    495
  Planarity :  0.005   0.046    617
  Dihedral  :  4.743  24.885    487
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 24.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.40), residues: 430
  helix: -3.48 (0.62), residues: 34
  sheet:  0.13 (0.46), residues: 123
  loop : -0.92 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L  37 
 HIS   0.003   0.001   HIS H 118 
 PHE   0.023   0.002   PHE A 392 
 TYR   0.024   0.002   TYR A 351 
 ARG   0.003   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  107)
  hydrogen bonds       : angle       6.43633 (  273)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       0.82165 (   12)
  covalent geometry    : bond        0.00316 ( 3461)
  covalent geometry    : angle       0.80628 ( 4707)

********************** 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
  137 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8212 (m-40) cc_final: 0.7695 (m-40)
REVERT: A  356 LYS cc_start: 0.8574 (tppt) cc_final: 0.8108 (tptt)
REVERT: A  398 ASP cc_start: 0.8210 (m-30) cc_final: 0.7642 (m-30)
REVERT: A  401 VAL cc_start: 0.8946 (t) cc_final: 0.8729 (t)
REVERT: A  414 GLN cc_start: 0.8396 (mp-120) cc_final: 0.8165 (mp10)
REVERT: A  472 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5409 (mt)
REVERT: A  493 GLN cc_start: 0.8072 (tp40) cc_final: 0.7835 (tp40)
REVERT: H    2 VAL cc_start: 0.8192 (m) cc_final: 0.7878 (p)
REVERT: H    3 GLN cc_start: 0.7396 (pm20) cc_final: 0.7114 (pm20)
REVERT: H   28 THR cc_start: 0.8738 (m) cc_final: 0.8413 (p)
REVERT: H   68 PHE cc_start: 0.7371 (m-80) cc_final: 0.7026 (m-80)
REVERT: H  117 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7855 (mt0)
REVERT: L   88 TYR cc_start: 0.8485 (m-10) cc_final: 0.8137 (m-10)
  outliers start: 27
  outliers final: 24
  residues processed: 126
  average time/residue: 0.1355
  time to fit residues: 21.1765
Evaluate side-chains
  133 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  472 ILE
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   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   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  100 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 35 optimal weight:    0.3980
   chunk 12 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    2.8788

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.118892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.101406 restraints weight = 9350.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.104802 restraints weight = 5125.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.107060 restraints weight = 3360.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.7371

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= 0.194
  Angle     :  0.837  16.023   4719  Z= 0.407
  Chirality :  0.049   0.219    495
  Planarity :  0.005   0.053    617
  Dihedral  :  5.022  24.740    487
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 20.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 25.27 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.40), residues: 430
  helix: -2.99 (0.79), residues: 28
  sheet:  0.18 (0.47), residues: 122
  loop : -0.95 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L  37 
 HIS   0.005   0.002   HIS H 118 
 PHE   0.024   0.002   PHE A 392 
 TYR   0.021   0.002   TYR A 365 
 ARG   0.004   0.001   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  107)
  hydrogen bonds       : angle       6.31871 (  273)
  SS BOND              : bond        0.00502 (    6)
  SS BOND              : angle       0.95695 (   12)
  covalent geometry    : bond        0.00452 ( 3461)
  covalent geometry    : angle       0.83697 ( 4707)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1624.44 seconds
wall clock time: 28 minutes 57.27 seconds (1737.27 seconds total)