Starting phenix.real_space_refine
on Wed Jun  4 15:18:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wlc_32581/06_2025/7wlc_32581.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wlc_32581/06_2025/7wlc_32581.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wlc_32581/06_2025/7wlc_32581.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wlc_32581/06_2025/7wlc_32581.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wlc_32581/06_2025/7wlc_32581.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wlc_32581/06_2025/7wlc_32581.cif"
  }
  resolution = 4.0
  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
-------------------------------------------------------------------------------
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=   0.005 sd=   0.009
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    2094      2.51       5
     N     563      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 3307
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187}
    Chain: "H"
      Number of atoms: 892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 892
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 803
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 2.59, per 1000 atoms: 0.78
  Number of scatterers: 3307
  At special positions: 0
  Unit cell: (53.04, 80.08, 95.68, 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     636      8.00
     N     563      7.00
     C    2094      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 380.5 milliseconds
  

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  784

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      8.8% alpha, 30.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'E' and resid 337 through 342
      removed outlier: 3.781A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 386 through 389
      removed outlier: 3.657A  pdb=" N   ASP E 389 " --> pdb=" O   LYS E 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 386 through 389'
    Processing helix  chain 'E' and resid 405 through 411
      removed outlier: 4.535A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA E 411 " --> pdb=" O   ARG E 408 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 417 through 422
      removed outlier: 3.569A  pdb=" N   ASN E 422 " --> pdb=" O   ILE E 418 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.730A  pdb=" N   GLN H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358
      removed outlier: 3.730A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 391 through 392
      removed outlier: 3.634A  pdb=" N   VAL E 524 " --> pdb=" O   PHE E 392 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 453 through 454
    Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474
      removed outlier: 3.694A  pdb=" N   TYR E 473 " --> pdb=" O   TYR E 489 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.789A  pdb=" N   GLU H  10 " --> pdb=" O   LEU H 116 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA H 118 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.625A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12
    Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23

    100 hydrogen bonds defined for protein.
    237 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.82

  Time building geometry restraints manager: 1.03 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: 1071
        1.34 -     1.47: 889
        1.47 -     1.59: 1416
        1.59 -     1.71: 0
        1.71 -     1.84: 16
  Bond restraints: 3392
  Sorted by residual:
  bond pdb=" CB  LYS H  13 "
       pdb=" CG  LYS H  13 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.24e+00
  bond pdb=" CB  ASN E 448 "
       pdb=" CG  ASN E 448 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 1.01e+00
  bond pdb=" N   GLY H 112 "
       pdb=" CA  GLY H 112 "
    ideal  model  delta    sigma   weight residual
    1.444  1.454 -0.010 9.60e-03 1.09e+04 9.95e-01
  bond pdb=" C   ASN E 331 "
       pdb=" N   ILE E 332 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.40e-02 5.10e+03 9.85e-01
  bond pdb=" CG  LYS H  13 "
       pdb=" CD  LYS H  13 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.82e-01
  ... (remaining 3387 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 4508
        1.92 -     3.83: 86
        3.83 -     5.75: 13
        5.75 -     7.67: 5
        7.67 -     9.59: 2
  Bond angle restraints: 4614
  Sorted by residual:
  angle pdb=" C   ASN E 331 "
        pdb=" N   ILE E 332 "
        pdb=" CA  ILE E 332 "
      ideal   model   delta    sigma   weight residual
     121.70  128.16   -6.46 1.80e+00 3.09e-01 1.29e+01
  angle pdb=" CA  MET H  81 "
        pdb=" CB  MET H  81 "
        pdb=" CG  MET H  81 "
      ideal   model   delta    sigma   weight residual
     114.10  121.07   -6.97 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" CB  LYS H  13 "
        pdb=" CG  LYS H  13 "
        pdb=" CD  LYS H  13 "
      ideal   model   delta    sigma   weight residual
     111.30  119.20   -7.90 2.30e+00 1.89e-01 1.18e+01
  angle pdb=" CB  MET H  81 "
        pdb=" CG  MET H  81 "
        pdb=" SD  MET H  81 "
      ideal   model   delta    sigma   weight residual
     112.70  103.11    9.59 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" CA  TRP H 111 "
        pdb=" CB  TRP H 111 "
        pdb=" CG  TRP H 111 "
      ideal   model   delta    sigma   weight residual
     113.60  119.66   -6.06 1.90e+00 2.77e-01 1.02e+01
  ... (remaining 4609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.37: 1779
       15.37 -    30.74: 175
       30.74 -    46.11: 29
       46.11 -    61.48: 13
       61.48 -    76.85: 8
  Dihedral angle restraints: 2004
    sinusoidal: 768
      harmonic: 1236
  Sorted by residual:
  dihedral pdb=" CB  CYS E 379 "
           pdb=" SG  CYS E 379 "
           pdb=" SG  CYS E 432 "
           pdb=" CB  CYS E 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.64   64.36     1      1.00e+01 1.00e-02 5.45e+01
  dihedral pdb=" CB  CYS E 336 "
           pdb=" SG  CYS E 336 "
           pdb=" SG  CYS E 361 "
           pdb=" CB  CYS E 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.26   58.74     1      1.00e+01 1.00e-02 4.62e+01
  dihedral pdb=" CA  MET H  81 "
           pdb=" C   MET H  81 "
           pdb=" N   GLU H  82 "
           pdb=" CA  GLU H  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.52   21.48     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 2001 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 244
       0.028 -    0.056: 160
       0.056 -    0.084: 57
       0.084 -    0.111: 25
       0.111 -    0.139: 11
  Chirality restraints: 497
  Sorted by residual:
  chirality pdb=" CA  ILE H  70 "
            pdb=" N   ILE H  70 "
            pdb=" C   ILE H  70 "
            pdb=" CB  ILE H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  PRO E 373 "
            pdb=" N   PRO E 373 "
            pdb=" C   PRO E 373 "
            pdb=" CB  PRO E 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE L  76 "
            pdb=" N   ILE L  76 "
            pdb=" C   ILE L  76 "
            pdb=" CB  ILE L  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 494 not shown)

  Planarity restraints: 601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  59 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO L  60 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO L  60 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO L  60 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 111 "   -0.015 2.00e-02 2.50e+03   9.52e-03 2.27e+00
        pdb=" CG  TRP H 111 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 111 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 111 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 111 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 111 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 111 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 111 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 111 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS E 336 "    0.022 5.00e-02 4.00e+02   3.36e-02 1.81e+00
        pdb=" N   PRO E 337 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO E 337 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E 337 "    0.019 5.00e-02 4.00e+02
  ... (remaining 598 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 234
        2.74 -     3.28: 3348
        3.28 -     3.82: 5244
        3.82 -     4.36: 5995
        4.36 -     4.90: 10460
  Nonbonded interactions: 25281
  Sorted by model distance:
  nonbonded pdb=" O   ASN E 448 "
            pdb=" OG  SER E 494 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" NZ  LYS H  23 "
            pdb=" O   THR H  76 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   SER H   7 "
            pdb=" OG1 THR H 115 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   TYR H 108 "
            pdb=" OH  TYR L  37 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ARG H  67 "
            pdb=" OG  SER H  84 "
     model   vdw
     2.271 3.040
  ... (remaining 25276 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:             0.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.940
  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:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3398  Z= 0.139
  Angle     :  0.705   9.586   4626  Z= 0.380
  Chirality :  0.044   0.139    497
  Planarity :  0.005   0.039    601
  Dihedral  : 13.708  76.851   1202
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.35 (0.42), residues: 424
  helix: -3.38 (0.98), residues: 18
  sheet:  0.25 (0.50), residues: 131
  loop : -1.37 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H 111 
 HIS   0.001   0.000   HIS H 110 
 PHE   0.021   0.002   PHE E 497 
 TYR   0.018   0.001   TYR E 351 
 ARG   0.006   0.000   ARG E 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13124 (   93)
  hydrogen bonds       : angle       8.67802 (  237)
  SS BOND              : bond        0.00423 (    6)
  SS BOND              : angle       1.58104 (   12)
  covalent geometry    : bond        0.00296 ( 3392)
  covalent geometry    : angle       0.70106 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  392 PHE cc_start: 0.8997 (m-80) cc_final: 0.8779 (m-80)
REVERT: E  467 ASP cc_start: 0.7961 (t70) cc_final: 0.7735 (t0)
REVERT: H   29 PHE cc_start: 0.7613 (t80) cc_final: 0.7264 (t80)
REVERT: H   67 ARG cc_start: 0.8905 (ptp-170) cc_final: 0.8544 (ttp-110)
REVERT: L   39 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7662 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1845
  time to fit residues: 21.5788
Evaluate side-chains
  80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  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:   50.0000
   chunk 31 optimal weight:    0.0070
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 21 optimal weight:   40.0000
   chunk 32 optimal weight:   50.0000
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:   30.0000
   chunk 24 optimal weight:   40.0000
   chunk 38 optimal weight:   20.0000
   chunk 11 optimal weight:    7.9990
   overall best weight:    3.9604

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 110 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.127690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.098145 restraints weight = 8956.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.101127 restraints weight = 5145.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.102987 restraints weight = 3546.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3398  Z= 0.135
  Angle     :  0.700  10.162   4626  Z= 0.360
  Chirality :  0.047   0.140    497
  Planarity :  0.005   0.039    601
  Dihedral  :  5.443  19.414    471
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.93 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.20 (0.42), residues: 424
  helix: -3.51 (1.23), residues: 12
  sheet:  0.24 (0.47), residues: 140
  loop : -1.29 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H 111 
 HIS   0.002   0.001   HIS H 110 
 PHE   0.023   0.002   PHE E 429 
 TYR   0.015   0.002   TYR E 449 
 ARG   0.007   0.001   ARG L  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03574 (   93)
  hydrogen bonds       : angle       6.82854 (  237)
  SS BOND              : bond        0.00431 (    6)
  SS BOND              : angle       1.17682 (   12)
  covalent geometry    : bond        0.00301 ( 3392)
  covalent geometry    : angle       0.69862 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  346 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7629 (mtp85)
REVERT: H   29 PHE cc_start: 0.7713 (t80) cc_final: 0.7267 (t80)
REVERT: H   48 MET cc_start: 0.8304 (mmp) cc_final: 0.7683 (tpp)
REVERT: H   67 ARG cc_start: 0.8812 (ptp-170) cc_final: 0.8587 (ttp-110)
REVERT: L   39 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7710 (tp-100)
  outliers start: 7
  outliers final: 4
  residues processed: 84
  average time/residue: 0.1905
  time to fit residues: 18.9569
Evaluate side-chains
  79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:   50.0000
   chunk 33 optimal weight:   20.0000
   chunk 34 optimal weight:   40.0000
   chunk 11 optimal weight:   40.0000
   chunk 16 optimal weight:   40.0000
   chunk 0 optimal weight:   30.0000
   chunk 38 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 13 optimal weight:   30.0000
   chunk 25 optimal weight:   40.0000
   chunk 20 optimal weight:   30.0000
   overall best weight:   22.0000

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.118900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.089682 restraints weight = 9156.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.092328 restraints weight = 5434.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.094046 restraints weight = 3856.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067   3398  Z= 0.372
  Angle     :  0.865  11.256   4626  Z= 0.455
  Chirality :  0.051   0.194    497
  Planarity :  0.006   0.047    601
  Dihedral  :  6.472  19.980    471
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 21.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.55 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.73 (0.40), residues: 424
  helix: -3.56 (0.92), residues: 18
  sheet: -0.09 (0.47), residues: 140
  loop : -1.64 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP H 111 
 HIS   0.005   0.001   HIS H 110 
 PHE   0.031   0.004   PHE E 338 
 TYR   0.015   0.002   TYR E 423 
 ARG   0.006   0.001   ARG L  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04568 (   93)
  hydrogen bonds       : angle       7.07488 (  237)
  SS BOND              : bond        0.00413 (    6)
  SS BOND              : angle       1.81509 (   12)
  covalent geometry    : bond        0.00818 ( 3392)
  covalent geometry    : angle       0.86094 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8197 (t80) cc_final: 0.7711 (t80)
REVERT: H   48 MET cc_start: 0.8266 (mmp) cc_final: 0.7920 (mmm)
REVERT: H   67 ARG cc_start: 0.8898 (ptp-170) cc_final: 0.8668 (ttp-110)
REVERT: L   46 LYS cc_start: 0.9592 (tppp) cc_final: 0.9356 (tppp)
  outliers start: 10
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1794
  time to fit residues: 16.8968
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  389 ASP
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  108 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:   30.0000
   chunk 23 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 37 optimal weight:   40.0000
   chunk 39 optimal weight:   30.0000
   chunk 41 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
** L  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.125595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095928 restraints weight = 9393.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.098854 restraints weight = 5477.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.100765 restraints weight = 3825.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3398  Z= 0.162
  Angle     :  0.742  10.602   4626  Z= 0.380
  Chirality :  0.047   0.147    497
  Planarity :  0.005   0.046    601
  Dihedral  :  5.898  19.677    471
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.89 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.57 (0.41), residues: 424
  helix: -3.48 (0.99), residues: 18
  sheet: -0.01 (0.47), residues: 140
  loop : -1.51 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP H 111 
 HIS   0.006   0.001   HIS H 110 
 PHE   0.013   0.002   PHE E 338 
 TYR   0.016   0.002   TYR L  86 
 ARG   0.004   0.000   ARG L  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (   93)
  hydrogen bonds       : angle       6.54346 (  237)
  SS BOND              : bond        0.00621 (    6)
  SS BOND              : angle       1.43357 (   12)
  covalent geometry    : bond        0.00366 ( 3392)
  covalent geometry    : angle       0.73927 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8026 (t80) cc_final: 0.7503 (t80)
REVERT: H   48 MET cc_start: 0.8313 (mmp) cc_final: 0.7732 (mmm)
REVERT: H   67 ARG cc_start: 0.8811 (ptp-170) cc_final: 0.8579 (ttp-110)
REVERT: L   36 TRP cc_start: 0.7932 (m100) cc_final: 0.7624 (m100)
REVERT: L   39 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7632 (tp-100)
  outliers start: 10
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1968
  time to fit residues: 20.7602
Evaluate side-chains
  86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  511 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:   30.0000
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:   40.0000
   chunk 22 optimal weight:   50.0000
   chunk 23 optimal weight:   30.0000
   chunk 37 optimal weight:   20.0000
   chunk 2 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:   30.0000
   overall best weight:    5.9992

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.126624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.097363 restraints weight = 9413.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.100196 restraints weight = 5568.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.102032 restraints weight = 3949.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3398  Z= 0.151
  Angle     :  0.728  10.707   4626  Z= 0.371
  Chirality :  0.047   0.141    497
  Planarity :  0.005   0.045    601
  Dihedral  :  5.708  19.948    471
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 19.78 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.48 (0.41), residues: 424
  helix: -3.34 (1.02), residues: 18
  sheet:  0.05 (0.47), residues: 140
  loop : -1.45 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H 111 
 HIS   0.004   0.001   HIS H 110 
 PHE   0.012   0.002   PHE E 338 
 TYR   0.011   0.001   TYR L  86 
 ARG   0.005   0.001   ARG L  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03377 (   93)
  hydrogen bonds       : angle       6.34598 (  237)
  SS BOND              : bond        0.00583 (    6)
  SS BOND              : angle       1.39750 (   12)
  covalent geometry    : bond        0.00342 ( 3392)
  covalent geometry    : angle       0.72534 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: E  474 GLN cc_start: 0.2838 (pp30) cc_final: 0.2448 (pp30)
REVERT: H   29 PHE cc_start: 0.7974 (t80) cc_final: 0.7266 (t80)
REVERT: H   48 MET cc_start: 0.8187 (mmp) cc_final: 0.7755 (mmm)
REVERT: H   67 ARG cc_start: 0.8846 (ptp-170) cc_final: 0.8600 (ttp-110)
REVERT: L   39 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7644 (tp-100)
  outliers start: 15
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1902
  time to fit residues: 19.6552
Evaluate side-chains
  93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  511 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   34 ILE
Chi-restraints excluded: chain L residue   40 LEU
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:   50.0000
   chunk 1 optimal weight:    0.4980
   chunk 3 optimal weight:   30.0000
   chunk 35 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 25 optimal weight:   40.0000
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:   30.0000
   chunk 37 optimal weight:   30.0000
   overall best weight:    5.0786

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.131429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.103418 restraints weight = 8990.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.106157 restraints weight = 5394.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.107979 restraints weight = 3849.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3398  Z= 0.140
  Angle     :  0.718  11.888   4626  Z= 0.361
  Chirality :  0.046   0.136    497
  Planarity :  0.005   0.046    601
  Dihedral  :  5.530  20.868    471
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 21.73 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.42 (0.41), residues: 424
  helix: -3.52 (0.93), residues: 18
  sheet:  0.08 (0.46), residues: 146
  loop : -1.41 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H 111 
 HIS   0.004   0.001   HIS H 110 
 PHE   0.015   0.002   PHE E 392 
 TYR   0.011   0.001   TYR E 495 
 ARG   0.006   0.001   ARG E 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03224 (   93)
  hydrogen bonds       : angle       6.15847 (  237)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       1.02652 (   12)
  covalent geometry    : bond        0.00322 ( 3392)
  covalent geometry    : angle       0.71726 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.7946 (t80) cc_final: 0.7187 (t80)
REVERT: H   48 MET cc_start: 0.7942 (mmp) cc_final: 0.7696 (mmm)
  outliers start: 12
  outliers final: 10
  residues processed: 93
  average time/residue: 0.1946
  time to fit residues: 21.3195
Evaluate side-chains
  89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  511 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   34 ILE
Chi-restraints excluded: chain L residue   40 LEU
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:   30.0000
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:   50.0000
   chunk 1 optimal weight:    9.9990
   chunk 23 optimal weight:   30.0000
   chunk 26 optimal weight:    8.9990
   chunk 24 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   chunk 41 optimal weight:   30.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.131573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.102687 restraints weight = 9053.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.105948 restraints weight = 5158.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.107998 restraints weight = 3558.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3398  Z= 0.145
  Angle     :  0.727  10.258   4626  Z= 0.365
  Chirality :  0.046   0.150    497
  Planarity :  0.005   0.046    601
  Dihedral  :  5.514  22.107    471
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 23.68 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.50 (0.41), residues: 424
  helix: -3.60 (0.85), residues: 18
  sheet:  0.02 (0.45), residues: 147
  loop : -1.46 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H 111 
 HIS   0.005   0.001   HIS H 110 
 PHE   0.017   0.002   PHE E 497 
 TYR   0.015   0.001   TYR E 351 
 ARG   0.006   0.001   ARG E 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (   93)
  hydrogen bonds       : angle       6.05217 (  237)
  SS BOND              : bond        0.00534 (    6)
  SS BOND              : angle       1.01185 (   12)
  covalent geometry    : bond        0.00329 ( 3392)
  covalent geometry    : angle       0.72591 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.7934 (t80) cc_final: 0.7222 (t80)
REVERT: H   48 MET cc_start: 0.7953 (mmp) cc_final: 0.7645 (mmm)
  outliers start: 12
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1789
  time to fit residues: 18.3888
Evaluate side-chains
  90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  511 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   34 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 25 optimal weight:    0.0270
   chunk 6 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 35 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:   30.0000
   chunk 14 optimal weight:   40.0000
   chunk 17 optimal weight:   20.0000
   chunk 12 optimal weight:    9.9990
   overall best weight:    6.6046

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.131580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.102629 restraints weight = 8921.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.105837 restraints weight = 5156.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.107817 restraints weight = 3571.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3398  Z= 0.150
  Angle     :  0.727   8.144   4626  Z= 0.365
  Chirality :  0.046   0.144    497
  Planarity :  0.005   0.046    601
  Dihedral  :  5.508  22.060    471
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 23.40 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.38 (0.41), residues: 424
  helix: -3.57 (0.87), residues: 18
  sheet:  0.14 (0.48), residues: 134
  loop : -1.34 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H 111 
 HIS   0.004   0.001   HIS H 110 
 PHE   0.017   0.002   PHE E 374 
 TYR   0.023   0.002   TYR E 351 
 ARG   0.007   0.001   ARG L  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03045 (   93)
  hydrogen bonds       : angle       6.00824 (  237)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       1.65743 (   12)
  covalent geometry    : bond        0.00337 ( 3392)
  covalent geometry    : angle       0.72277 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.7980 (t80) cc_final: 0.7280 (t80)
REVERT: H   48 MET cc_start: 0.7977 (mmp) cc_final: 0.7656 (mmm)
  outliers start: 14
  outliers final: 13
  residues processed: 90
  average time/residue: 0.1767
  time to fit residues: 19.1627
Evaluate side-chains
  91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  511 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   34 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 36 optimal weight:    0.4980
   chunk 22 optimal weight:   50.0000
   chunk 28 optimal weight:   10.0000
   chunk 14 optimal weight:   30.0000
   chunk 29 optimal weight:   30.0000
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    5.2988

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

Flipped N/Q/H residues before XYZ refinement:
** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.132195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.103843 restraints weight = 8965.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.106781 restraints weight = 5415.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.108426 restraints weight = 3845.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3398  Z= 0.138
  Angle     :  0.714   7.746   4626  Z= 0.360
  Chirality :  0.046   0.143    497
  Planarity :  0.005   0.046    601
  Dihedral  :  5.417  22.364    471
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.79 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.45 (0.41), residues: 424
  helix: -3.55 (0.89), residues: 18
  sheet:  0.05 (0.48), residues: 133
  loop : -1.36 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H 111 
 HIS   0.004   0.001   HIS H 110 
 PHE   0.019   0.002   PHE E 374 
 TYR   0.022   0.002   TYR E 351 
 ARG   0.007   0.001   ARG L  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03006 (   93)
  hydrogen bonds       : angle       5.92921 (  237)
  SS BOND              : bond        0.00385 (    6)
  SS BOND              : angle       1.59662 (   12)
  covalent geometry    : bond        0.00311 ( 3392)
  covalent geometry    : angle       0.71014 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.7949 (t80) cc_final: 0.7162 (t80)
REVERT: H   48 MET cc_start: 0.8011 (mmp) cc_final: 0.7663 (mmm)
  outliers start: 13
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1835
  time to fit residues: 18.9677
Evaluate side-chains
  91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  511 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   34 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 25 optimal weight:   50.0000
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:   50.0000
   chunk 26 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:   50.0000
   chunk 20 optimal weight:   40.0000
   chunk 37 optimal weight:    0.0010
   chunk 40 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   overall best weight:    4.3792

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.132958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.104888 restraints weight = 8875.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.107754 restraints weight = 5450.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.109567 restraints weight = 3928.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3398  Z= 0.139
  Angle     :  0.741   7.898   4626  Z= 0.372
  Chirality :  0.046   0.144    497
  Planarity :  0.005   0.046    601
  Dihedral  :  5.451  22.325    471
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 25.35 %
    Favored  : 71.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.42 (0.41), residues: 424
  helix: -3.61 (0.85), residues: 18
  sheet:  0.01 (0.48), residues: 134
  loop : -1.30 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H 111 
 HIS   0.004   0.001   HIS H 110 
 PHE   0.022   0.002   PHE E 374 
 TYR   0.023   0.002   TYR E 351 
 ARG   0.007   0.001   ARG E 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02971 (   93)
  hydrogen bonds       : angle       5.90227 (  237)
  SS BOND              : bond        0.00436 (    6)
  SS BOND              : angle       1.55878 (   12)
  covalent geometry    : bond        0.00315 ( 3392)
  covalent geometry    : angle       0.73819 ( 4614)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  392 PHE cc_start: 0.8856 (m-80) cc_final: 0.8645 (m-10)
REVERT: H   29 PHE cc_start: 0.7844 (t80) cc_final: 0.7031 (t80)
REVERT: H   48 MET cc_start: 0.7959 (mmp) cc_final: 0.7728 (mmm)
REVERT: L   38 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8568 (tp-100)
  outliers start: 12
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1846
  time to fit residues: 18.9318
Evaluate side-chains
  92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  345 THR
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  461 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  511 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   34 ILE
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 36 optimal weight:    0.0670
   chunk 39 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 19 optimal weight:    0.0570
   chunk 26 optimal weight:   40.0000
   chunk 22 optimal weight:   50.0000
   chunk 38 optimal weight:   50.0000
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:   50.0000
   overall best weight:    5.0242

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.132898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.104687 restraints weight = 9032.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.107617 restraints weight = 5448.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.109475 restraints weight = 3883.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3398  Z= 0.141
  Angle     :  0.739   7.679   4626  Z= 0.373
  Chirality :  0.046   0.143    497
  Planarity :  0.005   0.046    601
  Dihedral  :  5.441  22.162    471
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.74 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.47 (0.41), residues: 424
  helix: -3.62 (0.85), residues: 18
  sheet: -0.06 (0.47), residues: 140
  loop : -1.33 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H 111 
 HIS   0.003   0.001   HIS H 110 
 PHE   0.022   0.002   PHE E 374 
 TYR   0.023   0.002   TYR E 351 
 ARG   0.007   0.001   ARG E 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02966 (   93)
  hydrogen bonds       : angle       5.79856 (  237)
  SS BOND              : bond        0.00429 (    6)
  SS BOND              : angle       1.50826 (   12)
  covalent geometry    : bond        0.00324 ( 3392)
  covalent geometry    : angle       0.73563 ( 4614)

===============================================================================
Job complete
usr+sys time: 1417.24 seconds
wall clock time: 25 minutes 36.95 seconds (1536.95 seconds total)