Starting phenix.real_space_refine
on Fri Jul 25 04:35:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6z1i_11030/07_2025/6z1i_11030.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6z1i_11030/07_2025/6z1i_11030.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6z1i_11030/07_2025/6z1i_11030.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6z1i_11030/07_2025/6z1i_11030.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6z1i_11030/07_2025/6z1i_11030.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6z1i_11030/07_2025/6z1i_11030.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2250      2.51       5
     N     648      2.21       5
     O     738      1.98       5
     H    3492      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7140
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 1190
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 2, 'TRANS': 78}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.84, per 1000 atoms: 0.40
  Number of scatterers: 7140
  At special positions: 0
  Unit cell: (85.28, 73.84, 45.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     O     738      8.00
     N     648      7.00
     C    2250      6.00
     H    3492      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=1.99

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.53
  Conformation dependent library (CDL) restraints added in 577.8 milliseconds
  

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  888

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 44.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 23
    Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26
    Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 31
    Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 37
    Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 47
    Processing sheet with id=AA9, first strand: chain 'A' and resid 72 through 75
    Processing sheet with id=AB1, first strand: chain 'A' and resid 79 through 82
    Processing sheet with id=AB2, first strand: chain 'A' and resid 85 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 85 through 86
    current: chain 'B' and resid 85 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 85 through 86
    current: chain 'C' and resid 85 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 85 through 86
    current: chain 'D' and resid 85 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 85 through 86
    current: chain 'E' and resid 85 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 85 through 86
    current: chain 'F' and resid 85 through 86
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 91
    Processing sheet with id=AB4, first strand: chain 'A' and resid 95 through 97
      removed outlier: 3.531A  pdb=" N   HIS B  96 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   HIS C  96 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS D  96 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS E  96 " --> pdb=" O   ASN D  95 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   HIS F  96 " --> pdb=" O   ASN E  95 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 106

    170 hydrogen bonds defined for protein.
    510 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: 2.35

  Time building geometry restraints manager: 1.90 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 3492
        1.03 -     1.23: 138
        1.23 -     1.42: 1464
        1.42 -     1.62: 2088
        1.62 -     1.81: 12
  Bond restraints: 7194
  Sorted by residual:
  bond pdb=" N   LYS B  38 "
       pdb=" CA  LYS B  38 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.07e-02 8.73e+03 1.24e+01
  bond pdb=" N   LYS E  38 "
       pdb=" CA  LYS E  38 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.07e-02 8.73e+03 1.22e+01
  bond pdb=" N   LYS D  38 "
       pdb=" CA  LYS D  38 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.07e-02 8.73e+03 1.20e+01
  bond pdb=" N   LYS A  38 "
       pdb=" CA  LYS A  38 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.07e-02 8.73e+03 1.20e+01
  bond pdb=" N   LYS F  38 "
       pdb=" CA  LYS F  38 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.07e-02 8.73e+03 1.17e+01
  ... (remaining 7189 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 10349
        1.88 -     3.76: 1916
        3.76 -     5.64: 425
        5.64 -     7.52: 150
        7.52 -     9.40: 24
  Bond angle restraints: 12864
  Sorted by residual:
  angle pdb=" C   PRO D  39 "
        pdb=" CA  PRO D  39 "
        pdb=" CB  PRO D  39 "
      ideal   model   delta    sigma   weight residual
     111.11  103.02    8.09 1.17e+00 7.31e-01 4.78e+01
  angle pdb=" C   PRO A  39 "
        pdb=" CA  PRO A  39 "
        pdb=" CB  PRO A  39 "
      ideal   model   delta    sigma   weight residual
     111.11  103.02    8.09 1.17e+00 7.31e-01 4.78e+01
  angle pdb=" C   PRO E  39 "
        pdb=" CA  PRO E  39 "
        pdb=" CB  PRO E  39 "
      ideal   model   delta    sigma   weight residual
     111.11  103.02    8.09 1.17e+00 7.31e-01 4.78e+01
  angle pdb=" C   PRO F  39 "
        pdb=" CA  PRO F  39 "
        pdb=" CB  PRO F  39 "
      ideal   model   delta    sigma   weight residual
     111.11  103.04    8.07 1.17e+00 7.31e-01 4.75e+01
  angle pdb=" C   PRO B  39 "
        pdb=" CA  PRO B  39 "
        pdb=" CB  PRO B  39 "
      ideal   model   delta    sigma   weight residual
     111.11  103.05    8.06 1.17e+00 7.31e-01 4.75e+01
  ... (remaining 12859 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.85: 2755
       10.85 -    21.71: 342
       21.71 -    32.56: 175
       32.56 -    43.42: 103
       43.42 -    54.27: 48
  Dihedral angle restraints: 3423
    sinusoidal: 1827
      harmonic: 1596
  Sorted by residual:
  dihedral pdb=" C   CYS E  87 "
           pdb=" N   CYS E  87 "
           pdb=" CA  CYS E  87 "
           pdb=" CB  CYS E  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.19    9.59     0      2.50e+00 1.60e-01 1.47e+01
  dihedral pdb=" C   CYS D  87 "
           pdb=" N   CYS D  87 "
           pdb=" CA  CYS D  87 "
           pdb=" CB  CYS D  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.16    9.56     0      2.50e+00 1.60e-01 1.46e+01
  dihedral pdb=" C   CYS F  87 "
           pdb=" N   CYS F  87 "
           pdb=" CA  CYS F  87 "
           pdb=" CB  CYS F  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.16    9.56     0      2.50e+00 1.60e-01 1.46e+01
  ... (remaining 3420 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.075: 248
       0.075 -    0.147: 208
       0.147 -    0.220: 94
       0.220 -    0.292: 20
       0.292 -    0.365: 6
  Chirality restraints: 576
  Sorted by residual:
  chirality pdb=" CA  CYS E  87 "
            pdb=" N   CYS E  87 "
            pdb=" C   CYS E  87 "
            pdb=" CB  CYS E  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CA  CYS D  87 "
            pdb=" N   CYS D  87 "
            pdb=" C   CYS D  87 "
            pdb=" CB  CYS D  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.30e+00
  chirality pdb=" CA  CYS A  87 "
            pdb=" N   CYS A  87 "
            pdb=" C   CYS A  87 "
            pdb=" CB  CYS A  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.29e+00
  ... (remaining 573 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN F  41 "    0.196 2.00e-02 2.50e+03   2.26e-01 7.65e+02
        pdb=" CD  GLN F  41 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE1 GLN F  41 "   -0.188 2.00e-02 2.50e+03
        pdb=" NE2 GLN F  41 "   -0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN F  41 "   -0.339 2.00e-02 2.50e+03
        pdb="HE22 GLN F  41 "    0.343 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A  41 "    0.195 2.00e-02 2.50e+03   2.26e-01 7.65e+02
        pdb=" CD  GLN A  41 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE1 GLN A  41 "   -0.188 2.00e-02 2.50e+03
        pdb=" NE2 GLN A  41 "   -0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN A  41 "   -0.339 2.00e-02 2.50e+03
        pdb="HE22 GLN A  41 "    0.343 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN D  41 "    0.195 2.00e-02 2.50e+03   2.26e-01 7.64e+02
        pdb=" CD  GLN D  41 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE1 GLN D  41 "   -0.188 2.00e-02 2.50e+03
        pdb=" NE2 GLN D  41 "   -0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN D  41 "   -0.339 2.00e-02 2.50e+03
        pdb="HE22 GLN D  41 "    0.342 2.00e-02 2.50e+03
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.33: 1843
        2.33 -     2.90: 16264
        2.90 -     3.47: 16681
        3.47 -     4.03: 26517
        4.03 -     4.60: 36183
  Nonbonded interactions: 97488
  Sorted by model distance:
  nonbonded pdb=" HG1 THR D  75 "
            pdb=" O   SER C  92 "
     model   vdw
     1.764 2.450
  nonbonded pdb=" O   SER D  92 "
            pdb=" HG1 THR E  75 "
     model   vdw
     1.764 2.450
  nonbonded pdb=" HG1 THR B  75 "
            pdb=" O   SER A  92 "
     model   vdw
     1.765 2.450
  nonbonded pdb=" HG1 THR C  75 "
            pdb=" O   SER B  92 "
     model   vdw
     1.765 2.450
  nonbonded pdb=" O   SER E  92 "
            pdb=" HG1 THR F  75 "
     model   vdw
     1.765 2.450
  ... (remaining 97483 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  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:             0.140
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.620
  Find NCS groups from input model:        0.110
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
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      :  0.013   0.046   3703  Z= 0.903
  Angle     :  2.259   9.399   5024  Z= 1.593
  Chirality :  0.116   0.365    576
  Planarity :  0.012   0.045    654
  Dihedral  : 14.226  52.366   1290
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  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: -4.29 (0.28), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.007   TRP A  34 
 HIS   0.003   0.002   HIS E  96 
 PHE   0.018   0.007   PHE A  99 
 TYR   0.028   0.006   TYR C  86 
 ARG   0.001   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14092 (  170)
  hydrogen bonds       : angle       8.17674 (  510)
  SS BOND              : bond        0.04181 (    1)
  SS BOND              : angle       3.70323 (    2)
  covalent geometry    : bond        0.01288 ( 3702)
  covalent geometry    : angle       2.25793 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   30 TYR cc_start: 0.8351 (m-10) cc_final: 0.7753 (m-80)
REVERT: D   91 ASP cc_start: 0.8943 (t0) cc_final: 0.8568 (t70)
REVERT: E   35 TYR cc_start: 0.7139 (m-80) cc_final: 0.6712 (m-80)
REVERT: E   88 ASN cc_start: 0.8870 (m-40) cc_final: 0.8257 (m110)
REVERT: F   48 PHE cc_start: 0.8095 (m-80) cc_final: 0.6652 (p90)
REVERT: F   84 ASP cc_start: 0.8010 (t0) cc_final: 0.7226 (m-30)
REVERT: F   88 ASN cc_start: 0.7734 (m-40) cc_final: 0.7354 (m-40)
REVERT: F   90 ARG cc_start: 0.7610 (ttp80) cc_final: 0.6871 (ttp-170)
REVERT: F  103 THR cc_start: 0.7830 (m) cc_final: 0.7580 (t)
REVERT: C   17 THR cc_start: 0.8887 (m) cc_final: 0.8554 (t)
REVERT: C   34 TRP cc_start: 0.7715 (t-100) cc_final: 0.6109 (t-100)
REVERT: B   34 TRP cc_start: 0.7048 (t-100) cc_final: 0.5752 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.4996
  time to fit residues: 96.4181
Evaluate side-chains
  108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D  95 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.140359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.133813 restraints weight = 16949.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 2.11
r_work: 0.3966 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3857 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.5236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3703  Z= 0.170
  Angle     :  0.705   5.673   5024  Z= 0.389
  Chirality :  0.049   0.141    576
  Planarity :  0.006   0.041    654
  Dihedral  :  6.825  19.915    522
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.41 %
    Favored  : 80.51 %
  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: -3.94 (0.29), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  34 
 HIS   0.001   0.001   HIS E  96 
 PHE   0.011   0.001   PHE E  99 
 TYR   0.023   0.003   TYR E  86 
 ARG   0.005   0.001   ARG F  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02591 (  170)
  hydrogen bonds       : angle       5.84003 (  510)
  SS BOND              : bond        0.00557 (    1)
  SS BOND              : angle       0.65374 (    2)
  covalent geometry    : bond        0.00378 ( 3702)
  covalent geometry    : angle       0.70501 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   90 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8180 (ttp-170)
REVERT: F   48 PHE cc_start: 0.8209 (m-80) cc_final: 0.6459 (p90)
REVERT: B   30 TYR cc_start: 0.8843 (m-10) cc_final: 0.8323 (m-10)
REVERT: B   34 TRP cc_start: 0.7882 (t-100) cc_final: 0.6739 (t-100)
REVERT: A   23 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7570 (tm-30)
REVERT: A   28 ARG cc_start: 0.6945 (pmt-80) cc_final: 0.6718 (pmt-80)
REVERT: A   82 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7506 (mt-10)
  outliers start: 12
  outliers final: 10
  residues processed: 113
  average time/residue: 0.3209
  time to fit residues: 44.0802
Evaluate side-chains
  98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  106 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
F  88 ASN
F  96 HIS
A  36 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.121782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.115671 restraints weight = 17879.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 1.97
r_work: 0.3738 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.7025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3703  Z= 0.208
  Angle     :  0.695   5.654   5024  Z= 0.382
  Chirality :  0.048   0.122    576
  Planarity :  0.005   0.037    654
  Dihedral  :  6.544  18.028    522
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.72 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.78 (0.29), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  34 
 HIS   0.003   0.002   HIS D  96 
 PHE   0.012   0.002   PHE B  99 
 TYR   0.019   0.003   TYR F  85 
 ARG   0.004   0.001   ARG C  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02498 (  170)
  hydrogen bonds       : angle       5.30294 (  510)
  SS BOND              : bond        0.01231 (    1)
  SS BOND              : angle       1.44580 (    2)
  covalent geometry    : bond        0.00465 ( 3702)
  covalent geometry    : angle       0.69454 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.561 
Fit side-chains
REVERT: D   30 TYR cc_start: 0.8861 (m-10) cc_final: 0.8260 (m-10)
REVERT: E   48 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7300 (m-80)
REVERT: E   97 GLN cc_start: 0.8784 (mt0) cc_final: 0.8579 (mt0)
REVERT: F   30 TYR cc_start: 0.8524 (m-10) cc_final: 0.8195 (m-80)
REVERT: F   48 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6339 (p90)
REVERT: C   25 ASP cc_start: 0.7700 (p0) cc_final: 0.7405 (p0)
REVERT: A   23 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8184 (tt0)
REVERT: A   80 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7523 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2872
  time to fit residues: 38.1714
Evaluate side-chains
  92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain A residue   17 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.121402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.115455 restraints weight = 18066.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 1.95
r_work: 0.3749 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3648 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.7584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3703  Z= 0.164
  Angle     :  0.631   4.769   5024  Z= 0.345
  Chirality :  0.047   0.123    576
  Planarity :  0.004   0.032    654
  Dihedral  :  6.308  17.636    522
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.95 %
    Favored  : 78.72 %
  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: -3.57 (0.29), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  34 
 HIS   0.003   0.001   HIS A  96 
 PHE   0.007   0.001   PHE B  99 
 TYR   0.019   0.002   TYR F  85 
 ARG   0.002   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02008 (  170)
  hydrogen bonds       : angle       5.13468 (  510)
  SS BOND              : bond        0.00919 (    1)
  SS BOND              : angle       1.05364 (    2)
  covalent geometry    : bond        0.00364 ( 3702)
  covalent geometry    : angle       0.63091 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.524 
Fit side-chains
REVERT: D   30 TYR cc_start: 0.8859 (m-10) cc_final: 0.8455 (m-10)
REVERT: E   31 SER cc_start: 0.9275 (t) cc_final: 0.8990 (p)
REVERT: E   48 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7424 (m-80)
REVERT: F   48 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.6213 (p90)
REVERT: C   48 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7246 (m-80)
REVERT: B   48 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7876 (m-80)
REVERT: A   19 ARG cc_start: 0.6051 (mmp-170) cc_final: 0.5463 (mmp-170)
REVERT: A   23 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8032 (tt0)
REVERT: A   80 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7537 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 97
  average time/residue: 0.2668
  time to fit residues: 33.0309
Evaluate side-chains
  99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain A residue   17 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0970
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
C  96 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.119796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.113905 restraints weight = 18059.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 1.93
r_work: 0.3731 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.8070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3703  Z= 0.172
  Angle     :  0.625   5.132   5024  Z= 0.341
  Chirality :  0.046   0.123    576
  Planarity :  0.004   0.031    654
  Dihedral  :  6.235  18.935    522
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 18.97 %
    Favored  : 76.92 %
  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: -3.42 (0.29), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  34 
 HIS   0.004   0.001   HIS A  96 
 PHE   0.008   0.001   PHE B  99 
 TYR   0.018   0.002   TYR F  85 
 ARG   0.002   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02045 (  170)
  hydrogen bonds       : angle       4.97255 (  510)
  SS BOND              : bond        0.00953 (    1)
  SS BOND              : angle       1.11064 (    2)
  covalent geometry    : bond        0.00386 ( 3702)
  covalent geometry    : angle       0.62471 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: D   30 TYR cc_start: 0.8886 (m-10) cc_final: 0.8397 (m-10)
REVERT: D   34 TRP cc_start: 0.7920 (t-100) cc_final: 0.7688 (t-100)
REVERT: D   80 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7778 (mt-10)
REVERT: E   31 SER cc_start: 0.9279 (t) cc_final: 0.9047 (p)
REVERT: E   48 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7438 (m-80)
REVERT: F   48 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6124 (p90)
REVERT: C   25 ASP cc_start: 0.7672 (p0) cc_final: 0.7274 (p0)
REVERT: C   30 TYR cc_start: 0.9058 (m-10) cc_final: 0.8775 (m-80)
REVERT: C   48 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7239 (m-80)
REVERT: A   19 ARG cc_start: 0.6145 (mmp-170) cc_final: 0.4832 (mmp-170)
  outliers start: 16
  outliers final: 9
  residues processed: 94
  average time/residue: 0.2362
  time to fit residues: 28.9559
Evaluate side-chains
  92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain A residue   73 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.118589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.112749 restraints weight = 18125.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.90
r_work: 0.3709 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.8342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3703  Z= 0.200
  Angle     :  0.642   5.113   5024  Z= 0.351
  Chirality :  0.047   0.120    576
  Planarity :  0.004   0.030    654
  Dihedral  :  6.271  17.031    522
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.74 %
    Favored  : 75.64 %
  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: -3.38 (0.29), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  34 
 HIS   0.003   0.001   HIS A  96 
 PHE   0.008   0.001   PHE B  99 
 TYR   0.020   0.003   TYR B  35 
 ARG   0.003   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02065 (  170)
  hydrogen bonds       : angle       4.91987 (  510)
  SS BOND              : bond        0.01120 (    1)
  SS BOND              : angle       1.26335 (    2)
  covalent geometry    : bond        0.00450 ( 3702)
  covalent geometry    : angle       0.64155 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: D   30 TYR cc_start: 0.8955 (m-10) cc_final: 0.8601 (m-10)
REVERT: E   31 SER cc_start: 0.9285 (t) cc_final: 0.9043 (p)
REVERT: E   48 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7521 (m-80)
REVERT: F   48 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.6051 (p90)
REVERT: C   25 ASP cc_start: 0.7818 (p0) cc_final: 0.7458 (p0)
REVERT: C   34 TRP cc_start: 0.8883 (OUTLIER) cc_final: 0.8189 (t60)
REVERT: C   48 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7255 (m-80)
REVERT: A   19 ARG cc_start: 0.6069 (mmp-170) cc_final: 0.4698 (mmp-170)
REVERT: A   48 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.6572 (m-80)
REVERT: A   80 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7717 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 93
  average time/residue: 0.2640
  time to fit residues: 31.7775
Evaluate side-chains
  96 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   34 TRP
Chi-restraints excluded: chain C residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue   95 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  96 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.117524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.111719 restraints weight = 17901.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.87
r_work: 0.3715 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.8495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3703  Z= 0.191
  Angle     :  0.629   5.346   5024  Z= 0.345
  Chirality :  0.046   0.122    576
  Planarity :  0.004   0.029    654
  Dihedral  :  6.258  18.005    522
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.77 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.33 (0.29), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B  34 
 HIS   0.002   0.001   HIS B  96 
 PHE   0.007   0.001   PHE B  99 
 TYR   0.021   0.003   TYR C  30 
 ARG   0.003   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02115 (  170)
  hydrogen bonds       : angle       4.89788 (  510)
  SS BOND              : bond        0.01016 (    1)
  SS BOND              : angle       1.17220 (    2)
  covalent geometry    : bond        0.00429 ( 3702)
  covalent geometry    : angle       0.62906 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
REVERT: D   30 TYR cc_start: 0.8933 (m-10) cc_final: 0.8501 (m-10)
REVERT: E   31 SER cc_start: 0.9295 (t) cc_final: 0.9038 (p)
REVERT: E   48 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7590 (m-80)
REVERT: F   23 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8727 (tt0)
REVERT: F   48 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.6011 (p90)
REVERT: C   25 ASP cc_start: 0.7823 (p0) cc_final: 0.7398 (p0)
REVERT: C   30 TYR cc_start: 0.9004 (m-10) cc_final: 0.8736 (m-80)
REVERT: C   34 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8076 (t60)
REVERT: C   48 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7290 (m-80)
REVERT: B   68 ASN cc_start: 0.6332 (OUTLIER) cc_final: 0.5748 (m-40)
REVERT: A   19 ARG cc_start: 0.5669 (mmp-170) cc_final: 0.4189 (mmp-170)
REVERT: A   34 TRP cc_start: 0.6005 (t60) cc_final: 0.5628 (t60)
REVERT: A   48 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6581 (m-80)
REVERT: A   80 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7748 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 91
  average time/residue: 0.2816
  time to fit residues: 32.9648
Evaluate side-chains
  94 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain F residue   23 GLN
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   34 TRP
Chi-restraints excluded: chain C residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue   95 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 1 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.120383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.114535 restraints weight = 17999.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 1.90
r_work: 0.3762 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3664 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.8580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3703  Z= 0.135
  Angle     :  0.595   4.855   5024  Z= 0.326
  Chirality :  0.046   0.126    576
  Planarity :  0.004   0.029    654
  Dihedral  :  6.127  17.757    522
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 21.03 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.27 (0.30), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.23), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D  34 
 HIS   0.002   0.001   HIS B  96 
 PHE   0.005   0.001   PHE B  99 
 TYR   0.018   0.002   TYR C  30 
 ARG   0.003   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01972 (  170)
  hydrogen bonds       : angle       4.80724 (  510)
  SS BOND              : bond        0.00716 (    1)
  SS BOND              : angle       0.76049 (    2)
  covalent geometry    : bond        0.00307 ( 3702)
  covalent geometry    : angle       0.59492 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: D   30 TYR cc_start: 0.8932 (m-10) cc_final: 0.8521 (m-10)
REVERT: E   31 SER cc_start: 0.9308 (t) cc_final: 0.9078 (p)
REVERT: E   48 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7702 (m-80)
REVERT: F   48 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.6001 (p90)
REVERT: C   25 ASP cc_start: 0.7831 (p0) cc_final: 0.7415 (p0)
REVERT: C   30 TYR cc_start: 0.8987 (m-10) cc_final: 0.8738 (m-80)
REVERT: C   34 TRP cc_start: 0.8809 (OUTLIER) cc_final: 0.8051 (t60)
REVERT: C   48 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7280 (m-80)
REVERT: A   19 ARG cc_start: 0.5803 (mmp-170) cc_final: 0.4369 (mmp-170)
REVERT: A   34 TRP cc_start: 0.6030 (t60) cc_final: 0.5786 (t60)
REVERT: A   48 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.6449 (m-80)
REVERT: A   80 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7775 (mt-10)
  outliers start: 17
  outliers final: 9
  residues processed: 92
  average time/residue: 0.2415
  time to fit residues: 28.9375
Evaluate side-chains
  93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   34 TRP
Chi-restraints excluded: chain C residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain A residue   48 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 37 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.121700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.115852 restraints weight = 18084.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 1.89
r_work: 0.3769 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3669 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.8663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3703  Z= 0.139
  Angle     :  0.587   5.078   5024  Z= 0.321
  Chirality :  0.046   0.132    576
  Planarity :  0.003   0.028    654
  Dihedral  :  6.029  17.394    522
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.28 %
    Favored  : 74.87 %
  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: -3.25 (0.30), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.23), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D  34 
 HIS   0.002   0.001   HIS B  96 
 PHE   0.005   0.001   PHE B  99 
 TYR   0.017   0.002   TYR F  85 
 ARG   0.003   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01914 (  170)
  hydrogen bonds       : angle       4.71543 (  510)
  SS BOND              : bond        0.00760 (    1)
  SS BOND              : angle       0.89338 (    2)
  covalent geometry    : bond        0.00315 ( 3702)
  covalent geometry    : angle       0.58690 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: D   30 TYR cc_start: 0.8953 (m-10) cc_final: 0.8537 (m-10)
REVERT: E   31 SER cc_start: 0.9280 (t) cc_final: 0.9060 (p)
REVERT: E   48 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7648 (m-80)
REVERT: F   48 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.5976 (p90)
REVERT: C   25 ASP cc_start: 0.7775 (p0) cc_final: 0.7368 (p0)
REVERT: C   30 TYR cc_start: 0.9012 (m-10) cc_final: 0.8760 (m-80)
REVERT: C   34 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.7970 (t60)
REVERT: C   48 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7252 (m-80)
REVERT: C   91 ASP cc_start: 0.8644 (t0) cc_final: 0.8257 (t70)
REVERT: A   19 ARG cc_start: 0.5765 (mmp-170) cc_final: 0.4329 (mmp-170)
REVERT: A   34 TRP cc_start: 0.6128 (t60) cc_final: 0.5820 (t60)
REVERT: A   48 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.6414 (m-80)
REVERT: A   80 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7795 (mt-10)
REVERT: A   84 ASP cc_start: 0.7345 (m-30) cc_final: 0.5958 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 93
  average time/residue: 0.2389
  time to fit residues: 28.9276
Evaluate side-chains
  93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   34 TRP
Chi-restraints excluded: chain C residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   89 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.119657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.113842 restraints weight = 18155.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 1.87
r_work: 0.3731 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3634 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.8727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3703  Z= 0.177
  Angle     :  0.617   5.426   5024  Z= 0.337
  Chirality :  0.046   0.134    576
  Planarity :  0.004   0.027    654
  Dihedral  :  6.118  17.266    522
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.79 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.27 (0.30), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.23), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  34 
 HIS   0.002   0.001   HIS B  96 
 PHE   0.006   0.001   PHE B  99 
 TYR   0.016   0.002   TYR F  85 
 ARG   0.003   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02070 (  170)
  hydrogen bonds       : angle       4.73401 (  510)
  SS BOND              : bond        0.00961 (    1)
  SS BOND              : angle       1.02440 (    2)
  covalent geometry    : bond        0.00400 ( 3702)
  covalent geometry    : angle       0.61638 ( 5022)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: D   30 TYR cc_start: 0.8967 (m-10) cc_final: 0.8596 (m-10)
REVERT: E   31 SER cc_start: 0.9273 (t) cc_final: 0.9020 (p)
REVERT: E   48 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7751 (m-80)
REVERT: F   48 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.5978 (p90)
REVERT: F   90 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7806 (ttp-170)
REVERT: C   25 ASP cc_start: 0.7810 (p0) cc_final: 0.7403 (p0)
REVERT: C   30 TYR cc_start: 0.8993 (m-10) cc_final: 0.8746 (m-80)
REVERT: C   34 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.7836 (t60)
REVERT: C   48 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7646 (m-80)
REVERT: A   19 ARG cc_start: 0.5809 (mmp-170) cc_final: 0.4320 (mmp80)
REVERT: A   34 TRP cc_start: 0.6067 (t60) cc_final: 0.5757 (t60)
REVERT: A   48 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7362 (m-80)
REVERT: A   80 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7745 (mt-10)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.2936
  time to fit residues: 32.5820
Evaluate side-chains
  93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain E residue   34 TRP
Chi-restraints excluded: chain E residue   48 PHE
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   48 PHE
Chi-restraints excluded: chain C residue   34 TRP
Chi-restraints excluded: chain C residue   48 PHE
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   89 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.120997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.115164 restraints weight = 17958.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 1.89
r_work: 0.3767 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.8781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3703  Z= 0.146
  Angle     :  0.593   5.099   5024  Z= 0.324
  Chirality :  0.046   0.124    576
  Planarity :  0.003   0.026    654
  Dihedral  :  6.058  17.031    522
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.54 %
    Favored  : 74.87 %
  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: -3.26 (0.30), residues: 462
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.23), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  34 
 HIS   0.002   0.001   HIS B  96 
 PHE   0.005   0.001   PHE B  99 
 TYR   0.016   0.002   TYR F  85 
 ARG   0.003   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01970 (  170)
  hydrogen bonds       : angle       4.69050 (  510)
  SS BOND              : bond        0.00768 (    1)
  SS BOND              : angle       0.86060 (    2)
  covalent geometry    : bond        0.00331 ( 3702)
  covalent geometry    : angle       0.59271 ( 5022)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4759.45 seconds
wall clock time: 81 minutes 53.13 seconds (4913.13 seconds total)