Starting phenix.real_space_refine
on Tue Mar  3 12:10:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eqs_28544/03_2026/8eqs_28544_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eqs_28544/03_2026/8eqs_28544.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eqs_28544/03_2026/8eqs_28544_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eqs_28544/03_2026/8eqs_28544_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eqs_28544/03_2026/8eqs_28544.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eqs_28544/03_2026/8eqs_28544.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      20      5.16       5
     C    2406      2.51       5
     N     570      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3654
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1573
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 3, 'TRANS': 188}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 229
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'PEE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 26
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 0.99, per 1000 atoms: 0.27
  Number of scatterers: 3654
  At special positions: 0
  Unit cell: (73.428, 64.988, 89.464, 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      20     16.00
     P       2     15.00
     O     656      8.00
     N     570      7.00
     C    2406      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.31
  Conformation dependent library (CDL) restraints added in 134.4 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  824

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 2 sheets defined
      53.9% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 61
      removed outlier: 3.553A  pdb=" N   VAL A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 100
      removed outlier: 3.600A  pdb=" N   LEU A  71 " --> pdb=" O   LYS A  67 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A  72 " --> pdb=" O   ARG A  68 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN A  78 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 134
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 219 through 224
    Processing helix  chain 'B' and resid 43 through 61
      removed outlier: 3.553A  pdb=" N   VAL B  47 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 100
      removed outlier: 3.600A  pdb=" N   LEU B  71 " --> pdb=" O   LYS B  67 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA B  72 " --> pdb=" O   ARG B  68 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B  78 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 134
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 219 through 224
    Processing helix  chain 'C' and resid 26 through 48
      Proline residue:  C  34  - end of helix
      removed outlier: 4.378A  pdb=" N   GLN C  37 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 48
      Proline residue:  D  34  - end of helix
      removed outlier: 4.378A  pdb=" N   GLN D  37 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160
      removed outlier: 5.812A  pdb=" N   HIS A 150 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   TYR A 200 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   ILE A 232 " --> pdb=" O   GLU A 215 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   THR A 217 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE A 230 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160
      removed outlier: 5.812A  pdb=" N   HIS B 150 " --> pdb=" O   TYR B 200 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   TYR B 200 " --> pdb=" O   HIS B 150 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   ILE B 232 " --> pdb=" O   GLU B 215 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   THR B 217 " --> pdb=" O   PHE B 230 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE B 230 " --> pdb=" O   THR B 217 " (cutoff:3.500A)

    234 hydrogen bonds defined for protein.
    678 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: 0.52

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 566
        1.31 -     1.44: 1140
        1.44 -     1.56: 2016
        1.56 -     1.69: 4
        1.69 -     1.81: 24
  Bond restraints: 3750
  Sorted by residual:
  bond pdb=" C10 PEE B 401 "
       pdb=" O2  PEE B 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.424 -0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" C10 PEE A 401 "
       pdb=" O2  PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.423 -0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C30 PEE A 401 "
       pdb=" O3  PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.411 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" C30 PEE B 401 "
       pdb=" O3  PEE B 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.410 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C10 PEE A 401 "
       pdb=" C11 PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.504  1.549 -0.045 2.00e-02 2.50e+03 5.17e+00
  ... (remaining 3745 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 5049
        3.37 -     6.74: 29
        6.74 -    10.11: 4
       10.11 -    13.48: 2
       13.48 -    16.85: 2
  Bond angle restraints: 5086
  Sorted by residual:
  angle pdb=" O3P PEE B 401 "
        pdb=" P   PEE B 401 "
        pdb=" O4P PEE B 401 "
      ideal   model   delta    sigma   weight residual
      92.91  109.76  -16.85 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" O3P PEE A 401 "
        pdb=" P   PEE A 401 "
        pdb=" O4P PEE A 401 "
      ideal   model   delta    sigma   weight residual
      92.91  109.76  -16.85 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" O1P PEE A 401 "
        pdb=" P   PEE A 401 "
        pdb=" O2P PEE A 401 "
      ideal   model   delta    sigma   weight residual
     119.43  109.24   10.19 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" O1P PEE B 401 "
        pdb=" P   PEE B 401 "
        pdb=" O2P PEE B 401 "
      ideal   model   delta    sigma   weight residual
     119.43  109.24   10.19 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" C11 PEE B 401 "
        pdb=" C10 PEE B 401 "
        pdb=" O2  PEE B 401 "
      ideal   model   delta    sigma   weight residual
     111.70  120.37   -8.67 3.00e+00 1.11e-01 8.35e+00
  ... (remaining 5081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.50: 2070
       31.50 -    63.00: 58
       63.00 -    94.50: 12
       94.50 -   126.00: 0
      126.00 -   157.50: 6
  Dihedral angle restraints: 2146
    sinusoidal: 858
      harmonic: 1288
  Sorted by residual:
  dihedral pdb=" C3  PEE A 401 "
           pdb=" C1  PEE A 401 "
           pdb=" C2  PEE A 401 "
           pdb=" O3P PEE A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73  -94.77  157.50     1      3.00e+01 1.11e-03 2.05e+01
  dihedral pdb=" C3  PEE B 401 "
           pdb=" C1  PEE B 401 "
           pdb=" C2  PEE B 401 "
           pdb=" O3P PEE B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73  -94.74  157.47     1      3.00e+01 1.11e-03 2.05e+01
  dihedral pdb=" C2  PEE A 401 "
           pdb=" C10 PEE A 401 "
           pdb=" O2  PEE A 401 "
           pdb=" O4  PEE A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
       2.73 -153.71  156.44     1      3.00e+01 1.11e-03 2.04e+01
  ... (remaining 2143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 485
       0.063 -    0.125: 61
       0.125 -    0.188: 8
       0.188 -    0.251: 0
       0.251 -    0.314: 2
  Chirality restraints: 556
  Sorted by residual:
  chirality pdb=" C2  PEE B 401 "
            pdb=" C1  PEE B 401 "
            pdb=" C3  PEE B 401 "
            pdb=" O2  PEE B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.64    0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C2  PEE A 401 "
            pdb=" C1  PEE A 401 "
            pdb=" C3  PEE A 401 "
            pdb=" O2  PEE A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.64    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CA  ILE A 186 "
            pdb=" N   ILE A 186 "
            pdb=" C   ILE A 186 "
            pdb=" CB  ILE A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 553 not shown)

  Planarity restraints: 622
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  80 "    0.007 2.00e-02 2.50e+03   1.31e-02 1.73e+00
        pdb=" C   ILE A  80 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ILE A  80 "    0.009 2.00e-02 2.50e+03
        pdb=" N   CYS A  81 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  80 "   -0.007 2.00e-02 2.50e+03   1.31e-02 1.70e+00
        pdb=" C   ILE B  80 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ILE B  80 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   CYS B  81 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  82 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.66e+00
        pdb=" C   ASN A  82 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ASN A  82 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU A  83 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 619 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 532
        2.76 -     3.29: 3664
        3.29 -     3.83: 6165
        3.83 -     4.36: 7026
        4.36 -     4.90: 12093
  Nonbonded interactions: 29480
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  58 "
            pdb=" NE2 GLN B 116 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" NE2 GLN A 116 "
            pdb=" OG  SER B  58 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OH  TYR A 154 "
            pdb=" OE2 GLU A 191 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OH  TYR B 154 "
            pdb=" OE2 GLU B 191 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OE1 GLU C  38 "
            pdb=" ND2 ASN C  42 "
     model   vdw
     2.258 3.120
  ... (remaining 29475 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.460
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
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      :  0.005   0.092   3750  Z= 0.251
  Angle     :  0.737  16.848   5086  Z= 0.344
  Chirality :  0.045   0.314    556
  Planarity :  0.003   0.024    622
  Dihedral  : 19.168 157.496   1322
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.38), residues: 426
  helix:  1.25 (0.35), residues: 198
  sheet: -0.34 (0.60), residues: 82
  loop : -1.49 (0.38), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  51 
 TYR   0.004   0.001   TYR A  91 
 PHE   0.012   0.001   PHE A  56 
 TRP   0.019   0.002   TRP A 131 
 HIS   0.002   0.001   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 3750)
  covalent geometry    : angle       0.73687 ( 5086)
  hydrogen bonds       : bond        0.19056 (  234)
  hydrogen bonds       : angle       7.32231 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.8227 (m100) cc_final: 0.7956 (m100)
REVERT: A   67 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8474 (mmmm)
REVERT: A   87 PHE cc_start: 0.8744 (t80) cc_final: 0.8543 (t80)
REVERT: A  130 CYS cc_start: 0.8322 (p) cc_final: 0.7785 (p)
REVERT: A  136 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7438 (mmtt)
REVERT: A  152 HIS cc_start: 0.7813 (t-90) cc_final: 0.7579 (t70)
REVERT: A  198 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8446 (mmmm)
REVERT: B   41 LEU cc_start: 0.8950 (mm) cc_final: 0.8687 (mt)
REVERT: B   45 TRP cc_start: 0.8227 (m100) cc_final: 0.7955 (m100)
REVERT: B   67 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8478 (mmmm)
REVERT: B   87 PHE cc_start: 0.8753 (t80) cc_final: 0.8545 (t80)
REVERT: B  130 CYS cc_start: 0.8324 (p) cc_final: 0.7783 (p)
REVERT: B  136 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7446 (mmtt)
REVERT: B  152 HIS cc_start: 0.7806 (t-90) cc_final: 0.7576 (t70)
REVERT: B  198 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8446 (mmmm)
REVERT: C   25 PHE cc_start: 0.4370 (m-10) cc_final: 0.3971 (m-10)
REVERT: C   42 ASN cc_start: 0.8145 (m-40) cc_final: 0.7757 (m-40)
REVERT: D   25 PHE cc_start: 0.4364 (m-10) cc_final: 0.3958 (m-10)
REVERT: D   42 ASN cc_start: 0.8143 (m-40) cc_final: 0.7756 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0782
  time to fit residues: 12.8402
Evaluate side-chains
  121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  57 GLN
A  82 ASN
A 161 ASN
A 185 GLN
B  57 GLN
B  82 ASN
B 161 ASN
B 185 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.119272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.089745 restraints weight = 5955.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 3.14
r_work: 0.2986 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3750  Z= 0.153
  Angle     :  0.500   4.397   5086  Z= 0.278
  Chirality :  0.042   0.145    556
  Planarity :  0.003   0.027    622
  Dihedral  : 16.877 150.005    516
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.86 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.39), residues: 426
  helix:  2.52 (0.33), residues: 212
  sheet: -0.40 (0.57), residues: 88
  loop : -1.09 (0.46), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  68 
 TYR   0.015   0.001   TYR A  74 
 PHE   0.010   0.001   PHE B  56 
 TRP   0.012   0.001   TRP A 149 
 HIS   0.004   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3750)
  covalent geometry    : angle       0.50033 ( 5086)
  hydrogen bonds       : bond        0.03506 (  234)
  hydrogen bonds       : angle       4.50469 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8413 (mmmm)
REVERT: A  130 CYS cc_start: 0.8697 (p) cc_final: 0.7897 (p)
REVERT: A  193 ARG cc_start: 0.8922 (ptm160) cc_final: 0.8524 (ptm160)
REVERT: A  198 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8594 (mmmm)
REVERT: B   43 PHE cc_start: 0.7997 (m-10) cc_final: 0.7741 (m-80)
REVERT: B   67 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8425 (mmmm)
REVERT: B  130 CYS cc_start: 0.8702 (p) cc_final: 0.7906 (p)
REVERT: B  193 ARG cc_start: 0.8925 (ptm160) cc_final: 0.8526 (ptm160)
REVERT: B  198 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8585 (mmmm)
REVERT: C   42 ASN cc_start: 0.8527 (m-40) cc_final: 0.8093 (m-40)
REVERT: D   42 ASN cc_start: 0.8525 (m-40) cc_final: 0.8094 (m-40)
  outliers start: 8
  outliers final: 4
  residues processed: 133
  average time/residue: 0.0770
  time to fit residues: 12.2187
Evaluate side-chains
  122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 118
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
B  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.117226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.087501 restraints weight = 5894.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.15
r_work: 0.2926 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3750  Z= 0.153
  Angle     :  0.497   4.333   5086  Z= 0.274
  Chirality :  0.042   0.141    556
  Planarity :  0.003   0.027    622
  Dihedral  : 16.108 145.141    516
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 14.95 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.40), residues: 426
  helix:  2.85 (0.33), residues: 222
  sheet: -0.55 (0.55), residues: 88
  loop : -1.48 (0.46), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  68 
 TYR   0.008   0.001   TYR B 141 
 PHE   0.009   0.001   PHE A  56 
 TRP   0.010   0.001   TRP B 149 
 HIS   0.003   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3750)
  covalent geometry    : angle       0.49678 ( 5086)
  hydrogen bonds       : bond        0.03247 (  234)
  hydrogen bonds       : angle       4.29937 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  109 TYR cc_start: 0.9016 (m-80) cc_final: 0.8680 (m-80)
REVERT: A  128 TRP cc_start: 0.8546 (t60) cc_final: 0.7994 (t60)
REVERT: A  130 CYS cc_start: 0.8786 (p) cc_final: 0.8005 (p)
REVERT: A  150 HIS cc_start: 0.7684 (m-70) cc_final: 0.7182 (m-70)
REVERT: A  155 ASP cc_start: 0.8269 (m-30) cc_final: 0.7627 (t0)
REVERT: A  185 GLN cc_start: 0.9081 (tm130) cc_final: 0.8789 (tm130)
REVERT: A  193 ARG cc_start: 0.8961 (ptm160) cc_final: 0.8632 (ptm160)
REVERT: A  198 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8579 (mmmm)
REVERT: B   43 PHE cc_start: 0.8029 (m-10) cc_final: 0.7786 (m-80)
REVERT: B  109 TYR cc_start: 0.9006 (m-80) cc_final: 0.8672 (m-80)
REVERT: B  128 TRP cc_start: 0.8536 (t60) cc_final: 0.7982 (t60)
REVERT: B  130 CYS cc_start: 0.8785 (p) cc_final: 0.8005 (p)
REVERT: B  150 HIS cc_start: 0.7688 (m-70) cc_final: 0.7184 (m-70)
REVERT: B  155 ASP cc_start: 0.8268 (m-30) cc_final: 0.7635 (t0)
REVERT: B  185 GLN cc_start: 0.9093 (tm130) cc_final: 0.8803 (tm130)
REVERT: B  193 ARG cc_start: 0.8964 (ptm160) cc_final: 0.8632 (ptm160)
REVERT: B  198 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8588 (mmmm)
REVERT: C   29 ARG cc_start: 0.6995 (ttt-90) cc_final: 0.6559 (mtt-85)
REVERT: C   42 ASN cc_start: 0.8511 (m-40) cc_final: 0.8086 (m-40)
REVERT: D   29 ARG cc_start: 0.7011 (ttt-90) cc_final: 0.6571 (mtt-85)
REVERT: D   42 ASN cc_start: 0.8515 (m-40) cc_final: 0.8089 (m-40)
  outliers start: 12
  outliers final: 6
  residues processed: 126
  average time/residue: 0.0794
  time to fit residues: 11.9469
Evaluate side-chains
  118 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
A 144 ASN
B  82 ASN
B 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.115655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.086434 restraints weight = 5850.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 3.07
r_work: 0.2905 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3750  Z= 0.158
  Angle     :  0.478   4.391   5086  Z= 0.265
  Chirality :  0.041   0.141    556
  Planarity :  0.003   0.026    622
  Dihedral  : 15.839 142.693    516
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.72 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.41), residues: 426
  helix:  2.99 (0.33), residues: 224
  sheet: -0.67 (0.54), residues: 88
  loop : -1.40 (0.47), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  68 
 TYR   0.008   0.001   TYR A 109 
 PHE   0.016   0.001   PHE A 207 
 TRP   0.010   0.001   TRP B 149 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3750)
  covalent geometry    : angle       0.47813 ( 5086)
  hydrogen bonds       : bond        0.02995 (  234)
  hydrogen bonds       : angle       4.25672 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 CYS cc_start: 0.8749 (p) cc_final: 0.7985 (p)
REVERT: A  193 ARG cc_start: 0.8974 (ptm160) cc_final: 0.8610 (ptm160)
REVERT: A  198 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8621 (mmmm)
REVERT: B  130 CYS cc_start: 0.8766 (p) cc_final: 0.8009 (p)
REVERT: B  193 ARG cc_start: 0.8972 (ptm160) cc_final: 0.8605 (ptm160)
REVERT: B  198 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8620 (mmmm)
REVERT: C   42 ASN cc_start: 0.8483 (m-40) cc_final: 0.8044 (m-40)
REVERT: D   42 ASN cc_start: 0.8487 (m-40) cc_final: 0.8049 (m-40)
  outliers start: 9
  outliers final: 7
  residues processed: 115
  average time/residue: 0.0776
  time to fit residues: 10.6679
Evaluate side-chains
  110 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0060
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 213 GLN
B 144 ASN
B 213 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.116738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.087847 restraints weight = 5867.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 3.08
r_work: 0.2926 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3750  Z= 0.126
  Angle     :  0.471   4.360   5086  Z= 0.260
  Chirality :  0.040   0.138    556
  Planarity :  0.002   0.026    622
  Dihedral  : 15.488 140.798    516
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 14.43 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.40), residues: 426
  helix:  2.97 (0.33), residues: 224
  sheet: -0.61 (0.53), residues: 88
  loop : -1.35 (0.48), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.010   0.001   TYR A  74 
 PHE   0.014   0.001   PHE A 207 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3750)
  covalent geometry    : angle       0.47141 ( 5086)
  hydrogen bonds       : bond        0.02892 (  234)
  hydrogen bonds       : angle       4.22274 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.9067 (mmm) cc_final: 0.8697 (mmt)
REVERT: A  130 CYS cc_start: 0.8775 (p) cc_final: 0.8020 (p)
REVERT: A  150 HIS cc_start: 0.7509 (m-70) cc_final: 0.7058 (m-70)
REVERT: A  155 ASP cc_start: 0.8311 (m-30) cc_final: 0.7345 (t0)
REVERT: A  193 ARG cc_start: 0.8982 (ptm160) cc_final: 0.8581 (ptm160)
REVERT: A  198 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8631 (mmmm)
REVERT: B  125 MET cc_start: 0.9066 (mmm) cc_final: 0.8690 (mmt)
REVERT: B  130 CYS cc_start: 0.8784 (p) cc_final: 0.8034 (p)
REVERT: B  150 HIS cc_start: 0.7507 (m-70) cc_final: 0.7046 (m-70)
REVERT: B  155 ASP cc_start: 0.8316 (m-30) cc_final: 0.7348 (t0)
REVERT: B  193 ARG cc_start: 0.8988 (ptm160) cc_final: 0.8585 (ptm160)
REVERT: B  198 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8608 (mmmm)
REVERT: C   42 ASN cc_start: 0.8491 (m-40) cc_final: 0.8056 (m-40)
REVERT: D   42 ASN cc_start: 0.8496 (m-40) cc_final: 0.8063 (m-40)
  outliers start: 12
  outliers final: 7
  residues processed: 120
  average time/residue: 0.0739
  time to fit residues: 10.7278
Evaluate side-chains
  117 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 144 ASN
B  78 GLN
B 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.115716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.087014 restraints weight = 5905.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 3.03
r_work: 0.2907 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3750  Z= 0.146
  Angle     :  0.486   4.460   5086  Z= 0.268
  Chirality :  0.041   0.142    556
  Planarity :  0.003   0.026    622
  Dihedral  : 15.174 140.373    516
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.43 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.40), residues: 426
  helix:  3.06 (0.33), residues: 224
  sheet: -0.61 (0.53), residues: 88
  loop : -1.31 (0.48), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.009   0.001   TYR B  74 
 PHE   0.016   0.001   PHE A 207 
 TRP   0.012   0.001   TRP B 149 
 HIS   0.002   0.000   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3750)
  covalent geometry    : angle       0.48615 ( 5086)
  hydrogen bonds       : bond        0.02849 (  234)
  hydrogen bonds       : angle       4.27290 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.9072 (mmm) cc_final: 0.8676 (mmt)
REVERT: A  130 CYS cc_start: 0.8751 (p) cc_final: 0.7980 (p)
REVERT: A  150 HIS cc_start: 0.7455 (m-70) cc_final: 0.6943 (m-70)
REVERT: A  155 ASP cc_start: 0.8379 (m-30) cc_final: 0.7338 (t0)
REVERT: A  193 ARG cc_start: 0.8967 (ptm160) cc_final: 0.8539 (ptm160)
REVERT: A  198 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8615 (mmmm)
REVERT: B  125 MET cc_start: 0.9070 (mmm) cc_final: 0.8670 (mmt)
REVERT: B  130 CYS cc_start: 0.8760 (p) cc_final: 0.7990 (p)
REVERT: B  150 HIS cc_start: 0.7457 (m-70) cc_final: 0.7176 (m-70)
REVERT: B  193 ARG cc_start: 0.8978 (ptm160) cc_final: 0.8547 (ptm160)
REVERT: B  198 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8653 (mmmm)
REVERT: C   42 ASN cc_start: 0.8446 (m-40) cc_final: 0.8007 (m-40)
REVERT: D   42 ASN cc_start: 0.8454 (m-40) cc_final: 0.8016 (m-40)
  outliers start: 13
  outliers final: 9
  residues processed: 123
  average time/residue: 0.0784
  time to fit residues: 11.5755
Evaluate side-chains
  121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 144 ASN
B  78 GLN
B 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.116299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.087790 restraints weight = 6006.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 3.07
r_work: 0.2929 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3750  Z= 0.118
  Angle     :  0.484   4.728   5086  Z= 0.263
  Chirality :  0.041   0.144    556
  Planarity :  0.002   0.026    622
  Dihedral  : 14.670 140.025    516
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.46 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.40), residues: 426
  helix:  3.07 (0.33), residues: 224
  sheet: -0.61 (0.53), residues: 88
  loop : -1.22 (0.48), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.009   0.001   TYR A  74 
 PHE   0.016   0.001   PHE A 207 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.002   0.000   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3750)
  covalent geometry    : angle       0.48402 ( 5086)
  hydrogen bonds       : bond        0.02774 (  234)
  hydrogen bonds       : angle       4.20461 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.9057 (mmm) cc_final: 0.8673 (mmt)
REVERT: A  130 CYS cc_start: 0.8753 (p) cc_final: 0.7990 (p)
REVERT: A  134 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8405 (mmtt)
REVERT: A  150 HIS cc_start: 0.7390 (m-70) cc_final: 0.7128 (m-70)
REVERT: A  193 ARG cc_start: 0.8985 (ptm160) cc_final: 0.8547 (ptm160)
REVERT: A  198 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8622 (mmmm)
REVERT: B  125 MET cc_start: 0.9063 (mmm) cc_final: 0.8675 (mmt)
REVERT: B  130 CYS cc_start: 0.8762 (p) cc_final: 0.8016 (p)
REVERT: B  150 HIS cc_start: 0.7425 (m-70) cc_final: 0.6987 (m-70)
REVERT: B  155 ASP cc_start: 0.8362 (m-30) cc_final: 0.7243 (t0)
REVERT: B  193 ARG cc_start: 0.8985 (ptm160) cc_final: 0.8543 (ptm160)
REVERT: B  198 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8609 (mmmm)
REVERT: C   42 ASN cc_start: 0.8468 (m-40) cc_final: 0.8035 (m-40)
REVERT: D   42 ASN cc_start: 0.8476 (m-40) cc_final: 0.8048 (m-40)
  outliers start: 11
  outliers final: 8
  residues processed: 123
  average time/residue: 0.0648
  time to fit residues: 9.7113
Evaluate side-chains
  125 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0270
   overall best weight:    0.6642

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.115373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.086949 restraints weight = 5931.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 3.01
r_work: 0.2923 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3750  Z= 0.141
  Angle     :  0.498   5.498   5086  Z= 0.271
  Chirality :  0.041   0.149    556
  Planarity :  0.003   0.027    622
  Dihedral  : 13.958 140.245    516
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.01 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.40), residues: 426
  helix:  3.07 (0.33), residues: 224
  sheet: -0.54 (0.54), residues: 88
  loop : -1.15 (0.48), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.012   0.001   TYR A  74 
 PHE   0.024   0.002   PHE A 207 
 TRP   0.011   0.001   TRP A 149 
 HIS   0.002   0.000   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3750)
  covalent geometry    : angle       0.49828 ( 5086)
  hydrogen bonds       : bond        0.02878 (  234)
  hydrogen bonds       : angle       4.22956 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.9067 (mmm) cc_final: 0.8689 (mmt)
REVERT: A  130 CYS cc_start: 0.8776 (p) cc_final: 0.8033 (p)
REVERT: A  150 HIS cc_start: 0.7441 (m-70) cc_final: 0.7019 (m-70)
REVERT: A  155 ASP cc_start: 0.8429 (m-30) cc_final: 0.7355 (t0)
REVERT: A  193 ARG cc_start: 0.9001 (ptm160) cc_final: 0.8559 (ptm160)
REVERT: A  198 LYS cc_start: 0.8915 (mmtm) cc_final: 0.8623 (mmmm)
REVERT: B  125 MET cc_start: 0.9069 (mmm) cc_final: 0.8679 (mmt)
REVERT: B  130 CYS cc_start: 0.8779 (p) cc_final: 0.8016 (p)
REVERT: B  150 HIS cc_start: 0.7394 (m-70) cc_final: 0.6963 (m-70)
REVERT: B  155 ASP cc_start: 0.8407 (m-30) cc_final: 0.7342 (t0)
REVERT: B  193 ARG cc_start: 0.9001 (ptm160) cc_final: 0.8557 (ptm160)
REVERT: B  198 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8631 (mmmm)
REVERT: C   42 ASN cc_start: 0.8465 (m-40) cc_final: 0.8039 (m-40)
REVERT: D   42 ASN cc_start: 0.8476 (m-40) cc_final: 0.8052 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 122
  average time/residue: 0.0702
  time to fit residues: 10.1899
Evaluate side-chains
  120 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.114223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.085581 restraints weight = 5999.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 3.05
r_work: 0.2895 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3750  Z= 0.166
  Angle     :  0.533   5.901   5086  Z= 0.288
  Chirality :  0.042   0.151    556
  Planarity :  0.003   0.027    622
  Dihedral  : 13.092 136.707    516
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.01 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.40), residues: 426
  helix:  3.05 (0.33), residues: 224
  sheet: -0.45 (0.54), residues: 88
  loop : -1.11 (0.48), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 122 
 TYR   0.010   0.001   TYR B  74 
 PHE   0.025   0.002   PHE A 207 
 TRP   0.011   0.001   TRP A 149 
 HIS   0.002   0.000   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3750)
  covalent geometry    : angle       0.53337 ( 5086)
  hydrogen bonds       : bond        0.03037 (  234)
  hydrogen bonds       : angle       4.28065 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.9098 (mmm) cc_final: 0.8709 (mmt)
REVERT: A  130 CYS cc_start: 0.8784 (p) cc_final: 0.8063 (p)
REVERT: A  150 HIS cc_start: 0.7380 (m-70) cc_final: 0.6900 (m-70)
REVERT: A  155 ASP cc_start: 0.8454 (m-30) cc_final: 0.7361 (t0)
REVERT: A  193 ARG cc_start: 0.9006 (ptm160) cc_final: 0.8568 (ptm160)
REVERT: A  198 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8635 (mmmm)
REVERT: A  209 GLU cc_start: 0.8628 (tt0) cc_final: 0.8376 (tp30)
REVERT: B  125 MET cc_start: 0.9097 (mmm) cc_final: 0.8705 (mmt)
REVERT: B  130 CYS cc_start: 0.8785 (p) cc_final: 0.8086 (p)
REVERT: B  155 ASP cc_start: 0.8445 (m-30) cc_final: 0.8135 (t0)
REVERT: B  193 ARG cc_start: 0.9008 (ptm160) cc_final: 0.8568 (ptm160)
REVERT: B  198 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8650 (mmmm)
REVERT: B  209 GLU cc_start: 0.8648 (tt0) cc_final: 0.8374 (tp30)
REVERT: C   42 ASN cc_start: 0.8480 (m-40) cc_final: 0.8052 (m-40)
REVERT: D   42 ASN cc_start: 0.8483 (m-40) cc_final: 0.8056 (m-40)
  outliers start: 11
  outliers final: 9
  residues processed: 119
  average time/residue: 0.0706
  time to fit residues: 10.1417
Evaluate side-chains
  119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 40 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.115407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.086768 restraints weight = 6006.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 3.07
r_work: 0.2925 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3750  Z= 0.136
  Angle     :  0.514   6.039   5086  Z= 0.279
  Chirality :  0.041   0.151    556
  Planarity :  0.003   0.027    622
  Dihedral  : 12.380 132.915    516
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.01 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.40), residues: 426
  helix:  2.98 (0.33), residues: 224
  sheet: -0.41 (0.54), residues: 88
  loop : -0.99 (0.49), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 122 
 TYR   0.011   0.001   TYR B  74 
 PHE   0.027   0.002   PHE A 207 
 TRP   0.010   0.001   TRP A 149 
 HIS   0.002   0.000   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3750)
  covalent geometry    : angle       0.51426 ( 5086)
  hydrogen bonds       : bond        0.02919 (  234)
  hydrogen bonds       : angle       4.20888 (  678)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.9069 (mmm) cc_final: 0.8664 (mmt)
REVERT: A  130 CYS cc_start: 0.8799 (p) cc_final: 0.8092 (p)
REVERT: A  150 HIS cc_start: 0.7421 (m-70) cc_final: 0.6953 (m-70)
REVERT: A  155 ASP cc_start: 0.8442 (m-30) cc_final: 0.7402 (t0)
REVERT: A  193 ARG cc_start: 0.9016 (ptm160) cc_final: 0.8525 (ptm-80)
REVERT: A  198 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8604 (mmmm)
REVERT: A  209 GLU cc_start: 0.8656 (tt0) cc_final: 0.8345 (tp30)
REVERT: B  125 MET cc_start: 0.9083 (mmm) cc_final: 0.8670 (mmt)
REVERT: B  130 CYS cc_start: 0.8799 (p) cc_final: 0.8096 (p)
REVERT: B  155 ASP cc_start: 0.8424 (m-30) cc_final: 0.8144 (t0)
REVERT: B  193 ARG cc_start: 0.9014 (ptm160) cc_final: 0.8554 (ptm160)
REVERT: B  198 LYS cc_start: 0.8919 (mmtm) cc_final: 0.8627 (mmmm)
REVERT: B  209 GLU cc_start: 0.8670 (tt0) cc_final: 0.8364 (tp30)
REVERT: C   42 ASN cc_start: 0.8473 (m-40) cc_final: 0.8048 (m-40)
REVERT: D   42 ASN cc_start: 0.8491 (m-40) cc_final: 0.8074 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 120
  average time/residue: 0.0764
  time to fit residues: 11.0146
Evaluate side-chains
  121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 2 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.117102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.088482 restraints weight = 5866.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 3.06
r_work: 0.2947 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3750  Z= 0.122
  Angle     :  0.506   6.053   5086  Z= 0.278
  Chirality :  0.042   0.155    556
  Planarity :  0.003   0.027    622
  Dihedral  : 11.727 127.710    516
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 18.30 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.40), residues: 426
  helix:  2.97 (0.33), residues: 224
  sheet: -0.38 (0.54), residues: 88
  loop : -1.02 (0.48), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 122 
 TYR   0.012   0.001   TYR B  74 
 PHE   0.027   0.001   PHE A 207 
 TRP   0.013   0.001   TRP A 149 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3750)
  covalent geometry    : angle       0.50643 ( 5086)
  hydrogen bonds       : bond        0.02904 (  234)
  hydrogen bonds       : angle       4.14616 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1102.56 seconds
wall clock time: 19 minutes 34.14 seconds (1174.14 seconds total)