Starting phenix.real_space_refine
on Wed Sep 17 03:14:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vdf_43148/09_2025/8vdf_43148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vdf_43148/09_2025/8vdf_43148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vdf_43148/09_2025/8vdf_43148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vdf_43148/09_2025/8vdf_43148.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vdf_43148/09_2025/8vdf_43148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vdf_43148/09_2025/8vdf_43148.map"
  }
  resolution = 3.5
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    1637      2.51       5
     N     432      2.21       5
     O     495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2584
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 888
          Classifications: {'peptide': 103}
          Link IDs: {'TRANS': 102}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 935
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 761
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
  Time building chain proxies: 0.89, per 1000 atoms: 0.34
  Number of scatterers: 2584
  At special positions: 0
  Unit cell: (63.8, 67.425, 76.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     495      8.00
     N     432      7.00
     C    1637      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 601 " - pdb=" SG  CYS A 614 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  99 " - pdb=" SG  CYS H 100D" distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  85 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 87.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  594

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 5 sheets defined
      33.1% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 577 through 598
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 614 through 636
    Processing helix  chain 'A' and resid 652 through 657
    Processing helix  chain 'A' and resid 660 through 669
      removed outlier: 3.697A  pdb=" N   VAL A 664 " --> pdb=" O   PHE A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 685
      removed outlier: 3.575A  pdb=" N   TRP A 674 " --> pdb=" O   LYS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 714
      removed outlier: 3.715A  pdb=" N   ILE A 714 " --> pdb=" O   GLU A 710 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.758A  pdb=" N   SER H  87 " --> pdb=" O   ASP H  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 76 through 80
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7
      removed outlier: 4.126A  pdb=" N   LEU H  18 " --> pdb=" O   MET H  82 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR H  79 " --> pdb=" O   SER H  70 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   SER H  70 " --> pdb=" O   TYR H  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59
      removed outlier: 7.162A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY H  33 " --> pdb=" O   GLY H  95 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL H 102 " --> pdb=" O   LYS H  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59
      removed outlier: 7.162A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY H  33 " --> pdb=" O   GLY H  95 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR H  90 " --> pdb=" O   THR H 107 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12
      removed outlier: 4.042A  pdb=" N   MET L  10 " --> pdb=" O   LYS L 102 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   THR L 101 " --> pdb=" O   TYR L  83 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR L  83 " --> pdb=" O   THR L 101 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  35 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLN L  35 " --> pdb=" O   ASP L  82 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP L  32 " --> pdb=" O   VAL L  44 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 21
      removed outlier: 3.554A  pdb=" N   ALA L  18 " --> pdb=" O   ILE L  72 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE L  72 " --> pdb=" O   ALA L  18 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ILE L  20 " --> pdb=" O   LEU L  70 " (cutoff:3.500A)

    116 hydrogen bonds defined for protein.
    327 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: 0.29

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 816
        1.34 -     1.46: 666
        1.46 -     1.58: 1128
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 2640
  Sorted by residual:
  bond pdb=" CB  GLN H   3 "
       pdb=" CG  GLN H   3 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 3.00e-02 1.11e+03 2.24e+00
  bond pdb=" CB  ASN L  63 "
       pdb=" CG  ASN L  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.551 -0.035 2.50e-02 1.60e+03 1.91e+00
  bond pdb=" CG  GLN H   3 "
       pdb=" CD  GLN H   3 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.73e+00
  bond pdb=" C   ILE L  55 "
       pdb=" N   PRO L  56 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.25e-02 6.40e+03 1.71e+00
  bond pdb=" CB  GLN L  16 "
       pdb=" CG  GLN L  16 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.66e+00
  ... (remaining 2635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 3456
        2.20 -     4.40: 84
        4.40 -     6.60: 14
        6.60 -     8.80: 3
        8.80 -    11.00: 2
  Bond angle restraints: 3559
  Sorted by residual:
  angle pdb=" CA  TYR H 100E"
        pdb=" CB  TYR H 100E"
        pdb=" CG  TYR H 100E"
      ideal   model   delta    sigma   weight residual
     113.90  120.99   -7.09 1.80e+00 3.09e-01 1.55e+01
  angle pdb=" C   GLN L  47 "
        pdb=" N   ASP L  48 "
        pdb=" CA  ASP L  48 "
      ideal   model   delta    sigma   weight residual
     121.54  128.71   -7.17 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" CB  MET A 602 "
        pdb=" CG  MET A 602 "
        pdb=" SD  MET A 602 "
      ideal   model   delta    sigma   weight residual
     112.70  123.70  -11.00 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" CB  GLU A 658 "
        pdb=" CG  GLU A 658 "
        pdb=" CD  GLU A 658 "
      ideal   model   delta    sigma   weight residual
     112.60  118.08   -5.48 1.70e+00 3.46e-01 1.04e+01
  angle pdb=" CB  GLN H   3 "
        pdb=" CG  GLN H   3 "
        pdb=" CD  GLN H   3 "
      ideal   model   delta    sigma   weight residual
     112.60  118.08   -5.48 1.70e+00 3.46e-01 1.04e+01
  ... (remaining 3554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.96: 1434
       15.96 -    31.92: 89
       31.92 -    47.88: 20
       47.88 -    63.84: 13
       63.84 -    79.79: 4
  Dihedral angle restraints: 1560
    sinusoidal: 630
      harmonic: 930
  Sorted by residual:
  dihedral pdb=" CB  CYS A 601 "
           pdb=" SG  CYS A 601 "
           pdb=" SG  CYS A 614 "
           pdb=" CB  CYS A 614 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.33  -69.33     1      1.00e+01 1.00e-02 6.21e+01
  dihedral pdb=" CB  CYS H  99 "
           pdb=" SG  CYS H  99 "
           pdb=" SG  CYS H 100D"
           pdb=" CB  CYS H 100D"
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.60  -60.60     1      1.00e+01 1.00e-02 4.89e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.09   39.91     1      1.00e+01 1.00e-02 2.24e+01
  ... (remaining 1557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 255
       0.043 -    0.085: 85
       0.085 -    0.127: 32
       0.127 -    0.170: 6
       0.170 -    0.212: 1
  Chirality restraints: 379
  Sorted by residual:
  chirality pdb=" CB  ILE L  55 "
            pdb=" CA  ILE L  55 "
            pdb=" CG1 ILE L  55 "
            pdb=" CG2 ILE L  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CB  ILE H  69 "
            pdb=" CA  ILE H  69 "
            pdb=" CG1 ILE H  69 "
            pdb=" CG2 ILE H  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.00e-01
  chirality pdb=" CB  VAL A 625 "
            pdb=" CA  VAL A 625 "
            pdb=" CG1 VAL A 625 "
            pdb=" CG2 VAL A 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.35e-01
  ... (remaining 376 not shown)

  Planarity restraints: 448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  36 "   -0.017 2.00e-02 2.50e+03   1.69e-02 7.13e+00
        pdb=" CG  TRP H  36 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  36 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  36 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  36 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  36 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  36 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  36 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L  55 "   -0.036 5.00e-02 4.00e+02   5.54e-02 4.91e+00
        pdb=" N   PRO L  56 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO L  56 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO L  56 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG L  51 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.66e+00
        pdb=" N   PRO L  52 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO L  52 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO L  52 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 445 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 291
        2.76 -     3.29: 2361
        3.29 -     3.83: 4239
        3.83 -     4.36: 4873
        4.36 -     4.90: 8454
  Nonbonded interactions: 20218
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 658 "
            pdb=" OH  TYR H 100I"
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   GLY H 100H"
            pdb=" OG  SER L  31 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER L  13 "
            pdb=" OE1 GLN L  16 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" NZ  LYS A 684 "
            pdb=" OE1 GLU A 710 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" NH2 ARG L  58 "
            pdb=" OD2 ASP L  79 "
     model   vdw
     2.380 3.120
  ... (remaining 20213 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.160
  Find NCS groups from input model:        0.010
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6179
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      :  0.004   0.045   2644  Z= 0.196
  Angle     :  0.857  10.998   3567  Z= 0.461
  Chirality :  0.050   0.212    379
  Planarity :  0.006   0.055    448
  Dihedral  : 12.535  79.795    954
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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 aren not related in a simple way.
  whole: -1.98 (0.42), residues: 314
  helix: -1.12 (0.42), residues: 89
  sheet: -1.38 (0.55), residues: 79
  loop : -1.25 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  58 
 TYR   0.010   0.002   TYR L  27 
 PHE   0.025   0.003   PHE A 657 
 TRP   0.045   0.003   TRP H  36 
 HIS   0.002   0.001   HIS H  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 2640)
  covalent geometry    : angle       0.85555 ( 3559)
  SS BOND              : bond        0.00080 (    4)
  SS BOND              : angle       1.47408 (    8)
  hydrogen bonds       : bond        0.20567 (  104)
  hydrogen bonds       : angle       8.81646 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  665 MET cc_start: 0.7563 (mmp) cc_final: 0.6925 (mmt)
REVERT: A  678 MET cc_start: 0.8207 (mmt) cc_final: 0.7866 (mmt)
REVERT: A  683 ASN cc_start: 0.5921 (m-40) cc_final: 0.5702 (m110)
REVERT: H  100 TYR cc_start: 0.7242 (t80) cc_final: 0.6528 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0395
  time to fit residues: 2.5574
Evaluate side-chains
  42 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 603 ASN
** A 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.226679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.205436 restraints weight = 3117.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.209944 restraints weight = 1897.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.212985 restraints weight = 1301.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.215104 restraints weight = 971.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.216754 restraints weight = 772.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.4492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6440
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2644  Z= 0.150
  Angle     :  0.596   6.342   3567  Z= 0.316
  Chirality :  0.041   0.138    379
  Planarity :  0.004   0.030    448
  Dihedral  :  4.985  21.186    348
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  5.99 %
    Favored  : 91.90 %
  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 aren not related in a simple way.
  whole: -1.27 (0.45), residues: 314
  helix:  0.34 (0.49), residues: 92
  sheet: -1.33 (0.52), residues: 87
  loop : -1.22 (0.53), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  19 
 TYR   0.013   0.002   TYR L  46 
 PHE   0.014   0.002   PHE H  67 
 TRP   0.023   0.002   TRP H  36 
 HIS   0.001   0.001   HIS H  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2640)
  covalent geometry    : angle       0.59379 ( 3559)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       1.18408 (    8)
  hydrogen bonds       : bond        0.03516 (  104)
  hydrogen bonds       : angle       5.86670 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  665 MET cc_start: 0.7634 (mmp) cc_final: 0.7397 (mmt)
REVERT: A  678 MET cc_start: 0.8432 (mmt) cc_final: 0.8016 (mmt)
REVERT: H  100 TYR cc_start: 0.7406 (t80) cc_final: 0.6909 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 46
  average time/residue: 0.0469
  time to fit residues: 2.6375
Evaluate side-chains
  44 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   55 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 663 HIS
L  16 GLN
L  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.231199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.210078 restraints weight = 3157.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.214068 restraints weight = 2059.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.216892 restraints weight = 1487.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.218808 restraints weight = 1157.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.220251 restraints weight = 951.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2644  Z= 0.168
  Angle     :  0.579   5.636   3567  Z= 0.309
  Chirality :  0.041   0.135    379
  Planarity :  0.003   0.026    448
  Dihedral  :  5.005  22.464    348
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  :  8.45 %
    Favored  : 87.68 %
  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 aren not related in a simple way.
  whole: -1.20 (0.45), residues: 314
  helix:  0.95 (0.50), residues: 92
  sheet: -1.70 (0.49), residues: 93
  loop : -1.26 (0.53), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  71 
 TYR   0.013   0.002   TYR L  46 
 PHE   0.014   0.002   PHE H  29 
 TRP   0.015   0.002   TRP H  36 
 HIS   0.002   0.001   HIS H  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 2640)
  covalent geometry    : angle       0.57740 ( 3559)
  SS BOND              : bond        0.00418 (    4)
  SS BOND              : angle       0.99319 (    8)
  hydrogen bonds       : bond        0.03577 (  104)
  hydrogen bonds       : angle       5.65987 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.060 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 MET cc_start: 0.8431 (mmt) cc_final: 0.7983 (mmt)
REVERT: H  100 TYR cc_start: 0.7566 (t80) cc_final: 0.7013 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0497
  time to fit residues: 3.0341
Evaluate side-chains
  51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  663 HIS
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   24 MET
Chi-restraints excluded: chain L residue   45 ILE
Chi-restraints excluded: chain L residue   48 ASP
Chi-restraints excluded: chain L residue   55 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:    0.0060
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 663 HIS
L  16 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.234292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.213802 restraints weight = 3154.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.217725 restraints weight = 2058.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.220533 restraints weight = 1488.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.222472 restraints weight = 1159.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.223296 restraints weight = 954.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.4552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2644  Z= 0.123
  Angle     :  0.527   5.543   3567  Z= 0.284
  Chirality :  0.039   0.131    379
  Planarity :  0.003   0.024    448
  Dihedral  :  4.726  19.762    348
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.97 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.46), residues: 314
  helix:  1.48 (0.51), residues: 92
  sheet: -1.73 (0.49), residues: 87
  loop : -1.24 (0.51), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  71 
 TYR   0.008   0.001   TYR L  46 
 PHE   0.012   0.002   PHE H  67 
 TRP   0.012   0.001   TRP A 583 
 HIS   0.005   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 2640)
  covalent geometry    : angle       0.52723 ( 3559)
  SS BOND              : bond        0.00269 (    4)
  SS BOND              : angle       0.62849 (    8)
  hydrogen bonds       : bond        0.03317 (  104)
  hydrogen bonds       : angle       5.35928 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 MET cc_start: 0.8379 (mmt) cc_final: 0.7786 (mmt)
REVERT: H  100 TYR cc_start: 0.7523 (t80) cc_final: 0.7020 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 46
  average time/residue: 0.0416
  time to fit residues: 2.4680
Evaluate side-chains
  45 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  663 HIS
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   55 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 663 HIS
L  16 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.234235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.212195 restraints weight = 3212.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.216287 restraints weight = 2111.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.219229 restraints weight = 1544.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.221199 restraints weight = 1210.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.222757 restraints weight = 1002.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.4524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2644  Z= 0.146
  Angle     :  0.539   5.801   3567  Z= 0.289
  Chirality :  0.039   0.129    379
  Planarity :  0.003   0.024    448
  Dihedral  :  4.759  20.864    348
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 11.97 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.46), residues: 314
  helix:  1.76 (0.52), residues: 92
  sheet: -1.80 (0.48), residues: 93
  loop : -1.26 (0.53), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  71 
 TYR   0.009   0.001   TYR L  46 
 PHE   0.011   0.001   PHE H  29 
 TRP   0.011   0.002   TRP A 583 
 HIS   0.003   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2640)
  covalent geometry    : angle       0.53881 ( 3559)
  SS BOND              : bond        0.00379 (    4)
  SS BOND              : angle       0.70460 (    8)
  hydrogen bonds       : bond        0.03381 (  104)
  hydrogen bonds       : angle       5.32181 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 MET cc_start: 0.8410 (mmt) cc_final: 0.7930 (mmt)
REVERT: H  100 TYR cc_start: 0.7556 (t80) cc_final: 0.7126 (t80)
  outliers start: 10
  outliers final: 7
  residues processed: 49
  average time/residue: 0.0429
  time to fit residues: 2.6890
Evaluate side-chains
  48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  663 HIS
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   45 ILE
Chi-restraints excluded: chain L residue   55 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 17 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 663 HIS
L  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.238719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.216446 restraints weight = 3193.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.220633 restraints weight = 2090.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.223708 restraints weight = 1513.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.225558 restraints weight = 1172.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.227199 restraints weight = 972.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2644  Z= 0.125
  Angle     :  0.538   6.461   3567  Z= 0.288
  Chirality :  0.039   0.128    379
  Planarity :  0.003   0.024    448
  Dihedral  :  4.807  24.918    348
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 11.97 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.47), residues: 314
  helix:  2.00 (0.52), residues: 92
  sheet: -1.78 (0.49), residues: 87
  loop : -1.23 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  71 
 TYR   0.008   0.001   TYR L  27 
 PHE   0.014   0.002   PHE H  67 
 TRP   0.012   0.001   TRP A 583 
 HIS   0.002   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2640)
  covalent geometry    : angle       0.53454 ( 3559)
  SS BOND              : bond        0.00458 (    4)
  SS BOND              : angle       1.34346 (    8)
  hydrogen bonds       : bond        0.03264 (  104)
  hydrogen bonds       : angle       5.14341 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 MET cc_start: 0.8388 (mmt) cc_final: 0.7743 (mmt)
REVERT: H  100 TYR cc_start: 0.7481 (t80) cc_final: 0.7083 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0439
  time to fit residues: 2.7116
Evaluate side-chains
  47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   45 ILE
Chi-restraints excluded: chain L residue   55 ILE
Chi-restraints excluded: chain L residue  104 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0050
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5352

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

Flipped N/Q/H residues before XYZ refinement:
L  16 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.233790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.213527 restraints weight = 3180.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.217327 restraints weight = 2133.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.219930 restraints weight = 1573.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.221812 restraints weight = 1247.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.222374 restraints weight = 1039.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.4541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2644  Z= 0.139
  Angle     :  0.542   5.722   3567  Z= 0.291
  Chirality :  0.039   0.127    379
  Planarity :  0.003   0.024    448
  Dihedral  :  4.793  23.024    348
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 11.97 %
    Favored  : 84.15 %
  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 aren not related in a simple way.
  whole: -0.67 (0.48), residues: 314
  helix:  2.07 (0.52), residues: 92
  sheet: -2.04 (0.49), residues: 91
  loop : -0.97 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  71 
 TYR   0.010   0.001   TYR H  91 
 PHE   0.011   0.001   PHE H  29 
 TRP   0.011   0.001   TRP A 583 
 HIS   0.001   0.001   HIS A 577 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 2640)
  covalent geometry    : angle       0.53835 ( 3559)
  SS BOND              : bond        0.00385 (    4)
  SS BOND              : angle       1.50977 (    8)
  hydrogen bonds       : bond        0.03292 (  104)
  hydrogen bonds       : angle       5.24436 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 MET cc_start: 0.8392 (mmt) cc_final: 0.7844 (mmt)
REVERT: H  100 TYR cc_start: 0.7513 (t80) cc_final: 0.7100 (t80)
REVERT: L   10 MET cc_start: 0.4045 (OUTLIER) cc_final: 0.2059 (mtt)
  outliers start: 11
  outliers final: 7
  residues processed: 47
  average time/residue: 0.0507
  time to fit residues: 3.0723
Evaluate side-chains
  48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  663 HIS
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   10 MET
Chi-restraints excluded: chain L residue   45 ILE
Chi-restraints excluded: chain L residue   55 ILE
Chi-restraints excluded: chain L residue  104 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   chunk 5 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4629 r_free = 0.4629 target = 0.231211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.210633 restraints weight = 3240.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.214420 restraints weight = 2183.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.217109 restraints weight = 1614.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.218939 restraints weight = 1280.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.219950 restraints weight = 1070.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.4515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6601
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2644  Z= 0.157
  Angle     :  0.568   7.462   3567  Z= 0.304
  Chirality :  0.040   0.128    379
  Planarity :  0.003   0.024    448
  Dihedral  :  4.866  21.185    348
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 13.38 %
    Favored  : 83.10 %
  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 aren not related in a simple way.
  whole: -0.68 (0.48), residues: 314
  helix:  2.11 (0.52), residues: 92
  sheet: -2.10 (0.50), residues: 91
  loop : -0.97 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  71 
 TYR   0.008   0.001   TYR H  91 
 PHE   0.012   0.002   PHE H  29 
 TRP   0.011   0.002   TRP A 583 
 HIS   0.001   0.001   HIS A 577 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 2640)
  covalent geometry    : angle       0.56464 ( 3559)
  SS BOND              : bond        0.00215 (    4)
  SS BOND              : angle       1.44126 (    8)
  hydrogen bonds       : bond        0.03384 (  104)
  hydrogen bonds       : angle       5.35344 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  665 MET cc_start: 0.7622 (mmp) cc_final: 0.7322 (mmt)
REVERT: A  678 MET cc_start: 0.8402 (mmt) cc_final: 0.7812 (mmt)
REVERT: H  100 TYR cc_start: 0.7563 (t80) cc_final: 0.7151 (t80)
REVERT: L   10 MET cc_start: 0.4043 (OUTLIER) cc_final: 0.2006 (mtt)
  outliers start: 10
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0532
  time to fit residues: 3.1865
Evaluate side-chains
  50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  663 HIS
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   10 MET
Chi-restraints excluded: chain L residue   45 ILE
Chi-restraints excluded: chain L residue   55 ILE
Chi-restraints excluded: chain L residue  104 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 30 optimal weight:    0.0870
   chunk 11 optimal weight:    0.0980
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.4647 r_free = 0.4647 target = 0.233358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.213183 restraints weight = 3214.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.217036 restraints weight = 2108.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.219877 restraints weight = 1534.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.221764 restraints weight = 1191.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.222637 restraints weight = 978.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2644  Z= 0.122
  Angle     :  0.533   6.859   3567  Z= 0.288
  Chirality :  0.039   0.128    379
  Planarity :  0.003   0.026    448
  Dihedral  :  4.759  19.155    348
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.44 %
    Favored  : 82.39 %
  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 aren not related in a simple way.
  whole: -0.46 (0.49), residues: 314
  helix:  2.42 (0.52), residues: 92
  sheet: -1.97 (0.51), residues: 91
  loop : -0.95 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  66 
 TYR   0.008   0.001   TYR L  27 
 PHE   0.016   0.002   PHE H  67 
 TRP   0.013   0.001   TRP H  36 
 HIS   0.001   0.000   HIS A 577 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2640)
  covalent geometry    : angle       0.53066 ( 3559)
  SS BOND              : bond        0.00194 (    4)
  SS BOND              : angle       1.16842 (    8)
  hydrogen bonds       : bond        0.03242 (  104)
  hydrogen bonds       : angle       5.11957 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 MET cc_start: 0.8382 (mmt) cc_final: 0.7847 (mmt)
REVERT: H  100 TYR cc_start: 0.7481 (t80) cc_final: 0.7107 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 45
  average time/residue: 0.0598
  time to fit residues: 3.3386
Evaluate side-chains
  47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  663 HIS
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   45 ILE
Chi-restraints excluded: chain L residue   55 ILE
Chi-restraints excluded: chain L residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    0.1980
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4637 r_free = 0.4637 target = 0.232314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.212096 restraints weight = 3231.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.215836 restraints weight = 2162.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.218070 restraints weight = 1596.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.220261 restraints weight = 1285.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.221632 restraints weight = 1054.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2644  Z= 0.145
  Angle     :  0.563   6.563   3567  Z= 0.303
  Chirality :  0.040   0.126    379
  Planarity :  0.003   0.027    448
  Dihedral  :  4.863  20.643    348
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.79 %
    Favored  : 82.39 %
  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 aren not related in a simple way.
  whole: -0.47 (0.49), residues: 314
  helix:  2.42 (0.52), residues: 92
  sheet: -2.06 (0.51), residues: 93
  loop : -0.86 (0.56), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  71 
 TYR   0.008   0.001   TYR L  27 
 PHE   0.011   0.002   PHE H  29 
 TRP   0.012   0.001   TRP A 583 
 HIS   0.001   0.001   HIS A 577 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2640)
  covalent geometry    : angle       0.56019 ( 3559)
  SS BOND              : bond        0.00285 (    4)
  SS BOND              : angle       1.28379 (    8)
  hydrogen bonds       : bond        0.03375 (  104)
  hydrogen bonds       : angle       5.19832 (  327)

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

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

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  628 Ramachandran restraints generated.
    314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 MET cc_start: 0.8412 (mmt) cc_final: 0.7833 (mmt)
REVERT: H   82 MET cc_start: 0.6112 (mpp) cc_final: 0.5569 (mpp)
REVERT: H  100 TYR cc_start: 0.7516 (t80) cc_final: 0.7107 (t80)
  outliers start: 8
  outliers final: 8
  residues processed: 44
  average time/residue: 0.0521
  time to fit residues: 2.9251
Evaluate side-chains
  47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  663 HIS
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain L residue   45 ILE
Chi-restraints excluded: chain L residue   55 ILE
Chi-restraints excluded: chain L residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.3978

-------------------------------------------------------------------------------
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 = 0.4634 r_free = 0.4634 target = 0.232235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.211962 restraints weight = 3169.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.215859 restraints weight = 2062.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.218672 restraints weight = 1493.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.220610 restraints weight = 1160.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.221801 restraints weight = 948.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2644  Z= 0.121
  Angle     :  0.529   6.378   3567  Z= 0.286
  Chirality :  0.039   0.126    379
  Planarity :  0.003   0.026    448
  Dihedral  :  4.742  19.180    348
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.14 %
    Favored  : 82.39 %
  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 aren not related in a simple way.
  whole: -0.32 (0.49), residues: 314
  helix:  2.57 (0.52), residues: 92
  sheet: -1.90 (0.52), residues: 94
  loop : -0.84 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  71 
 TYR   0.008   0.001   TYR L  27 
 PHE   0.010   0.001   PHE H  29 
 TRP   0.012   0.001   TRP A 583 
 HIS   0.001   0.001   HIS A 577 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 2640)
  covalent geometry    : angle       0.52665 ( 3559)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       1.08468 (    8)
  hydrogen bonds       : bond        0.03224 (  104)
  hydrogen bonds       : angle       5.02974 (  327)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 766.84 seconds
wall clock time: 13 minutes 54.77 seconds (834.77 seconds total)