Starting phenix.real_space_refine
on Fri Aug 22 13:38:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5e_37287/08_2025/8w5e_37287.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5e_37287/08_2025/8w5e_37287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5e_37287/08_2025/8w5e_37287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5e_37287/08_2025/8w5e_37287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5e_37287/08_2025/8w5e_37287.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5e_37287/08_2025/8w5e_37287.cif"
  }
  resolution = 3.8
  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=   0.007 sd=   0.119
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      11      5.16       5
     C    2128      2.51       5
     N     575      2.21       5
     O     680      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3396
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 782
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 944
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 8, 'TRANS': 118}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 7, 'TRANS': 86}
  Restraints were copied for chains:
    c
  Time building chain proxies: 1.19, per 1000 atoms: 0.35
  Number of scatterers: 3396
  At special positions: 0
  Unit cell: (91.8, 66.15, 85.05, 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      11     16.00
     P       2     15.00
     O     680      8.00
     N     575      7.00
     C    2128      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " 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: 0.30
  Conformation dependent library (CDL) restraints added in 137.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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:  832

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      10.3% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'c' and resid 101 through 116
      removed outlier: 3.884A  pdb=" N   VAL c 108 " --> pdb=" O   GLU c 104 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG c 109 " --> pdb=" O   ARG c 105 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 120 through 126
      removed outlier: 3.533A  pdb=" N   ASP c 126 " --> pdb=" O   ILE c 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 116
      removed outlier: 3.885A  pdb=" N   VAL C 108 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG C 109 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 126
      removed outlier: 3.533A  pdb=" N   ASP C 126 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 10
      removed outlier: 3.729A  pdb=" N   ASN H  80 " --> pdb=" O   ARG H  75 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 37 through 39
      removed outlier: 3.824A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'c' and resid 22 through 27
      removed outlier: 4.996A  pdb=" N   SER c  34 " --> pdb=" O   ARG c  24 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   VAL c  26 " --> pdb=" O   VAL c  32 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   VAL c  32 " --> pdb=" O   VAL c  26 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASN c  70 " --> pdb=" O   ALA c  88 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG c  86 " --> pdb=" O   THR c  72 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   CYS c  74 " --> pdb=" O   VAL c  84 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   VAL c  84 " --> pdb=" O   CYS c  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 22 through 27
      removed outlier: 4.996A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  24 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   VAL C  26 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   VAL C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASN C  70 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG C  86 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   CYS C  74 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   VAL C  84 " --> pdb=" O   CYS C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 8 through 9
    Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 49
      removed outlier: 3.799A  pdb=" N   ASP L  88 " --> pdb=" O   GLN L  41 " (cutoff:3.500A)

    99 hydrogen bonds defined for protein.
    264 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: 0.40

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 973
        1.33 -     1.45: 599
        1.45 -     1.57: 1863
        1.57 -     1.70: 8
        1.70 -     1.82: 14
  Bond restraints: 3457
  Sorted by residual:
  bond pdb=" C   VAL H   8 "
       pdb=" O   VAL H   8 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.024 1.07e-02 8.73e+03 5.08e+00
  bond pdb=" CA  VAL H   8 "
       pdb=" CB  VAL H   8 "
    ideal  model  delta    sigma   weight residual
    1.540  1.513  0.028 1.23e-02 6.61e+03 5.01e+00
  bond pdb=" CA  SER H  10 "
       pdb=" CB  SER H  10 "
    ideal  model  delta    sigma   weight residual
    1.534  1.500  0.033 1.78e-02 3.16e+03 3.50e+00
  bond pdb=" C   SER H  10 "
       pdb=" O   SER H  10 "
    ideal  model  delta    sigma   weight residual
    1.234  1.212  0.022 1.22e-02 6.72e+03 3.37e+00
  bond pdb=" N   THR L  81 "
       pdb=" CA  THR L  81 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.027 1.54e-02 4.22e+03 3.02e+00
  ... (remaining 3452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 4560
        2.81 -     5.61: 117
        5.61 -     8.42: 23
        8.42 -    11.22: 5
       11.22 -    14.03: 4
  Bond angle restraints: 4709
  Sorted by residual:
  angle pdb=" N   VAL H   8 "
        pdb=" CA  VAL H   8 "
        pdb=" C   VAL H   8 "
      ideal   model   delta    sigma   weight residual
     108.11  122.14  -14.03 1.40e+00 5.10e-01 1.00e+02
  angle pdb=" N   VAL H   8 "
        pdb=" CA  VAL H   8 "
        pdb=" CB  VAL H   8 "
      ideal   model   delta    sigma   weight residual
     111.41  104.80    6.61 1.38e+00 5.25e-01 2.29e+01
  angle pdb=" N   ILE L  51 "
        pdb=" CA  ILE L  51 "
        pdb=" C   ILE L  51 "
      ideal   model   delta    sigma   weight residual
     109.34  119.25   -9.91 2.08e+00 2.31e-01 2.27e+01
  angle pdb=" C   LEU L  50 "
        pdb=" N   ILE L  51 "
        pdb=" CA  ILE L  51 "
      ideal   model   delta    sigma   weight residual
     121.97  130.29   -8.32 1.80e+00 3.09e-01 2.14e+01
  angle pdb=" C   VAL H   8 "
        pdb=" CA  VAL H   8 "
        pdb=" CB  VAL H   8 "
      ideal   model   delta    sigma   weight residual
     110.63  103.90    6.73 1.48e+00 4.57e-01 2.07e+01
  ... (remaining 4704 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.23: 1970
       15.23 -    30.46: 83
       30.46 -    45.69: 24
       45.69 -    60.92: 7
       60.92 -    76.14: 4
  Dihedral angle restraints: 2088
    sinusoidal: 799
      harmonic: 1289
  Sorted by residual:
  dihedral pdb=" CA  LEU L  50 "
           pdb=" C   LEU L  50 "
           pdb=" N   ILE L  51 "
           pdb=" CA  ILE L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.45  -30.55     0      5.00e+00 4.00e-02 3.73e+01
  dihedral pdb=" CA  ASN L  96 "
           pdb=" C   ASN L  96 "
           pdb=" N   MET L  97 "
           pdb=" CA  MET L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.34  -23.66     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  ILE L  78 "
           pdb=" C   ILE L  78 "
           pdb=" N   GLU L  79 "
           pdb=" CA  GLU L  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.63  -22.37     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 2085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 332
       0.048 -    0.096: 144
       0.096 -    0.145: 52
       0.145 -    0.193: 15
       0.193 -    0.241: 4
  Chirality restraints: 547
  Sorted by residual:
  chirality pdb=" CB  ILE c  68 "
            pdb=" CA  ILE c  68 "
            pdb=" CG1 ILE c  68 "
            pdb=" CG2 ILE c  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  ILE C  68 "
            pdb=" CA  ILE C  68 "
            pdb=" CG1 ILE C  68 "
            pdb=" CG2 ILE C  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  VAL L  61 "
            pdb=" CA  VAL L  61 "
            pdb=" CG1 VAL L  61 "
            pdb=" CG2 VAL L  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 544 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE L  78 "    0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   ILE L  78 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   ILE L  78 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU L  79 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN c  70 "   -0.033 5.00e-02 4.00e+02   5.07e-02 4.12e+00
        pdb=" N   PRO c  71 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO c  71 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO c  71 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  70 "   -0.033 5.00e-02 4.00e+02   5.04e-02 4.07e+00
        pdb=" N   PRO C  71 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO C  71 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  71 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 38
        2.61 -     3.19: 2878
        3.19 -     3.76: 4920
        3.76 -     4.33: 6298
        4.33 -     4.90: 10746
  Nonbonded interactions: 24880
  Sorted by model distance:
  nonbonded pdb=" SG  CYS L  26 "
            pdb=" SG  CYS L  91 "
     model   vdw
     2.042 3.760
  nonbonded pdb=" OE1 GLU H   9 "
            pdb=" C   ARG H 115 "
     model   vdw
     2.158 3.270
  nonbonded pdb=" OD1 ASP c  91 "
            pdb=" OG1 THR C  93 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG1 THR c  93 "
            pdb=" OD1 ASP C  91 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   SER L  52 "
            pdb=" OG1 THR L  56 "
     model   vdw
     2.318 3.040
  ... (remaining 24875 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 'C'
  selection = chain 'c'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  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:                    0.020
  Process input model:                     4.750
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
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      :  0.007   0.039   3458  Z= 0.317
  Angle     :  1.177  14.027   4711  Z= 0.621
  Chirality :  0.064   0.241    547
  Planarity :  0.008   0.051    612
  Dihedral  : 11.145  76.144   1253
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  9.86 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  5.91 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -4.58 (0.34), residues: 426
  helix: -3.63 (0.59), residues: 44
  sheet: -2.33 (0.39), residues: 158
  loop : -3.50 (0.32), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 109 
 TYR   0.022   0.003   TYR c  62 
 PHE   0.021   0.003   PHE H 110 
 TRP   0.024   0.003   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 ( 3457)
  covalent geometry    : angle       1.17757 ( 4709)
  SS BOND              : bond        0.00205 (    1)
  SS BOND              : angle       0.79572 (    2)
  hydrogen bonds       : bond        0.14312 (   99)
  hydrogen bonds       : angle       7.14855 (  264)

*********************** 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
  184 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.6838 (ptp-170) cc_final: 0.5626 (mmm160)
REVERT: H   55 SER cc_start: 0.9381 (t) cc_final: 0.9086 (t)
REVERT: H   80 ASN cc_start: 0.8341 (p0) cc_final: 0.8121 (p0)
REVERT: H  101 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7662 (ptt90)
REVERT: H  106 SER cc_start: 0.8089 (t) cc_final: 0.7332 (t)
REVERT: c   13 LYS cc_start: 0.8920 (tppp) cc_final: 0.7828 (tppp)
REVERT: c   27 ASN cc_start: 0.8595 (t0) cc_final: 0.8182 (t0)
REVERT: c   32 VAL cc_start: 0.9273 (t) cc_final: 0.9022 (m)
REVERT: c   34 SER cc_start: 0.9509 (m) cc_final: 0.9064 (t)
REVERT: c   87 GLN cc_start: 0.8429 (mp-120) cc_final: 0.8206 (mm-40)
REVERT: c  100 SER cc_start: 0.9434 (m) cc_final: 0.9152 (p)
REVERT: c  103 GLU cc_start: 0.8355 (tp30) cc_final: 0.8145 (mm-30)
REVERT: c  122 ILE cc_start: 0.9094 (pp) cc_final: 0.8707 (pp)
REVERT: c  123 ASP cc_start: 0.7901 (t70) cc_final: 0.7489 (t0)
REVERT: C   13 LYS cc_start: 0.8795 (tppp) cc_final: 0.8399 (tppp)
REVERT: C   34 SER cc_start: 0.9452 (m) cc_final: 0.9033 (p)
REVERT: C   36 SER cc_start: 0.8738 (p) cc_final: 0.8398 (p)
REVERT: C   91 ASP cc_start: 0.8553 (p0) cc_final: 0.8334 (p0)
REVERT: C  104 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: C  122 ILE cc_start: 0.8522 (pp) cc_final: 0.8300 (tt)
REVERT: C  123 ASP cc_start: 0.8563 (t70) cc_final: 0.7669 (t0)
REVERT: C  127 GLN cc_start: 0.9275 (mp10) cc_final: 0.8690 (mp-120)
REVERT: C  129 ASN cc_start: 0.8495 (m-40) cc_final: 0.8094 (m110)
REVERT: L    9 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8104 (mp10)
REVERT: L   13 SER cc_start: 0.7775 (m) cc_final: 0.7295 (p)
REVERT: L   27 ILE cc_start: 0.8314 (tt) cc_final: 0.7935 (tt)
REVERT: L   35 ASP cc_start: 0.7146 (m-30) cc_final: 0.6701 (m-30)
REVERT: L   45 GLU cc_start: 0.8116 (pm20) cc_final: 0.7532 (pm20)
REVERT: L   93 GLN cc_start: 0.8762 (pm20) cc_final: 0.8380 (pm20)
  outliers start: 2
  outliers final: 1
  residues processed: 183
  average time/residue: 0.0723
  time to fit residues: 15.5182
Evaluate side-chains
  141 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   67 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  10 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.104828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.084869 restraints weight = 7551.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.087369 restraints weight = 3465.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.088969 restraints weight = 2058.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.090017 restraints weight = 1442.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.090689 restraints weight = 1136.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3458  Z= 0.169
  Angle     :  0.814   9.702   4711  Z= 0.411
  Chirality :  0.048   0.176    547
  Planarity :  0.006   0.051    612
  Dihedral  :  5.657  25.749    483
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.33 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 14.52 %
    Favored  : 79.03 %
  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: -4.02 (0.36), residues: 426
  helix: -2.15 (0.68), residues: 46
  sheet: -2.24 (0.39), residues: 162
  loop : -3.14 (0.34), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  75 
 TYR   0.017   0.002   TYR L  90 
 PHE   0.012   0.002   PHE L  74 
 TRP   0.018   0.003   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3457)
  covalent geometry    : angle       0.81393 ( 4709)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.53473 (    2)
  hydrogen bonds       : bond        0.03774 (   99)
  hydrogen bonds       : angle       5.84578 (  264)

*********************** 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
  164 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ARG cc_start: 0.7573 (ptp-170) cc_final: 0.6004 (mmm160)
REVERT: H   45 ARG cc_start: 0.8285 (tpp-160) cc_final: 0.7958 (mmp-170)
REVERT: H   54 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8001 (tp)
REVERT: H   55 SER cc_start: 0.9132 (t) cc_final: 0.8859 (t)
REVERT: H   62 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5904 (p90)
REVERT: H   79 LYS cc_start: 0.8713 (mttt) cc_final: 0.8269 (ptmt)
REVERT: H  115 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7815 (mmm160)
REVERT: c    4 GLU cc_start: 0.7826 (tp30) cc_final: 0.7572 (tp30)
REVERT: c    6 VAL cc_start: 0.9187 (t) cc_final: 0.8966 (p)
REVERT: c   13 LYS cc_start: 0.9233 (tppp) cc_final: 0.8943 (tppp)
REVERT: c   27 ASN cc_start: 0.8824 (t0) cc_final: 0.8401 (t0)
REVERT: c   32 VAL cc_start: 0.9383 (t) cc_final: 0.9180 (m)
REVERT: c   87 GLN cc_start: 0.8304 (mp-120) cc_final: 0.8102 (mm-40)
REVERT: c  100 SER cc_start: 0.9623 (m) cc_final: 0.9336 (p)
REVERT: c  102 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7771 (t0)
REVERT: c  122 ILE cc_start: 0.9062 (pp) cc_final: 0.8737 (pp)
REVERT: c  123 ASP cc_start: 0.7813 (t70) cc_final: 0.7458 (t0)
REVERT: C   87 GLN cc_start: 0.8952 (mp10) cc_final: 0.8698 (mt0)
REVERT: C   91 ASP cc_start: 0.8742 (p0) cc_final: 0.8520 (p0)
REVERT: C  123 ASP cc_start: 0.8576 (t70) cc_final: 0.7765 (t0)
REVERT: C  127 GLN cc_start: 0.9333 (mp10) cc_final: 0.8863 (mp-120)
REVERT: C  129 ASN cc_start: 0.8670 (m-40) cc_final: 0.8275 (m110)
REVERT: L   13 SER cc_start: 0.7578 (m) cc_final: 0.7217 (p)
REVERT: L   45 GLU cc_start: 0.8099 (pm20) cc_final: 0.7501 (pm20)
REVERT: L   70 TYR cc_start: 0.7548 (t80) cc_final: 0.6945 (t80)
REVERT: L   74 PHE cc_start: 0.8611 (m-80) cc_final: 0.8325 (m-10)
REVERT: L   93 GLN cc_start: 0.8699 (pm20) cc_final: 0.8464 (pm20)
  outliers start: 24
  outliers final: 15
  residues processed: 153
  average time/residue: 0.0815
  time to fit residues: 14.5679
Evaluate side-chains
  141 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   53 SER
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  102 ASP
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   88 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 8 optimal weight:   20.0000
   chunk 16 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.102586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.082167 restraints weight = 7615.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.084652 restraints weight = 3545.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.086248 restraints weight = 2121.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.087252 restraints weight = 1503.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.087893 restraints weight = 1198.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3458  Z= 0.203
  Angle     :  0.812  12.431   4711  Z= 0.408
  Chirality :  0.048   0.171    547
  Planarity :  0.005   0.037    612
  Dihedral  :  5.359  23.650    483
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.21 %
    Favored  : 87.56 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 18.28 %
    Favored  : 74.46 %
  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: -3.84 (0.36), residues: 426
  helix: -1.33 (0.73), residues: 46
  sheet: -2.23 (0.39), residues: 160
  loop : -3.11 (0.34), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  47 
 TYR   0.014   0.002   TYR L  89 
 PHE   0.016   0.002   PHE H  53 
 TRP   0.018   0.003   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 3457)
  covalent geometry    : angle       0.81202 ( 4709)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.59176 (    2)
  hydrogen bonds       : bond        0.03736 (   99)
  hydrogen bonds       : angle       5.63594 (  264)

*********************** 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
  152 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.9075 (m) cc_final: 0.8840 (p)
REVERT: H   22 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8428 (ttmm)
REVERT: H   32 PHE cc_start: 0.8905 (t80) cc_final: 0.8698 (t80)
REVERT: H   41 ARG cc_start: 0.7604 (ptp-170) cc_final: 0.5844 (mmm160)
REVERT: H   45 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7904 (mmp-170)
REVERT: H   54 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8245 (tp)
REVERT: H   55 SER cc_start: 0.9155 (t) cc_final: 0.8831 (t)
REVERT: H   62 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6395 (p90)
REVERT: H   79 LYS cc_start: 0.8586 (mttt) cc_final: 0.8141 (ptmt)
REVERT: c    4 GLU cc_start: 0.7957 (tp30) cc_final: 0.7742 (tp30)
REVERT: c   27 ASN cc_start: 0.8854 (t0) cc_final: 0.8336 (t0)
REVERT: c   87 GLN cc_start: 0.8304 (mp-120) cc_final: 0.7978 (mm-40)
REVERT: c  100 SER cc_start: 0.9629 (m) cc_final: 0.9359 (p)
REVERT: c  123 ASP cc_start: 0.8085 (t70) cc_final: 0.7654 (t0)
REVERT: C   30 ASN cc_start: 0.9274 (p0) cc_final: 0.9024 (p0)
REVERT: C   87 GLN cc_start: 0.8931 (mp10) cc_final: 0.8719 (mt0)
REVERT: C   91 ASP cc_start: 0.8876 (p0) cc_final: 0.8592 (p0)
REVERT: C  123 ASP cc_start: 0.8683 (t70) cc_final: 0.7780 (t0)
REVERT: C  127 GLN cc_start: 0.9383 (mp10) cc_final: 0.8911 (mp-120)
REVERT: C  129 ASN cc_start: 0.8632 (m-40) cc_final: 0.8080 (m110)
REVERT: L   13 SER cc_start: 0.7355 (m) cc_final: 0.6953 (p)
REVERT: L   20 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8236 (pm20)
REVERT: L   45 GLU cc_start: 0.8119 (pm20) cc_final: 0.7549 (pm20)
  outliers start: 27
  outliers final: 16
  residues processed: 142
  average time/residue: 0.0688
  time to fit residues: 11.7567
Evaluate side-chains
  139 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  102 ASP
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   20 GLU
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 35 optimal weight:   20.0000
   chunk 23 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0270
   chunk 41 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    2.5044

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.103478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.082927 restraints weight = 7479.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.085382 restraints weight = 3501.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.086978 restraints weight = 2112.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.088026 restraints weight = 1497.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.088630 restraints weight = 1193.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3458  Z= 0.156
  Angle     :  0.785  12.427   4711  Z= 0.392
  Chirality :  0.048   0.167    547
  Planarity :  0.005   0.038    612
  Dihedral  :  5.197  23.723    483
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.33 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 19.09 %
    Favored  : 74.19 %
  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: -3.59 (0.37), residues: 426
  helix: -1.12 (0.77), residues: 46
  sheet: -1.98 (0.39), residues: 163
  loop : -3.01 (0.36), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  47 
 TYR   0.026   0.002   TYR H  35 
 PHE   0.007   0.001   PHE H 104 
 TRP   0.011   0.002   TRP H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3457)
  covalent geometry    : angle       0.78512 ( 4709)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.46071 (    2)
  hydrogen bonds       : bond        0.03389 (   99)
  hydrogen bonds       : angle       5.48983 (  264)

*********************** 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
  148 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.8953 (m) cc_final: 0.8666 (p)
REVERT: H   22 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8444 (ttmm)
REVERT: H   41 ARG cc_start: 0.7535 (ptp-170) cc_final: 0.5803 (mmm160)
REVERT: H   53 PHE cc_start: 0.8796 (t80) cc_final: 0.8553 (t80)
REVERT: H   54 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8119 (tp)
REVERT: H   62 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.5986 (p90)
REVERT: H   79 LYS cc_start: 0.8539 (mttt) cc_final: 0.8294 (ptmt)
REVERT: c    4 GLU cc_start: 0.7924 (tp30) cc_final: 0.7700 (tp30)
REVERT: c   27 ASN cc_start: 0.8841 (t0) cc_final: 0.8301 (t0)
REVERT: c   87 GLN cc_start: 0.8265 (mp-120) cc_final: 0.8064 (mm-40)
REVERT: c  100 SER cc_start: 0.9600 (m) cc_final: 0.9327 (p)
REVERT: c  102 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8174 (t0)
REVERT: c  103 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: c  123 ASP cc_start: 0.8094 (t70) cc_final: 0.7621 (t0)
REVERT: C   91 ASP cc_start: 0.8874 (p0) cc_final: 0.8604 (p0)
REVERT: C  123 ASP cc_start: 0.8676 (t70) cc_final: 0.7781 (t0)
REVERT: C  127 GLN cc_start: 0.9381 (mp10) cc_final: 0.8944 (mp-120)
REVERT: C  129 ASN cc_start: 0.8617 (m-40) cc_final: 0.8025 (m110)
REVERT: L   13 SER cc_start: 0.7348 (m) cc_final: 0.6966 (p)
REVERT: L   45 GLU cc_start: 0.8138 (pm20) cc_final: 0.7688 (pm20)
REVERT: L   50 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8810 (mm)
REVERT: L   97 MET cc_start: 0.7729 (mmm) cc_final: 0.5556 (mmm)
  outliers start: 25
  outliers final: 17
  residues processed: 137
  average time/residue: 0.0741
  time to fit residues: 12.2287
Evaluate side-chains
  144 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   80 CYS
Chi-restraints excluded: chain c residue  102 ASP
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 40 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.101647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.080928 restraints weight = 7627.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.083321 restraints weight = 3632.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.084811 restraints weight = 2216.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.085867 restraints weight = 1591.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.086490 restraints weight = 1272.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3458  Z= 0.205
  Angle     :  0.807  13.208   4711  Z= 0.403
  Chirality :  0.049   0.168    547
  Planarity :  0.005   0.038    612
  Dihedral  :  5.281  23.692    483
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 13.15 %
    Favored  : 86.62 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 20.70 %
    Favored  : 72.31 %
  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: -3.45 (0.38), residues: 426
  helix: -1.11 (0.77), residues: 46
  sheet: -1.90 (0.39), residues: 163
  loop : -2.90 (0.37), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 109 
 TYR   0.023   0.002   TYR H  35 
 PHE   0.016   0.002   PHE c  94 
 TRP   0.012   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 3457)
  covalent geometry    : angle       0.80674 ( 4709)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       0.35169 (    2)
  hydrogen bonds       : bond        0.03591 (   99)
  hydrogen bonds       : angle       5.47444 (  264)

*********************** 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
  148 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.8734 (m) cc_final: 0.8440 (p)
REVERT: H   41 ARG cc_start: 0.7588 (ptp-170) cc_final: 0.5817 (mmm160)
REVERT: H   53 PHE cc_start: 0.8877 (t80) cc_final: 0.8635 (t80)
REVERT: H   54 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8174 (tp)
REVERT: H   62 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6182 (p90)
REVERT: c   27 ASN cc_start: 0.8873 (t0) cc_final: 0.8365 (t0)
REVERT: c   87 GLN cc_start: 0.8223 (mp-120) cc_final: 0.8023 (mm110)
REVERT: c  102 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8074 (t0)
REVERT: c  103 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: c  104 GLU cc_start: 0.8596 (pt0) cc_final: 0.8370 (pt0)
REVERT: c  123 ASP cc_start: 0.8102 (t70) cc_final: 0.7625 (t0)
REVERT: C   13 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8653 (tppp)
REVERT: C   30 ASN cc_start: 0.9258 (p0) cc_final: 0.9048 (p0)
REVERT: C   89 TYR cc_start: 0.8907 (m-80) cc_final: 0.8690 (m-80)
REVERT: C  123 ASP cc_start: 0.8737 (t70) cc_final: 0.7875 (t0)
REVERT: C  127 GLN cc_start: 0.9392 (mp10) cc_final: 0.8963 (mp-120)
REVERT: C  129 ASN cc_start: 0.8704 (m-40) cc_final: 0.8137 (m110)
REVERT: L   13 SER cc_start: 0.7374 (m) cc_final: 0.6949 (p)
REVERT: L   45 GLU cc_start: 0.8331 (pm20) cc_final: 0.7809 (pm20)
REVERT: L   50 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8589 (mm)
REVERT: L   97 MET cc_start: 0.7774 (mmm) cc_final: 0.5378 (mmm)
  outliers start: 26
  outliers final: 18
  residues processed: 137
  average time/residue: 0.0718
  time to fit residues: 11.7424
Evaluate side-chains
  140 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   41 VAL
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  102 ASP
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0370
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0970
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
C  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.105364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.084743 restraints weight = 7364.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.087240 restraints weight = 3450.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.088837 restraints weight = 2066.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.089858 restraints weight = 1461.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.090471 restraints weight = 1162.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.4742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3458  Z= 0.129
  Angle     :  0.782  11.349   4711  Z= 0.389
  Chirality :  0.047   0.156    547
  Planarity :  0.005   0.042    612
  Dihedral  :  5.074  23.490    483
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.39 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 22.58 %
    Favored  : 71.51 %
  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: -3.16 (0.38), residues: 426
  helix: -0.85 (0.83), residues: 44
  sheet: -1.70 (0.40), residues: 160
  loop : -2.70 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.017   0.001   TYR H  35 
 PHE   0.013   0.001   PHE c  94 
 TRP   0.011   0.002   TRP L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3457)
  covalent geometry    : angle       0.78196 ( 4709)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       0.36127 (    2)
  hydrogen bonds       : bond        0.03077 (   99)
  hydrogen bonds       : angle       5.32434 (  264)

*********************** 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
  156 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.8710 (m) cc_final: 0.8439 (p)
REVERT: H   41 ARG cc_start: 0.6985 (ptp-170) cc_final: 0.5836 (mmm160)
REVERT: H   45 ARG cc_start: 0.8011 (tpp-160) cc_final: 0.7610 (mmp-170)
REVERT: H   54 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8448 (mm)
REVERT: c   27 ASN cc_start: 0.8804 (t0) cc_final: 0.8274 (t0)
REVERT: c   46 LYS cc_start: 0.9179 (mttp) cc_final: 0.8952 (mttm)
REVERT: c   65 GLN cc_start: 0.7739 (pt0) cc_final: 0.7389 (tt0)
REVERT: c  103 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7680 (tm-30)
REVERT: c  104 GLU cc_start: 0.8592 (pt0) cc_final: 0.8198 (pt0)
REVERT: c  123 ASP cc_start: 0.7872 (t70) cc_final: 0.7360 (t0)
REVERT: C  123 ASP cc_start: 0.8664 (t70) cc_final: 0.7684 (t0)
REVERT: C  127 GLN cc_start: 0.9389 (mp10) cc_final: 0.8930 (mp-120)
REVERT: C  129 ASN cc_start: 0.8602 (m-40) cc_final: 0.8017 (m110)
REVERT: L   13 SER cc_start: 0.7360 (m) cc_final: 0.6971 (p)
REVERT: L   36 MET cc_start: 0.7091 (tpt) cc_final: 0.6555 (tpt)
REVERT: L   45 GLU cc_start: 0.8197 (pm20) cc_final: 0.7727 (pm20)
REVERT: L   50 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8522 (mm)
REVERT: L   70 TYR cc_start: 0.7927 (t80) cc_final: 0.7701 (t80)
REVERT: L   97 MET cc_start: 0.7595 (mmm) cc_final: 0.7373 (tpt)
  outliers start: 22
  outliers final: 16
  residues processed: 144
  average time/residue: 0.0718
  time to fit residues: 12.1762
Evaluate side-chains
  145 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    3.7786

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

Flipped N/Q/H residues before XYZ refinement:
c  69 GLN
C  17 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.101599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.080973 restraints weight = 7613.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.083388 restraints weight = 3619.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.084958 restraints weight = 2194.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.085956 restraints weight = 1555.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086629 restraints weight = 1237.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.4928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3458  Z= 0.197
  Angle     :  0.803  12.827   4711  Z= 0.400
  Chirality :  0.049   0.159    547
  Planarity :  0.005   0.044    612
  Dihedral  :  5.186  23.656    483
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 22.85 %
    Favored  : 70.70 %
  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 aren not related in a simple way.
  whole: -3.24 (0.38), residues: 426
  helix: -1.02 (0.78), residues: 46
  sheet: -1.82 (0.40), residues: 162
  loop : -2.69 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  47 
 TYR   0.018   0.002   TYR H  35 
 PHE   0.031   0.003   PHE L  74 
 TRP   0.009   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 3457)
  covalent geometry    : angle       0.80317 ( 4709)
  SS BOND              : bond        0.00192 (    1)
  SS BOND              : angle       0.32558 (    2)
  hydrogen bonds       : bond        0.03391 (   99)
  hydrogen bonds       : angle       5.42594 (  264)

*********************** 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
  148 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.8769 (m) cc_final: 0.8484 (p)
REVERT: H   41 ARG cc_start: 0.6976 (ptp-170) cc_final: 0.5948 (mmm160)
REVERT: H   49 GLU cc_start: 0.6181 (tt0) cc_final: 0.5845 (tt0)
REVERT: H   54 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8178 (tp)
REVERT: H   80 ASN cc_start: 0.8160 (p0) cc_final: 0.7926 (p0)
REVERT: c   27 ASN cc_start: 0.8781 (t0) cc_final: 0.8273 (t0)
REVERT: c   87 GLN cc_start: 0.7844 (mm110) cc_final: 0.7465 (mm-40)
REVERT: c  103 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7896 (tm-30)
REVERT: c  104 GLU cc_start: 0.8648 (pt0) cc_final: 0.8419 (pt0)
REVERT: c  123 ASP cc_start: 0.7879 (t70) cc_final: 0.7450 (t0)
REVERT: C  123 ASP cc_start: 0.8764 (t70) cc_final: 0.7856 (t0)
REVERT: C  127 GLN cc_start: 0.9413 (mp10) cc_final: 0.8911 (mp-120)
REVERT: C  129 ASN cc_start: 0.8716 (m-40) cc_final: 0.8140 (m110)
REVERT: L   13 SER cc_start: 0.7423 (m) cc_final: 0.6989 (p)
REVERT: L   45 GLU cc_start: 0.8245 (pm20) cc_final: 0.7704 (pm20)
REVERT: L   50 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8505 (mm)
REVERT: L   93 GLN cc_start: 0.9137 (pm20) cc_final: 0.8316 (pm20)
REVERT: L   97 MET cc_start: 0.7766 (mmm) cc_final: 0.7558 (tpt)
  outliers start: 24
  outliers final: 17
  residues processed: 136
  average time/residue: 0.0729
  time to fit residues: 11.7989
Evaluate side-chains
  143 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   98 GLN
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0270
   overall best weight:    3.0046

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN
c  69 GLN
L  40 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.102703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.082002 restraints weight = 7629.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.084429 restraints weight = 3607.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.086019 restraints weight = 2177.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.086958 restraints weight = 1544.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.087640 restraints weight = 1236.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3458  Z= 0.173
  Angle     :  0.800  12.254   4711  Z= 0.400
  Chirality :  0.049   0.163    547
  Planarity :  0.005   0.039    612
  Dihedral  :  5.230  23.452    483
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 22.58 %
    Favored  : 70.16 %
  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: -3.19 (0.39), residues: 426
  helix: -0.96 (0.78), residues: 46
  sheet: -1.80 (0.40), residues: 162
  loop : -2.63 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  47 
 TYR   0.015   0.001   TYR H  35 
 PHE   0.046   0.003   PHE L  74 
 TRP   0.008   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3457)
  covalent geometry    : angle       0.79980 ( 4709)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       0.32907 (    2)
  hydrogen bonds       : bond        0.03381 (   99)
  hydrogen bonds       : angle       5.50633 (  264)

*********************** 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
  159 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.8783 (m) cc_final: 0.8501 (p)
REVERT: H   41 ARG cc_start: 0.7028 (ptp-170) cc_final: 0.5599 (tpt90)
REVERT: H   49 GLU cc_start: 0.6131 (tt0) cc_final: 0.5796 (tt0)
REVERT: H   54 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8442 (tp)
REVERT: c   27 ASN cc_start: 0.8774 (t0) cc_final: 0.8262 (t0)
REVERT: c   65 GLN cc_start: 0.7885 (pt0) cc_final: 0.7604 (tt0)
REVERT: c   87 GLN cc_start: 0.8003 (mm110) cc_final: 0.7422 (mm-40)
REVERT: c  103 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: c  104 GLU cc_start: 0.8626 (pt0) cc_final: 0.8277 (pt0)
REVERT: c  123 ASP cc_start: 0.7841 (t70) cc_final: 0.7404 (t0)
REVERT: C  123 ASP cc_start: 0.8720 (t70) cc_final: 0.7788 (t0)
REVERT: C  127 GLN cc_start: 0.9435 (mp10) cc_final: 0.8928 (mp-120)
REVERT: C  129 ASN cc_start: 0.8685 (m-40) cc_final: 0.8106 (m110)
REVERT: L   13 SER cc_start: 0.7467 (m) cc_final: 0.7051 (p)
REVERT: L   45 GLU cc_start: 0.8252 (pm20) cc_final: 0.7748 (pm20)
REVERT: L   50 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8500 (mm)
REVERT: L   92 LEU cc_start: 0.6866 (pp) cc_final: 0.6073 (mt)
REVERT: L   93 GLN cc_start: 0.9116 (pm20) cc_final: 0.8662 (pm20)
  outliers start: 27
  outliers final: 22
  residues processed: 146
  average time/residue: 0.0736
  time to fit residues: 12.8039
Evaluate side-chains
  150 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   69 GLN
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   98 GLN
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue    7 VAL
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:    0.2980
   chunk 34 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    4.4386

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN
c 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.100919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.080459 restraints weight = 7515.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.082804 restraints weight = 3565.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.084354 restraints weight = 2147.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.085323 restraints weight = 1515.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.086003 restraints weight = 1211.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.5157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3458  Z= 0.223
  Angle     :  0.863  13.288   4711  Z= 0.427
  Chirality :  0.051   0.171    547
  Planarity :  0.005   0.049    612
  Dihedral  :  5.343  22.800    483
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 23.92 %
    Favored  : 69.89 %
  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: -3.26 (0.38), residues: 426
  helix: -1.25 (0.74), residues: 46
  sheet: -1.85 (0.40), residues: 162
  loop : -2.62 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  47 
 TYR   0.014   0.002   TYR H  35 
 PHE   0.043   0.003   PHE L  74 
 TRP   0.011   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 3457)
  covalent geometry    : angle       0.86334 ( 4709)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.30420 (    2)
  hydrogen bonds       : bond        0.03579 (   99)
  hydrogen bonds       : angle       5.57155 (  264)

*********************** 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
  147 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.8703 (m) cc_final: 0.8421 (p)
REVERT: H   41 ARG cc_start: 0.7051 (ptp-170) cc_final: 0.5486 (tpt90)
REVERT: H   49 GLU cc_start: 0.6205 (tt0) cc_final: 0.5708 (tt0)
REVERT: H   62 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6454 (p90)
REVERT: H  112 TYR cc_start: 0.8871 (m-10) cc_final: 0.8388 (m-10)
REVERT: c   27 ASN cc_start: 0.8775 (t0) cc_final: 0.8267 (t0)
REVERT: c   87 GLN cc_start: 0.8104 (mm110) cc_final: 0.7376 (mm-40)
REVERT: c  103 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7892 (tm-30)
REVERT: c  104 GLU cc_start: 0.8662 (pt0) cc_final: 0.8438 (pt0)
REVERT: c  123 ASP cc_start: 0.7912 (t70) cc_final: 0.7456 (t0)
REVERT: C  123 ASP cc_start: 0.8809 (t70) cc_final: 0.7856 (t0)
REVERT: C  127 GLN cc_start: 0.9451 (mp10) cc_final: 0.8903 (mp-120)
REVERT: C  129 ASN cc_start: 0.8737 (m-40) cc_final: 0.8168 (m110)
REVERT: L   13 SER cc_start: 0.7296 (m) cc_final: 0.6893 (p)
REVERT: L   45 GLU cc_start: 0.8259 (pm20) cc_final: 0.7756 (pm20)
REVERT: L   50 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8469 (mm)
REVERT: L   92 LEU cc_start: 0.6976 (pp) cc_final: 0.6085 (mt)
REVERT: L   93 GLN cc_start: 0.9180 (pm20) cc_final: 0.8802 (pm20)
  outliers start: 23
  outliers final: 20
  residues processed: 137
  average time/residue: 0.0739
  time to fit residues: 12.0681
Evaluate side-chains
  145 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   73 ILE
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   98 GLN
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue    7 VAL
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   88 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0770
   chunk 6 optimal weight:    7.9990
   chunk 40 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0020
   chunk 10 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    3.2152

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN
c  69 GLN
L  40 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.101882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.081669 restraints weight = 7547.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.084035 restraints weight = 3585.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.085572 restraints weight = 2152.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.086508 restraints weight = 1515.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.087228 restraints weight = 1212.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.5316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3458  Z= 0.179
  Angle     :  0.829  11.983   4711  Z= 0.411
  Chirality :  0.050   0.155    547
  Planarity :  0.005   0.048    612
  Dihedral  :  5.262  21.912    483
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.86 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 22.85 %
    Favored  : 70.43 %
  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: -3.15 (0.38), residues: 426
  helix: -1.13 (0.74), residues: 46
  sheet: -1.75 (0.40), residues: 162
  loop : -2.59 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  47 
 TYR   0.013   0.001   TYR H  35 
 PHE   0.038   0.002   PHE L  74 
 TRP   0.008   0.001   TRP H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3457)
  covalent geometry    : angle       0.82920 ( 4709)
  SS BOND              : bond        0.00192 (    1)
  SS BOND              : angle       0.29998 (    2)
  hydrogen bonds       : bond        0.03392 (   99)
  hydrogen bonds       : angle       5.51248 (  264)

********************** 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
  148 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 VAL cc_start: 0.8701 (m) cc_final: 0.8440 (p)
REVERT: H   41 ARG cc_start: 0.7119 (ptp-170) cc_final: 0.5593 (tpt90)
REVERT: H   49 GLU cc_start: 0.6140 (tt0) cc_final: 0.5611 (tt0)
REVERT: H   62 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6404 (p90)
REVERT: c   27 ASN cc_start: 0.8770 (t0) cc_final: 0.8274 (t0)
REVERT: c   87 GLN cc_start: 0.8088 (mm110) cc_final: 0.7408 (mm-40)
REVERT: c  104 GLU cc_start: 0.8624 (pt0) cc_final: 0.8323 (pt0)
REVERT: c  123 ASP cc_start: 0.7874 (t70) cc_final: 0.7392 (t0)
REVERT: C  123 ASP cc_start: 0.8768 (t70) cc_final: 0.7777 (t0)
REVERT: C  127 GLN cc_start: 0.9441 (mp10) cc_final: 0.8858 (mp-120)
REVERT: C  129 ASN cc_start: 0.8606 (m-40) cc_final: 0.8069 (m110)
REVERT: L   45 GLU cc_start: 0.8203 (pm20) cc_final: 0.7703 (pm20)
REVERT: L   50 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8462 (mm)
REVERT: L   93 GLN cc_start: 0.9208 (pm20) cc_final: 0.8874 (pm20)
  outliers start: 25
  outliers final: 21
  residues processed: 135
  average time/residue: 0.0746
  time to fit residues: 11.9461
Evaluate side-chains
  142 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   62 TYR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   73 ILE
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain c residue   34 SER
Chi-restraints excluded: chain c residue   49 THR
Chi-restraints excluded: chain c residue   50 VAL
Chi-restraints excluded: chain c residue   69 GLN
Chi-restraints excluded: chain c residue  118 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   98 GLN
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain L residue    7 VAL
Chi-restraints excluded: chain L residue   35 ASP
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   88 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
c  17 GLN
c  22 ASN
c  69 GLN
L  40 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.098988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.078812 restraints weight = 7716.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.081139 restraints weight = 3620.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.082642 restraints weight = 2181.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.083495 restraints weight = 1548.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.084210 restraints weight = 1257.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.5356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   3458  Z= 0.274
  Angle     :  0.927  13.992   4711  Z= 0.454
  Chirality :  0.052   0.174    547
  Planarity :  0.005   0.045    612
  Dihedral  :  5.470  22.404    483
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.68 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 23.12 %
    Favored  : 69.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.25 (0.38), residues: 426
  helix: -1.43 (0.72), residues: 46
  sheet: -1.86 (0.40), residues: 159
  loop : -2.54 (0.38), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  47 
 TYR   0.018   0.002   TYR H  35 
 PHE   0.029   0.003   PHE L  74 
 TRP   0.013   0.002   TRP L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 ( 3457)
  covalent geometry    : angle       0.92739 ( 4709)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       0.31890 (    2)
  hydrogen bonds       : bond        0.03772 (   99)
  hydrogen bonds       : angle       5.64246 (  264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 732.37 seconds
wall clock time: 13 minutes 20.41 seconds (800.41 seconds total)