Starting phenix.real_space_refine
on Thu Sep 10 23:17:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/28oa_56663/09_2026/28oa_56663.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/28oa_56663/09_2026/28oa_56663.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/28oa_56663/09_2026/28oa_56663.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/28oa_56663/09_2026/28oa_56663.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/28oa_56663/09_2026/28oa_56663.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/28oa_56663/09_2026/28oa_56663.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    3370      2.51       5
     N     850      2.21       5
     O     885      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5130
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1026
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 6, 'TRANS': 125}
          Chain breaks: 1
  Restraints were copied for chains:
    C, D, E, B
  Time building chain proxies: 1.04, per 1000 atoms: 0.20
  Number of scatterers: 5130
  At special positions: 0
  Unit cell: (75.624, 74.802, 125.766, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O     885      8.00
     N     850      7.00
     C    3370      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 144.7 milliseconds
  

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      77.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 14
      removed outlier: 3.526A  pdb=" N   LYS A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 4.216A  pdb=" N   VAL A  21 " --> pdb=" O   VAL A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 50
    Processing helix  chain 'A' and resid 74 through 106
      removed outlier: 4.095A  pdb=" N   PHE A  78 " --> pdb=" O   HIS A  74 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 135
    Processing helix  chain 'C' and resid 2 through 14
    Processing helix  chain 'C' and resid 15 through 40
      removed outlier: 4.217A  pdb=" N   VAL C  21 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 50
    Processing helix  chain 'C' and resid 74 through 106
      removed outlier: 4.095A  pdb=" N   PHE C  78 " --> pdb=" O   HIS C  74 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS C 106 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 135
    Processing helix  chain 'D' and resid 2 through 14
    Processing helix  chain 'D' and resid 15 through 40
      removed outlier: 4.216A  pdb=" N   VAL D  21 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 50
    Processing helix  chain 'D' and resid 74 through 106
      removed outlier: 4.094A  pdb=" N   PHE D  78 " --> pdb=" O   HIS D  74 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS D 106 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 116 through 135
    Processing helix  chain 'E' and resid 2 through 14
    Processing helix  chain 'E' and resid 15 through 40
      removed outlier: 4.216A  pdb=" N   VAL E  21 " --> pdb=" O   VAL E  17 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 50
    Processing helix  chain 'E' and resid 74 through 106
      removed outlier: 4.094A  pdb=" N   PHE E  78 " --> pdb=" O   HIS E  74 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS E 106 " --> pdb=" O   LEU E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 116 through 135
    Processing helix  chain 'B' and resid 2 through 14
    Processing helix  chain 'B' and resid 15 through 40
      removed outlier: 4.216A  pdb=" N   VAL B  21 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 50
    Processing helix  chain 'B' and resid 74 through 106
      removed outlier: 4.094A  pdb=" N   PHE B  78 " --> pdb=" O   HIS B  74 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 135

    395 hydrogen bonds defined for protein.
    1185 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: 0.74

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1630
        1.34 -     1.46: 517
        1.46 -     1.57: 3013
        1.57 -     1.69: 0
        1.69 -     1.80: 50
  Bond restraints: 5210
  Sorted by residual:
  bond pdb=" C   GLU A 108 "
       pdb=" N   PRO A 109 "
    ideal  model  delta    sigma   weight residual
    1.331  1.341 -0.011 1.31e-02 5.83e+03 6.58e-01
  bond pdb=" C   GLU E 108 "
       pdb=" N   PRO E 109 "
    ideal  model  delta    sigma   weight residual
    1.331  1.341 -0.011 1.31e-02 5.83e+03 6.57e-01
  bond pdb=" CB  LEU C  19 "
       pdb=" CG  LEU C  19 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 2.00e-02 2.50e+03 6.51e-01
  bond pdb=" C   GLU D 108 "
       pdb=" N   PRO D 109 "
    ideal  model  delta    sigma   weight residual
    1.331  1.341 -0.011 1.31e-02 5.83e+03 6.44e-01
  bond pdb=" C   GLU B 108 "
       pdb=" N   PRO B 109 "
    ideal  model  delta    sigma   weight residual
    1.331  1.341 -0.010 1.31e-02 5.83e+03 6.21e-01
  ... (remaining 5205 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 6694
        1.25 -     2.50: 238
        2.50 -     3.75: 48
        3.75 -     5.00: 35
        5.00 -     6.25: 10
  Bond angle restraints: 7025
  Sorted by residual:
  angle pdb=" CA  GLN C  56 "
        pdb=" CB  GLN C  56 "
        pdb=" CG  GLN C  56 "
      ideal   model   delta    sigma   weight residual
     114.10  118.58   -4.48 2.00e+00 2.50e-01 5.02e+00
  angle pdb=" CA  GLN B  56 "
        pdb=" CB  GLN B  56 "
        pdb=" CG  GLN B  56 "
      ideal   model   delta    sigma   weight residual
     114.10  118.54   -4.44 2.00e+00 2.50e-01 4.93e+00
  angle pdb=" CA  GLN D  56 "
        pdb=" CB  GLN D  56 "
        pdb=" CG  GLN D  56 "
      ideal   model   delta    sigma   weight residual
     114.10  118.53   -4.43 2.00e+00 2.50e-01 4.91e+00
  angle pdb=" CA  GLN E  56 "
        pdb=" CB  GLN E  56 "
        pdb=" CG  GLN E  56 "
      ideal   model   delta    sigma   weight residual
     114.10  118.53   -4.43 2.00e+00 2.50e-01 4.90e+00
  angle pdb=" N   MET A  42 "
        pdb=" CA  MET A  42 "
        pdb=" C   MET A  42 "
      ideal   model   delta    sigma   weight residual
     109.81  114.68   -4.87 2.21e+00 2.05e-01 4.86e+00
  ... (remaining 7020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.58: 2755
       14.58 -    29.16: 265
       29.16 -    43.74: 130
       43.74 -    58.32: 15
       58.32 -    72.90: 20
  Dihedral angle restraints: 3185
    sinusoidal: 1290
      harmonic: 1895
  Sorted by residual:
  dihedral pdb=" N   ASN B 100 "
           pdb=" CA  ASN B 100 "
           pdb=" CB  ASN B 100 "
           pdb=" CG  ASN B 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.39   59.39     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   ASN E 100 "
           pdb=" CA  ASN E 100 "
           pdb=" CB  ASN E 100 "
           pdb=" CG  ASN E 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.38   59.38     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   ASN A 100 "
           pdb=" CA  ASN A 100 "
           pdb=" CB  ASN A 100 "
           pdb=" CG  ASN A 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.38   59.38     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3182 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 476
       0.027 -    0.054: 223
       0.054 -    0.081: 109
       0.081 -    0.108: 22
       0.108 -    0.136: 15
  Chirality restraints: 845
  Sorted by residual:
  chirality pdb=" CA  GLU B 108 "
            pdb=" N   GLU B 108 "
            pdb=" C   GLU B 108 "
            pdb=" CB  GLU B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  GLU C 108 "
            pdb=" N   GLU C 108 "
            pdb=" C   GLU C 108 "
            pdb=" CB  GLU C 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  GLU E 108 "
            pdb=" N   GLU E 108 "
            pdb=" C   GLU E 108 "
            pdb=" CB  GLU E 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.50e-01
  ... (remaining 842 not shown)

  Planarity restraints: 885
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E  42 "    0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO E  43 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  42 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A  43 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  42 "   -0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO D  43 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D  43 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D  43 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 882 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1701
        2.85 -     3.36: 5856
        3.36 -     3.88: 8460
        3.88 -     4.39: 8748
        4.39 -     4.90: 14344
  Nonbonded interactions: 39109
  Sorted by model distance:
  nonbonded pdb=" O   VAL D 120 "
            pdb=" OG1 THR D 123 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" O   VAL A 120 "
            pdb=" OG1 THR A 123 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" O   VAL B 120 "
            pdb=" OG1 THR B 123 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   VAL E 120 "
            pdb=" OG1 THR E 123 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   VAL C 120 "
            pdb=" OG1 THR C 123 "
     model   vdw
     2.341 3.040
  ... (remaining 39104 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.790
  Find NCS groups from input model:        0.050
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5210  Z= 0.162
  Angle     :  0.668   6.252   7025  Z= 0.356
  Chirality :  0.039   0.136    845
  Planarity :  0.004   0.043    885
  Dihedral  : 15.432  72.899   1945
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  :  5.45 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.25), residues: 640
  helix: -1.33 (0.16), residues: 470
  sheet:  None (None), residues: 0
  loop : -1.88 (0.44), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 135 
 TYR   0.006   0.002   TYR D  75 
 PHE   0.014   0.001   PHE E  93 
 HIS   0.003   0.002   HIS B  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 5210)
  covalent geometry    : angle       0.66760 /  0.36 ( 7025)
  hydrogen bonds       : bond        0.10563 /  7.50 (  395)
  hydrogen bonds       : angle       4.46165 /  3.26 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 235
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6946 (mtp) cc_final: 0.6447 (ptt)
REVERT: A    5 LYS cc_start: 0.9332 (mttt) cc_final: 0.9088 (mttm)
REVERT: A   62 ARG cc_start: 0.7708 (tpm170) cc_final: 0.7361 (tmm-80)
REVERT: A   90 PHE cc_start: 0.8294 (t80) cc_final: 0.7976 (t80)
REVERT: A  124 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8782 (mt-10)
REVERT: A  127 ASP cc_start: 0.8767 (m-30) cc_final: 0.8565 (m-30)
REVERT: C    1 MET cc_start: 0.7394 (mtp) cc_final: 0.6819 (ptt)
REVERT: C    5 LYS cc_start: 0.9323 (mttt) cc_final: 0.8994 (mttm)
REVERT: C   62 ARG cc_start: 0.7730 (tpm170) cc_final: 0.7466 (tmm-80)
REVERT: C  118 GLU cc_start: 0.8105 (pm20) cc_final: 0.7840 (pm20)
REVERT: C  124 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8856 (mt-10)
REVERT: C  127 ASP cc_start: 0.8795 (m-30) cc_final: 0.8566 (m-30)
REVERT: D    5 LYS cc_start: 0.9347 (mttt) cc_final: 0.9025 (mttm)
REVERT: D   73 MET cc_start: 0.9022 (tpt) cc_final: 0.8770 (tpt)
REVERT: D   94 MET cc_start: 0.8187 (mmm) cc_final: 0.7730 (mtp)
REVERT: D  118 GLU cc_start: 0.7896 (pm20) cc_final: 0.7612 (pm20)
REVERT: D  124 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8566 (pt0)
REVERT: E    5 LYS cc_start: 0.9294 (mttt) cc_final: 0.9014 (mttm)
REVERT: E   19 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8674 (tt)
REVERT: E   90 PHE cc_start: 0.8027 (t80) cc_final: 0.7685 (t80)
REVERT: E   94 MET cc_start: 0.8045 (mmm) cc_final: 0.7570 (ttm)
REVERT: E  118 GLU cc_start: 0.7922 (pm20) cc_final: 0.7592 (pm20)
REVERT: E  124 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8676 (pt0)
REVERT: B    1 MET cc_start: 0.7501 (mtp) cc_final: 0.6886 (ptt)
REVERT: B   62 ARG cc_start: 0.7788 (tpm170) cc_final: 0.6995 (tmm-80)
REVERT: B   94 MET cc_start: 0.8212 (mmm) cc_final: 0.7963 (mtp)
REVERT: B   97 LYS cc_start: 0.8572 (tptt) cc_final: 0.8365 (tmtt)
REVERT: B  106 LYS cc_start: 0.7643 (mtmt) cc_final: 0.7358 (ptpt)
REVERT: B  118 GLU cc_start: 0.7962 (pm20) cc_final: 0.7531 (pm20)
  outliers start: 20
  outliers final: 0
  residues processed: 245
  average time/residue: 0.0872
  time to fit residues: 26.1615
Evaluate side-chains
  212 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 211
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.0370
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.3462

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  74 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.162682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115023 restraints weight = 9025.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.116484 restraints weight = 7282.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.117560 restraints weight = 6399.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.118036 restraints weight = 5890.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.118037 restraints weight = 5618.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5210  Z= 0.187
  Angle     :  0.689   6.145   7025  Z= 0.357
  Chirality :  0.040   0.127    845
  Planarity :  0.005   0.045    885
  Dihedral  :  4.470  16.014    685
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.91 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.29), residues: 640
  helix:  0.48 (0.20), residues: 475
  sheet:  None (None), residues: 0
  loop : -1.19 (0.49), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  13 
 TYR   0.005   0.002   TYR D  75 
 PHE   0.014   0.002   PHE E  93 
 HIS   0.002   0.001   HIS E  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.19 ( 5210)
  covalent geometry    : angle       0.68936 /  0.36 ( 7025)
  hydrogen bonds       : bond        0.04406 /  3.11 (  395)
  hydrogen bonds       : angle       3.99262 /  2.92 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 232
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6808 (mtp) cc_final: 0.6482 (ptt)
REVERT: A    5 LYS cc_start: 0.9293 (mttt) cc_final: 0.8686 (mttm)
REVERT: A    8 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7460 (ttp80)
REVERT: A   54 PHE cc_start: 0.6682 (m-10) cc_final: 0.6444 (m-10)
REVERT: A   62 ARG cc_start: 0.7766 (tpm170) cc_final: 0.7405 (tmm-80)
REVERT: A   90 PHE cc_start: 0.8247 (t80) cc_final: 0.8030 (t80)
REVERT: A  118 GLU cc_start: 0.7977 (pp20) cc_final: 0.7757 (pm20)
REVERT: A  124 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8727 (mt-10)
REVERT: C    1 MET cc_start: 0.7191 (mtp) cc_final: 0.6706 (ptt)
REVERT: C    5 LYS cc_start: 0.9301 (mttt) cc_final: 0.9033 (mttm)
REVERT: C   45 LEU cc_start: 0.8850 (tp) cc_final: 0.8648 (mm)
REVERT: C   54 PHE cc_start: 0.6626 (m-10) cc_final: 0.6367 (m-10)
REVERT: C  124 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8770 (mt-10)
REVERT: C  127 ASP cc_start: 0.8780 (m-30) cc_final: 0.8428 (m-30)
REVERT: D    5 LYS cc_start: 0.9292 (mttt) cc_final: 0.8967 (mttm)
REVERT: D   62 ARG cc_start: 0.8367 (tmm-80) cc_final: 0.7741 (tmm-80)
REVERT: D   90 PHE cc_start: 0.8217 (t80) cc_final: 0.7820 (t80)
REVERT: D   94 MET cc_start: 0.8260 (mmm) cc_final: 0.7902 (ttp)
REVERT: D  118 GLU cc_start: 0.7800 (pm20) cc_final: 0.7561 (pm20)
REVERT: D  123 THR cc_start: 0.9483 (p) cc_final: 0.9264 (p)
REVERT: D  124 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8689 (mt-10)
REVERT: D  127 ASP cc_start: 0.8951 (m-30) cc_final: 0.8723 (m-30)
REVERT: E    5 LYS cc_start: 0.9254 (mttt) cc_final: 0.8952 (mttm)
REVERT: E   62 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.7877 (tmm-80)
REVERT: E   90 PHE cc_start: 0.8118 (t80) cc_final: 0.7896 (t80)
REVERT: E   94 MET cc_start: 0.8205 (mmm) cc_final: 0.7638 (ttm)
REVERT: E  118 GLU cc_start: 0.7727 (pm20) cc_final: 0.7371 (pm20)
REVERT: E  123 THR cc_start: 0.9458 (p) cc_final: 0.9231 (p)
REVERT: E  124 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8630 (mt-10)
REVERT: B    1 MET cc_start: 0.7363 (mtp) cc_final: 0.6876 (ptt)
REVERT: B   55 LYS cc_start: 0.7822 (tmmt) cc_final: 0.7528 (tmmt)
REVERT: B   61 LEU cc_start: 0.8075 (mm) cc_final: 0.7777 (mm)
REVERT: B   62 ARG cc_start: 0.7784 (tpm170) cc_final: 0.7299 (tmm-80)
REVERT: B   94 MET cc_start: 0.8348 (mmm) cc_final: 0.8064 (mtp)
REVERT: B  118 GLU cc_start: 0.7858 (pm20) cc_final: 0.7444 (pm20)
REVERT: B  124 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8486 (mt-10)
  outliers start: 3
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0880
  time to fit residues: 25.2600
Evaluate side-chains
  207 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.0582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.162964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.110161 restraints weight = 9443.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.111273 restraints weight = 7885.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112555 restraints weight = 7053.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.113013 restraints weight = 6534.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.113240 restraints weight = 6259.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5210  Z= 0.166
  Angle     :  0.693   5.989   7025  Z= 0.359
  Chirality :  0.042   0.156    845
  Planarity :  0.006   0.047    885
  Dihedral  :  4.231  15.853    685
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.30), residues: 640
  helix:  1.14 (0.20), residues: 475
  sheet:  None (None), residues: 0
  loop : -1.07 (0.49), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  13 
 TYR   0.004   0.001   TYR A  75 
 PHE   0.021   0.002   PHE B  90 
 HIS   0.008   0.002   HIS B  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 ( 5210)
  covalent geometry    : angle       0.69310 /  0.36 ( 7025)
  hydrogen bonds       : bond        0.04141 /  2.88 (  395)
  hydrogen bonds       : angle       3.86146 /  2.84 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6941 (mtp) cc_final: 0.6231 (ptt)
REVERT: A    4 ILE cc_start: 0.9250 (mp) cc_final: 0.8904 (mt)
REVERT: A    5 LYS cc_start: 0.9237 (mttt) cc_final: 0.8946 (mttm)
REVERT: A   61 LEU cc_start: 0.8110 (mm) cc_final: 0.7894 (mm)
REVERT: A   62 ARG cc_start: 0.7787 (tpm170) cc_final: 0.7478 (tmm-80)
REVERT: A  124 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8678 (mt-10)
REVERT: A  127 ASP cc_start: 0.9063 (m-30) cc_final: 0.8845 (m-30)
REVERT: C    1 MET cc_start: 0.7345 (mtp) cc_final: 0.6814 (ptt)
REVERT: C    5 LYS cc_start: 0.9255 (mttt) cc_final: 0.9020 (mttm)
REVERT: C   62 ARG cc_start: 0.8385 (tmm-80) cc_final: 0.7967 (ttt-90)
REVERT: C  124 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8705 (mt-10)
REVERT: D   45 LEU cc_start: 0.8806 (tp) cc_final: 0.8554 (mm)
REVERT: D   62 ARG cc_start: 0.8431 (tmm-80) cc_final: 0.7734 (tmm-80)
REVERT: D   90 PHE cc_start: 0.8177 (t80) cc_final: 0.7781 (t80)
REVERT: D   94 MET cc_start: 0.8275 (mmm) cc_final: 0.7833 (ttp)
REVERT: D  124 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8644 (mt-10)
REVERT: D  127 ASP cc_start: 0.9049 (m-30) cc_final: 0.8828 (m-30)
REVERT: E   62 ARG cc_start: 0.8477 (tmm-80) cc_final: 0.7980 (tmm-80)
REVERT: E   94 MET cc_start: 0.8224 (mmm) cc_final: 0.7600 (ttm)
REVERT: E  123 THR cc_start: 0.9491 (p) cc_final: 0.9281 (p)
REVERT: E  124 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8560 (mt-10)
REVERT: E  127 ASP cc_start: 0.9054 (m-30) cc_final: 0.8797 (m-30)
REVERT: B    1 MET cc_start: 0.7408 (mtp) cc_final: 0.6837 (ptt)
REVERT: B   61 LEU cc_start: 0.8223 (mm) cc_final: 0.7974 (mm)
REVERT: B   62 ARG cc_start: 0.7860 (tpm170) cc_final: 0.7474 (tmm-80)
REVERT: B   94 MET cc_start: 0.8450 (mmm) cc_final: 0.7938 (mtp)
REVERT: B  118 GLU cc_start: 0.7953 (pm20) cc_final: 0.7565 (pm20)
REVERT: B  123 THR cc_start: 0.9507 (p) cc_final: 0.9197 (p)
REVERT: B  124 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8407 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.0891
  time to fit residues: 24.6556
Evaluate side-chains
  203 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0270
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.9242

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.162819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.109958 restraints weight = 9595.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.111262 restraints weight = 7748.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112680 restraints weight = 6832.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.112845 restraints weight = 6289.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113055 restraints weight = 6168.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5210  Z= 0.154
  Angle     :  0.674   5.876   7025  Z= 0.346
  Chirality :  0.041   0.153    845
  Planarity :  0.005   0.046    885
  Dihedral  :  4.167  15.375    685
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.30), residues: 640
  helix:  1.57 (0.20), residues: 475
  sheet:  None (None), residues: 0
  loop : -0.93 (0.50), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A   8 
 TYR   0.005   0.001   TYR B  75 
 PHE   0.010   0.001   PHE A  10 
 HIS   0.007   0.002   HIS B  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 5210)
  covalent geometry    : angle       0.67402 /  0.35 ( 7025)
  hydrogen bonds       : bond        0.03814 /  2.67 (  395)
  hydrogen bonds       : angle       3.70284 /  2.71 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7143 (mtp) cc_final: 0.6368 (ptt)
REVERT: A    4 ILE cc_start: 0.9227 (mp) cc_final: 0.8918 (mt)
REVERT: A   42 MET cc_start: 0.8017 (mmp) cc_final: 0.7634 (mtp)
REVERT: A   90 PHE cc_start: 0.8237 (t80) cc_final: 0.7892 (t80)
REVERT: A  124 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8593 (mt-10)
REVERT: C    1 MET cc_start: 0.7400 (mtp) cc_final: 0.6781 (ptt)
REVERT: C    5 LYS cc_start: 0.9264 (mttt) cc_final: 0.9056 (mttm)
REVERT: C   55 LYS cc_start: 0.7401 (tmmt) cc_final: 0.7119 (ttpp)
REVERT: C   62 ARG cc_start: 0.8444 (tmm-80) cc_final: 0.7964 (ttt-90)
REVERT: C   90 PHE cc_start: 0.8202 (t80) cc_final: 0.7936 (t80)
REVERT: C  124 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8729 (mt-10)
REVERT: D   45 LEU cc_start: 0.8940 (tp) cc_final: 0.8697 (mm)
REVERT: D   62 ARG cc_start: 0.8402 (tmm-80) cc_final: 0.7844 (tmm-80)
REVERT: D   90 PHE cc_start: 0.8178 (t80) cc_final: 0.7822 (t80)
REVERT: D   94 MET cc_start: 0.8327 (mmm) cc_final: 0.7869 (ttp)
REVERT: D  123 THR cc_start: 0.9530 (p) cc_final: 0.9328 (p)
REVERT: D  124 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8664 (mt-10)
REVERT: D  127 ASP cc_start: 0.9072 (m-30) cc_final: 0.8741 (m-30)
REVERT: E    1 MET cc_start: 0.6013 (ptt) cc_final: 0.5686 (ptp)
REVERT: E   62 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.7609 (tmm160)
REVERT: E   90 PHE cc_start: 0.8314 (t80) cc_final: 0.7826 (t80)
REVERT: E   94 MET cc_start: 0.8333 (mmm) cc_final: 0.7595 (ttm)
REVERT: E  123 THR cc_start: 0.9517 (p) cc_final: 0.9303 (p)
REVERT: E  124 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8570 (mt-10)
REVERT: E  127 ASP cc_start: 0.9071 (m-30) cc_final: 0.8759 (m-30)
REVERT: B    1 MET cc_start: 0.7445 (mtp) cc_final: 0.6765 (ptt)
REVERT: B   62 ARG cc_start: 0.7874 (tpm170) cc_final: 0.7554 (tmm-80)
REVERT: B   94 MET cc_start: 0.8490 (mmm) cc_final: 0.7872 (mtp)
REVERT: B  118 GLU cc_start: 0.7880 (pm20) cc_final: 0.7503 (pm20)
REVERT: B  123 THR cc_start: 0.9519 (p) cc_final: 0.9232 (p)
REVERT: B  124 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8394 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0898
  time to fit residues: 24.6063
Evaluate side-chains
  210 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.6782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.164511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.110482 restraints weight = 9661.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112493 restraints weight = 7385.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.113736 restraints weight = 6261.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.114763 restraints weight = 5683.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114768 restraints weight = 5333.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5210  Z= 0.140
  Angle     :  0.682   6.075   7025  Z= 0.349
  Chirality :  0.040   0.140    845
  Planarity :  0.005   0.047    885
  Dihedral  :  4.130  15.730    685
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.30), residues: 640
  helix:  1.92 (0.20), residues: 475
  sheet:  None (None), residues: 0
  loop : -1.10 (0.48), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D   8 
 TYR   0.006   0.002   TYR A  75 
 PHE   0.023   0.001   PHE B  90 
 HIS   0.007   0.002   HIS B  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 ( 5210)
  covalent geometry    : angle       0.68231 /  0.35 ( 7025)
  hydrogen bonds       : bond        0.03607 /  2.52 (  395)
  hydrogen bonds       : angle       3.58030 /  2.62 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7290 (mtp) cc_final: 0.6539 (ptp)
REVERT: A    4 ILE cc_start: 0.9236 (mp) cc_final: 0.8960 (mt)
REVERT: A   42 MET cc_start: 0.8140 (mmp) cc_final: 0.7558 (mtp)
REVERT: A   62 ARG cc_start: 0.8247 (ttt-90) cc_final: 0.7452 (tmm-80)
REVERT: A   90 PHE cc_start: 0.8273 (t80) cc_final: 0.7856 (t80)
REVERT: A  124 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8527 (mt-10)
REVERT: C    1 MET cc_start: 0.7402 (mtp) cc_final: 0.6729 (ptt)
REVERT: C   62 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.7955 (ttt-90)
REVERT: C   90 PHE cc_start: 0.8244 (t80) cc_final: 0.7945 (t80)
REVERT: C  124 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8707 (mt-10)
REVERT: D   45 LEU cc_start: 0.8897 (tp) cc_final: 0.8674 (mm)
REVERT: D   62 ARG cc_start: 0.8394 (tmm-80) cc_final: 0.7837 (tmm-80)
REVERT: D   90 PHE cc_start: 0.8190 (t80) cc_final: 0.7801 (t80)
REVERT: D   94 MET cc_start: 0.8321 (mmm) cc_final: 0.7848 (ttp)
REVERT: D  123 THR cc_start: 0.9517 (p) cc_final: 0.9307 (p)
REVERT: D  124 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8612 (mt-10)
REVERT: D  127 ASP cc_start: 0.9083 (m-30) cc_final: 0.8754 (m-30)
REVERT: E   62 ARG cc_start: 0.8538 (tmm-80) cc_final: 0.7706 (tmm160)
REVERT: E   90 PHE cc_start: 0.8289 (t80) cc_final: 0.7829 (t80)
REVERT: E   94 MET cc_start: 0.8320 (mmm) cc_final: 0.7607 (ttm)
REVERT: E  123 THR cc_start: 0.9509 (p) cc_final: 0.9297 (p)
REVERT: E  124 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8797 (mt-10)
REVERT: E  127 ASP cc_start: 0.9109 (m-30) cc_final: 0.8761 (m-30)
REVERT: B    1 MET cc_start: 0.7365 (mtp) cc_final: 0.6767 (ptt)
REVERT: B   61 LEU cc_start: 0.8132 (mm) cc_final: 0.7886 (mm)
REVERT: B   94 MET cc_start: 0.8384 (mmm) cc_final: 0.7902 (ttp)
REVERT: B  118 GLU cc_start: 0.7933 (pm20) cc_final: 0.7558 (pm20)
REVERT: B  123 THR cc_start: 0.9534 (p) cc_final: 0.9256 (p)
REVERT: B  124 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8354 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0799
  time to fit residues: 21.2120
Evaluate side-chains
  209 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  74 HIS
B  74 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.165082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110934 restraints weight = 9717.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112786 restraints weight = 7432.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114210 restraints weight = 6326.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114210 restraints weight = 5654.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114210 restraints weight = 5654.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5210  Z= 0.140
  Angle     :  0.700   6.017   7025  Z= 0.358
  Chirality :  0.040   0.131    845
  Planarity :  0.005   0.046    885
  Dihedral  :  4.059  14.441    685
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.30), residues: 640
  helix:  2.09 (0.21), residues: 475
  sheet:  None (None), residues: 0
  loop : -1.14 (0.47), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D   8 
 TYR   0.005   0.002   TYR D  75 
 PHE   0.014   0.001   PHE B  54 
 HIS   0.006   0.002   HIS B  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 5210)
  covalent geometry    : angle       0.70045 /  0.36 ( 7025)
  hydrogen bonds       : bond        0.03519 /  2.47 (  395)
  hydrogen bonds       : angle       3.56358 /  2.63 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7309 (mtp) cc_final: 0.6445 (ptt)
REVERT: A    8 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7593 (ttp80)
REVERT: A   62 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7355 (tmm-80)
REVERT: A   90 PHE cc_start: 0.8289 (t80) cc_final: 0.8004 (t80)
REVERT: A  124 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8513 (mt-10)
REVERT: A  132 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8594 (tp-100)
REVERT: C    1 MET cc_start: 0.7100 (mtp) cc_final: 0.6665 (ptt)
REVERT: C   62 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.8010 (ttt-90)
REVERT: C   90 PHE cc_start: 0.8269 (t80) cc_final: 0.7944 (t80)
REVERT: C  124 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8715 (mt-10)
REVERT: D   45 LEU cc_start: 0.8926 (tp) cc_final: 0.8684 (mm)
REVERT: D   49 ILE cc_start: 0.8482 (tp) cc_final: 0.8266 (tt)
REVERT: D   62 ARG cc_start: 0.8438 (tmm-80) cc_final: 0.7795 (tmm-80)
REVERT: D   90 PHE cc_start: 0.8179 (t80) cc_final: 0.7949 (t80)
REVERT: D   94 MET cc_start: 0.8342 (mmm) cc_final: 0.7803 (ttp)
REVERT: D  123 THR cc_start: 0.9519 (p) cc_final: 0.9299 (p)
REVERT: D  124 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8597 (mt-10)
REVERT: D  127 ASP cc_start: 0.9078 (m-30) cc_final: 0.8738 (m-30)
REVERT: E    8 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7675 (ttp80)
REVERT: E   42 MET cc_start: 0.8317 (mmp) cc_final: 0.7765 (mmm)
REVERT: E   62 ARG cc_start: 0.8560 (tmm-80) cc_final: 0.7808 (ttp-170)
REVERT: E   90 PHE cc_start: 0.8245 (t80) cc_final: 0.7805 (t80)
REVERT: E   94 MET cc_start: 0.8383 (mmm) cc_final: 0.7717 (ttm)
REVERT: E  123 THR cc_start: 0.9518 (p) cc_final: 0.9288 (p)
REVERT: E  124 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8761 (mt-10)
REVERT: E  127 ASP cc_start: 0.9097 (m-30) cc_final: 0.8756 (m-30)
REVERT: B    1 MET cc_start: 0.7440 (mtp) cc_final: 0.6740 (ptp)
REVERT: B   94 MET cc_start: 0.8452 (mmm) cc_final: 0.7917 (ttp)
REVERT: B  118 GLU cc_start: 0.7944 (pm20) cc_final: 0.7565 (pm20)
REVERT: B  123 THR cc_start: 0.9542 (p) cc_final: 0.9284 (p)
REVERT: B  124 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8377 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0863
  time to fit residues: 23.0597
Evaluate side-chains
  199 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    0.3980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.163976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.112708 restraints weight = 9586.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.114260 restraints weight = 7849.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.114898 restraints weight = 6903.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.115635 restraints weight = 6436.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.116296 restraints weight = 6110.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5210  Z= 0.139
  Angle     :  0.710   6.364   7025  Z= 0.357
  Chirality :  0.040   0.146    845
  Planarity :  0.005   0.044    885
  Dihedral  :  4.084  15.622    685
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.31), residues: 640
  helix:  2.07 (0.21), residues: 475
  sheet:  None (None), residues: 0
  loop : -1.07 (0.47), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D   8 
 TYR   0.005   0.002   TYR C  75 
 PHE   0.023   0.001   PHE B  90 
 HIS   0.006   0.002   HIS A  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 5210)
  covalent geometry    : angle       0.71004 /  0.36 ( 7025)
  hydrogen bonds       : bond        0.03459 /  2.42 (  395)
  hydrogen bonds       : angle       3.56292 /  2.60 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7264 (mtp) cc_final: 0.6413 (ptt)
REVERT: A   42 MET cc_start: 0.8198 (mmp) cc_final: 0.7643 (mtm)
REVERT: A   62 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7372 (tmm-80)
REVERT: A  102 LEU cc_start: 0.9389 (tt) cc_final: 0.9154 (tt)
REVERT: A  124 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8531 (mt-10)
REVERT: C    1 MET cc_start: 0.7128 (mtp) cc_final: 0.6637 (ptt)
REVERT: C   62 ARG cc_start: 0.8486 (tmm-80) cc_final: 0.7977 (ttt-90)
REVERT: C   90 PHE cc_start: 0.8225 (t80) cc_final: 0.7919 (t80)
REVERT: C  124 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8716 (mt-10)
REVERT: D   45 LEU cc_start: 0.8850 (tp) cc_final: 0.8627 (mm)
REVERT: D   49 ILE cc_start: 0.8459 (tp) cc_final: 0.8227 (tt)
REVERT: D   62 ARG cc_start: 0.8432 (tmm-80) cc_final: 0.7731 (tmm-80)
REVERT: D   94 MET cc_start: 0.8324 (mmm) cc_final: 0.7793 (ttp)
REVERT: D  123 THR cc_start: 0.9532 (p) cc_final: 0.9320 (p)
REVERT: D  124 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8624 (mt-10)
REVERT: D  127 ASP cc_start: 0.9080 (m-30) cc_final: 0.8749 (m-30)
REVERT: E    8 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7686 (ttp80)
REVERT: E   42 MET cc_start: 0.8375 (mmp) cc_final: 0.7889 (mmm)
REVERT: E   62 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.7711 (ttp80)
REVERT: E   90 PHE cc_start: 0.8243 (t80) cc_final: 0.8035 (t80)
REVERT: E   94 MET cc_start: 0.8343 (mmm) cc_final: 0.7664 (ttm)
REVERT: E  123 THR cc_start: 0.9524 (p) cc_final: 0.9300 (p)
REVERT: E  124 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8738 (mt-10)
REVERT: E  127 ASP cc_start: 0.9107 (m-30) cc_final: 0.8765 (m-30)
REVERT: B    1 MET cc_start: 0.7400 (mtp) cc_final: 0.6725 (ptp)
REVERT: B   94 MET cc_start: 0.8499 (mmm) cc_final: 0.7995 (ttp)
REVERT: B  118 GLU cc_start: 0.7918 (pm20) cc_final: 0.7541 (pm20)
REVERT: B  123 THR cc_start: 0.9550 (p) cc_final: 0.9286 (p)
REVERT: B  124 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8395 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0837
  time to fit residues: 23.0598
Evaluate side-chains
  197 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 53 optimal weight:    0.1980
   chunk 44 optimal weight:    0.0570
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.4980
   overall best weight:    0.4898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.166250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112539 restraints weight = 9665.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.114446 restraints weight = 7370.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116018 restraints weight = 6265.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.116535 restraints weight = 5653.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117116 restraints weight = 5369.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5210  Z= 0.137
  Angle     :  0.734   6.460   7025  Z= 0.369
  Chirality :  0.040   0.148    845
  Planarity :  0.005   0.044    885
  Dihedral  :  4.006  16.125    685
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.31), residues: 640
  helix:  2.17 (0.21), residues: 475
  sheet:  None (None), residues: 0
  loop : -1.02 (0.48), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  13 
 TYR   0.004   0.001   TYR A  75 
 PHE   0.022   0.001   PHE A  90 
 HIS   0.006   0.002   HIS A  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.14 ( 5210)
  covalent geometry    : angle       0.73428 /  0.37 ( 7025)
  hydrogen bonds       : bond        0.03390 /  2.35 (  395)
  hydrogen bonds       : angle       3.48567 /  2.55 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7251 (mtp) cc_final: 0.6393 (ptt)
REVERT: A   42 MET cc_start: 0.8346 (mmp) cc_final: 0.7662 (mtm)
REVERT: A   62 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7346 (tmm-80)
REVERT: A  102 LEU cc_start: 0.9401 (tt) cc_final: 0.9183 (tt)
REVERT: A  124 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8511 (mt-10)
REVERT: C    1 MET cc_start: 0.7112 (mtp) cc_final: 0.6621 (ptt)
REVERT: C   62 ARG cc_start: 0.8480 (tmm-80) cc_final: 0.8024 (ttt-90)
REVERT: C  124 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8696 (mt-10)
REVERT: D   62 ARG cc_start: 0.8431 (tmm-80) cc_final: 0.7728 (tmm-80)
REVERT: D   90 PHE cc_start: 0.8218 (t80) cc_final: 0.7963 (t80)
REVERT: D   94 MET cc_start: 0.8349 (mmm) cc_final: 0.7809 (ttp)
REVERT: D  123 THR cc_start: 0.9529 (p) cc_final: 0.9325 (p)
REVERT: D  124 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8614 (mt-10)
REVERT: D  127 ASP cc_start: 0.9103 (m-30) cc_final: 0.8781 (m-30)
REVERT: E    8 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7687 (ttp80)
REVERT: E   42 MET cc_start: 0.8445 (mmp) cc_final: 0.7898 (mmm)
REVERT: E   90 PHE cc_start: 0.8279 (t80) cc_final: 0.8067 (t80)
REVERT: E   94 MET cc_start: 0.8373 (mmm) cc_final: 0.7679 (ttp)
REVERT: E  123 THR cc_start: 0.9523 (p) cc_final: 0.9300 (p)
REVERT: E  124 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8725 (mt-10)
REVERT: E  127 ASP cc_start: 0.9125 (m-30) cc_final: 0.8773 (m-30)
REVERT: B    1 MET cc_start: 0.7396 (mtp) cc_final: 0.6697 (ptp)
REVERT: B   62 ARG cc_start: 0.7721 (tmm-80) cc_final: 0.7471 (tmm-80)
REVERT: B   94 MET cc_start: 0.8498 (mmm) cc_final: 0.7974 (ttp)
REVERT: B  118 GLU cc_start: 0.7918 (pm20) cc_final: 0.7542 (pm20)
REVERT: B  123 THR cc_start: 0.9534 (p) cc_final: 0.9282 (p)
REVERT: B  124 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8370 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0691
  time to fit residues: 18.6233
Evaluate side-chains
  200 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0050
   chunk 56 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.165754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.114374 restraints weight = 9507.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.115845 restraints weight = 7746.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.117030 restraints weight = 6808.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.117766 restraints weight = 6272.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.117766 restraints weight = 5944.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.5077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5210  Z= 0.141
  Angle     :  0.736   6.729   7025  Z= 0.374
  Chirality :  0.041   0.131    845
  Planarity :  0.005   0.050    885
  Dihedral  :  3.955  14.709    685
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.31), residues: 640
  helix:  2.13 (0.21), residues: 475
  sheet:  None (None), residues: 0
  loop : -0.93 (0.48), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  13 
 TYR   0.004   0.001   TYR E  75 
 PHE   0.022   0.001   PHE C  90 
 HIS   0.005   0.001   HIS A  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 5210)
  covalent geometry    : angle       0.73586 /  0.37 ( 7025)
  hydrogen bonds       : bond        0.03423 /  2.40 (  395)
  hydrogen bonds       : angle       3.53315 /  2.58 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7136 (mtp) cc_final: 0.6527 (ptp)
REVERT: A   42 MET cc_start: 0.8372 (mmp) cc_final: 0.7687 (mtm)
REVERT: A   62 ARG cc_start: 0.8008 (ttt-90) cc_final: 0.7340 (tmm-80)
REVERT: A  102 LEU cc_start: 0.9390 (tt) cc_final: 0.9182 (tt)
REVERT: A  124 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8524 (mt-10)
REVERT: C    1 MET cc_start: 0.7041 (mtp) cc_final: 0.6610 (ptt)
REVERT: C   62 ARG cc_start: 0.8510 (tmm-80) cc_final: 0.7588 (ttp80)
REVERT: C  124 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8701 (mt-10)
REVERT: C  127 ASP cc_start: 0.9161 (m-30) cc_final: 0.8948 (m-30)
REVERT: D   62 ARG cc_start: 0.8393 (tmm-80) cc_final: 0.7705 (tmm-80)
REVERT: D   94 MET cc_start: 0.8361 (mmm) cc_final: 0.7809 (ttp)
REVERT: D  123 THR cc_start: 0.9529 (p) cc_final: 0.9321 (p)
REVERT: D  124 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8621 (mt-10)
REVERT: D  127 ASP cc_start: 0.9074 (m-30) cc_final: 0.8741 (m-30)
REVERT: E    8 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7655 (ttp80)
REVERT: E   42 MET cc_start: 0.8467 (mmp) cc_final: 0.7909 (mmm)
REVERT: E   94 MET cc_start: 0.8346 (mmm) cc_final: 0.7676 (ttp)
REVERT: E  123 THR cc_start: 0.9521 (p) cc_final: 0.9298 (p)
REVERT: E  124 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8713 (mt-10)
REVERT: E  127 ASP cc_start: 0.9089 (m-30) cc_final: 0.8747 (m-30)
REVERT: B    1 MET cc_start: 0.7380 (mtp) cc_final: 0.6637 (ptp)
REVERT: B   62 ARG cc_start: 0.7747 (tmm-80) cc_final: 0.7478 (tmm-80)
REVERT: B   93 PHE cc_start: 0.7937 (t80) cc_final: 0.6612 (m-80)
REVERT: B   94 MET cc_start: 0.8463 (mmm) cc_final: 0.7855 (ttp)
REVERT: B  118 GLU cc_start: 0.7853 (pm20) cc_final: 0.7482 (pm20)
REVERT: B  123 THR cc_start: 0.9540 (p) cc_final: 0.9283 (p)
REVERT: B  124 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8402 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0784
  time to fit residues: 21.6800
Evaluate side-chains
  205 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 4 optimal weight:    0.0050
   chunk 43 optimal weight:    0.0980
   chunk 47 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 63 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0980
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.2194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 132 GLN
** C  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  74 HIS
** D  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 HIS
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.189923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.141083 restraints weight = 9368.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.143466 restraints weight = 6943.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.145277 restraints weight = 5705.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.146298 restraints weight = 5012.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.146351 restraints weight = 4613.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.5325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5210  Z= 0.138
  Angle     :  0.743   7.279   7025  Z= 0.374
  Chirality :  0.040   0.142    845
  Planarity :  0.005   0.052    885
  Dihedral  :  3.886  15.638    685
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.18 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.29 (0.32), residues: 640
  helix:  2.32 (0.21), residues: 475
  sheet:  None (None), residues: 0
  loop : -0.94 (0.48), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A   8 
 TYR   0.008   0.002   TYR E  75 
 PHE   0.023   0.001   PHE B  90 
 HIS   0.004   0.001   HIS A  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 ( 5210)
  covalent geometry    : angle       0.74333 /  0.37 ( 7025)
  hydrogen bonds       : bond        0.03261 /  2.27 (  395)
  hydrogen bonds       : angle       3.43240 /  2.52 ( 1185)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7076 (mtp) cc_final: 0.6513 (ptp)
REVERT: A   42 MET cc_start: 0.8394 (mmp) cc_final: 0.7833 (mmm)
REVERT: A   62 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7320 (tmm-80)
REVERT: A  124 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8493 (mt-10)
REVERT: C    1 MET cc_start: 0.7008 (mtp) cc_final: 0.6580 (ptt)
REVERT: C   42 MET cc_start: 0.6143 (ttt) cc_final: 0.5860 (mmm)
REVERT: C   62 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.7585 (ttp80)
REVERT: C  124 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8679 (mt-10)
REVERT: D   42 MET cc_start: 0.8132 (mmp) cc_final: 0.7490 (mtp)
REVERT: D   62 ARG cc_start: 0.8270 (tmm-80) cc_final: 0.7688 (tmm-80)
REVERT: D   94 MET cc_start: 0.8293 (mmm) cc_final: 0.7827 (ttp)
REVERT: D  123 THR cc_start: 0.9493 (p) cc_final: 0.9266 (p)
REVERT: D  124 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8591 (mt-10)
REVERT: D  127 ASP cc_start: 0.9012 (m-30) cc_final: 0.8673 (m-30)
REVERT: E    1 MET cc_start: 0.5765 (ptt) cc_final: 0.5416 (ptp)
REVERT: E    8 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7663 (ttp80)
REVERT: E   42 MET cc_start: 0.8419 (mmp) cc_final: 0.7846 (mmm)
REVERT: E   94 MET cc_start: 0.8291 (mmm) cc_final: 0.7665 (ttm)
REVERT: E  123 THR cc_start: 0.9473 (p) cc_final: 0.9227 (p)
REVERT: E  124 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8692 (mt-10)
REVERT: E  127 ASP cc_start: 0.9028 (m-30) cc_final: 0.8673 (m-30)
REVERT: B    1 MET cc_start: 0.7315 (mtp) cc_final: 0.6653 (ptp)
REVERT: B   62 ARG cc_start: 0.7577 (tmm-80) cc_final: 0.7323 (tmm-80)
REVERT: B   93 PHE cc_start: 0.7977 (t80) cc_final: 0.6671 (m-80)
REVERT: B   94 MET cc_start: 0.8488 (mmm) cc_final: 0.7895 (ttp)
REVERT: B  118 GLU cc_start: 0.7616 (pm20) cc_final: 0.7234 (pm20)
REVERT: B  123 THR cc_start: 0.9503 (p) cc_final: 0.9210 (p)
REVERT: B  124 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8355 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 223
  average time/residue: 0.0763
  time to fit residues: 21.4383
Evaluate side-chains
  212 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0870
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0270
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 132 GLN
** C  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 HIS
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.187885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.140031 restraints weight = 9243.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.142253 restraints weight = 6889.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.143805 restraints weight = 5651.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.145034 restraints weight = 4940.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.145398 restraints weight = 4534.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5210  Z= 0.139
  Angle     :  0.731   6.790   7025  Z= 0.371
  Chirality :  0.040   0.131    845
  Planarity :  0.005   0.048    885
  Dihedral  :  3.943  15.135    685
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.31), residues: 640
  helix:  2.25 (0.21), residues: 475
  sheet:  None (None), residues: 0
  loop : -0.91 (0.48), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D   8 
 TYR   0.006   0.002   TYR E  75 
 PHE   0.024   0.001   PHE B  90 
 HIS   0.005   0.002   HIS D  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 5210)
  covalent geometry    : angle       0.73119 /  0.37 ( 7025)
  hydrogen bonds       : bond        0.03339 /  2.33 (  395)
  hydrogen bonds       : angle       3.47578 /  2.56 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1116.53 seconds
wall clock time: 20 minutes 7.21 seconds (1207.21 seconds total)