Starting phenix.real_space_refine
on Tue Mar  3 13:38:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rug_24705/03_2026/7rug_24705.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rug_24705/03_2026/7rug_24705.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rug_24705/03_2026/7rug_24705.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rug_24705/03_2026/7rug_24705.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rug_24705/03_2026/7rug_24705.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rug_24705/03_2026/7rug_24705.map"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    1815      2.51       5
     N     413      2.21       5
     O     454      1.98       5
     H    2728      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5429
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 5151
          Classifications: {'peptide': 315}
          Link IDs: {'PTRANS': 8, 'TRANS': 306}
          Chain breaks: 4
    Chain: "L"
      Number of atoms: 278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 278
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
  Time building chain proxies: 1.18, per 1000 atoms: 0.22
  Number of scatterers: 5429
  At special positions: 0
  Unit cell: (70.35, 82.41, 67.335, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     O     454      8.00
     N     413      7.00
     C    1815      6.00
     H    2728      1.00
    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: 0.53
  Conformation dependent library (CDL) restraints added in 285.1 milliseconds
  

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  630

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 1 sheets defined
      85.8% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 57
    Processing helix  chain 'A' and resid 58 through 67
      removed outlier: 3.639A  pdb=" N   GLU A  62 " --> pdb=" O   ARG A  58 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   THR A  63 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   TYR A  64 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS A  67 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 116
    Processing helix  chain 'A' and resid 124 through 132
    Processing helix  chain 'A' and resid 133 through 150
      removed outlier: 3.777A  pdb=" N   PHE A 149 " --> pdb=" O   MET A 145 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   TYR A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 197
    Processing helix  chain 'A' and resid 198 through 229
      removed outlier: 3.685A  pdb=" N   TRP A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   THR A 229 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 255
      removed outlier: 3.521A  pdb=" N   SER A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 264
    Processing helix  chain 'A' and resid 268 through 289
      removed outlier: 3.880A  pdb=" N   SER A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 353
    Processing helix  chain 'A' and resid 404 through 424
    Processing helix  chain 'A' and resid 440 through 463
    Processing helix  chain 'A' and resid 464 through 466
      No H-bonds generated for 'chain 'A' and resid 464 through 466'
    Processing helix  chain 'L' and resid 113 through 117
      removed outlier: 3.535A  pdb=" N   ARG L 117 " --> pdb=" O   GLY L 114 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 105 through 106
      removed outlier: 3.989A  pdb=" N   SER L 112 " --> pdb=" O   ARG L 105 " (cutoff:3.500A)

    216 hydrogen bonds defined for protein.
    642 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: 0.84

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2723
        1.03 -     1.23: 5
        1.23 -     1.42: 1231
        1.42 -     1.61: 1518
        1.61 -     1.81: 31
  Bond restraints: 5508
  Sorted by residual:
  bond pdb=" CA  ILE A 151 "
       pdb=" CB  ILE A 151 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.012 1.29e-02 6.01e+03 9.35e-01
  bond pdb=" C   TRP L 108 "
       pdb=" N   TYR L 109 "
    ideal  model  delta    sigma   weight residual
    1.335  1.323  0.012 1.35e-02 5.49e+03 7.39e-01
  bond pdb=" CB  TRP L 108 "
       pdb=" CG  TRP L 108 "
    ideal  model  delta    sigma   weight residual
    1.498  1.477  0.021 3.10e-02 1.04e+03 4.63e-01
  bond pdb=" CG  LEU A 206 "
       pdb=" CD2 LEU A 206 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 3.86e-01
  bond pdb=" CA  MET A 105 "
       pdb=" HA  MET A 105 "
    ideal  model  delta    sigma   weight residual
    0.970  0.958  0.012 2.00e-02 2.50e+03 3.51e-01
  ... (remaining 5503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.85: 8849
        0.85 -     1.70: 974
        1.70 -     2.55: 65
        2.55 -     3.40: 13
        3.40 -     4.25: 11
  Bond angle restraints: 9912
  Sorted by residual:
  angle pdb=" C   ILE A 107 "
        pdb=" N   PHE A 108 "
        pdb=" CA  PHE A 108 "
      ideal   model   delta    sigma   weight residual
     120.29  116.85    3.44 1.42e+00 4.96e-01 5.87e+00
  angle pdb=" N   TYR L 103 "
        pdb=" CA  TYR L 103 "
        pdb=" C   TYR L 103 "
      ideal   model   delta    sigma   weight residual
     108.24  111.62   -3.38 1.81e+00 3.05e-01 3.48e+00
  angle pdb=" N   VAL A 462 "
        pdb=" CA  VAL A 462 "
        pdb=" C   VAL A 462 "
      ideal   model   delta    sigma   weight residual
     111.81  113.20   -1.39 8.60e-01 1.35e+00 2.62e+00
  angle pdb=" N   PHE A 108 "
        pdb=" CA  PHE A 108 "
        pdb=" CB  PHE A 108 "
      ideal   model   delta    sigma   weight residual
     110.16  112.48   -2.32 1.48e+00 4.57e-01 2.46e+00
  angle pdb=" CA  PHE A 108 "
        pdb=" CB  PHE A 108 "
        pdb=" CG  PHE A 108 "
      ideal   model   delta    sigma   weight residual
     113.80  115.34   -1.54 1.00e+00 1.00e+00 2.39e+00
  ... (remaining 9907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.36: 2349
       15.36 -    30.72: 171
       30.72 -    46.08: 50
       46.08 -    61.44: 31
       61.44 -    76.80: 4
  Dihedral angle restraints: 2605
    sinusoidal: 1323
      harmonic: 1282
  Sorted by residual:
  dihedral pdb=" CB  MET A 105 "
           pdb=" CG  MET A 105 "
           pdb=" SD  MET A 105 "
           pdb=" CE  MET A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  107.71  -47.71     3      1.50e+01 4.44e-03 8.53e+00
  dihedral pdb=" CB  MET A 116 "
           pdb=" CG  MET A 116 "
           pdb=" SD  MET A 116 "
           pdb=" CE  MET A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  106.93  -46.93     3      1.50e+01 4.44e-03 8.41e+00
  dihedral pdb=" CA  ASP A 181 "
           pdb=" CB  ASP A 181 "
           pdb=" CG  ASP A 181 "
           pdb=" OD1 ASP A 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -79.34   49.34     1      2.00e+01 2.50e-03 8.36e+00
  ... (remaining 2602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 299
       0.029 -    0.058: 75
       0.058 -    0.087: 37
       0.087 -    0.116: 14
       0.116 -    0.145: 2
  Chirality restraints: 427
  Sorted by residual:
  chirality pdb=" CG  LEU A 417 "
            pdb=" CB  LEU A 417 "
            pdb=" CD1 LEU A 417 "
            pdb=" CD2 LEU A 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  ILE A 151 "
            pdb=" N   ILE A 151 "
            pdb=" C   ILE A 151 "
            pdb=" CB  ILE A 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  PRO A 265 "
            pdb=" N   PRO A 265 "
            pdb=" C   PRO A 265 "
            pdb=" CB  PRO A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.11 2.00e-01 2.50e+01 3.23e-01
  ... (remaining 424 not shown)

  Planarity restraints: 757
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 105 "   -0.138 9.50e-02 1.11e+02   4.61e-02 2.57e+00
        pdb=" NE  ARG L 105 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 105 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 105 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 105 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG L 105 "    0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG L 105 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG L 105 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG L 105 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 112 "    0.008 2.00e-02 2.50e+03   8.23e-03 2.03e+00
        pdb=" CG  PHE A 112 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 112 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 112 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 112 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 112 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 112 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 112 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 112 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 112 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 112 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 112 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 108 "    0.014 2.00e-02 2.50e+03   7.67e-03 1.77e+00
        pdb=" CG  PHE A 108 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 108 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 108 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 108 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 108 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 108 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 108 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 108 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 108 "    0.001 2.00e-02 2.50e+03
  ... (remaining 754 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 639
        2.25 -     2.83: 12403
        2.83 -     3.42: 14521
        3.42 -     4.01: 18216
        4.01 -     4.60: 28153
  Nonbonded interactions: 73932
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 292 "
            pdb=" H   ASN A 296 "
     model   vdw
     1.657 2.450
  nonbonded pdb=" O   CYS A 413 "
            pdb=" HG  SER A 416 "
     model   vdw
     1.668 2.450
  nonbonded pdb=" O   TYR A 418 "
            pdb=" HG1 THR A 422 "
     model   vdw
     1.708 2.450
  nonbonded pdb=" O   ILE A 447 "
            pdb=" HG  SER A 450 "
     model   vdw
     1.724 2.450
  nonbonded pdb=" O   SER A 288 "
            pdb="HD21 ASN A 296 "
     model   vdw
     1.728 2.450
  ... (remaining 73927 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.660
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
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      :  0.003   0.021   2780  Z= 0.148
  Angle     :  0.498   4.253   3774  Z= 0.284
  Chirality :  0.035   0.145    427
  Planarity :  0.004   0.061    440
  Dihedral  : 12.584  76.800    950
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  3.26 (0.46), residues: 319
  helix:  2.50 (0.30), residues: 257
  sheet:  None (None), residues: 0
  loop :  0.77 (0.90), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L 105 
 TYR   0.013   0.001   TYR A 225 
 PHE   0.024   0.002   PHE A 112 
 TRP   0.011   0.002   TRP A 284 
 HIS   0.005   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 2780)
  covalent geometry    : angle       0.49780 ( 3774)
  hydrogen bonds       : bond        0.10173 (  216)
  hydrogen bonds       : angle       4.69106 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8826 (tm-30)
REVERT: A  244 ASN cc_start: 0.8707 (m-40) cc_final: 0.8365 (m-40)
REVERT: A  411 MET cc_start: 0.8543 (mtm) cc_final: 0.8319 (mtt)
REVERT: A  420 MET cc_start: 0.8259 (ttt) cc_final: 0.8049 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0971
  time to fit residues: 10.0123
Evaluate side-chains
  65 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.123297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.106650 restraints weight = 30781.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.110753 restraints weight = 14121.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.113329 restraints weight = 7818.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.114806 restraints weight = 5017.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.115857 restraints weight = 3729.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2780  Z= 0.225
  Angle     :  0.553   4.414   3774  Z= 0.326
  Chirality :  0.036   0.122    427
  Planarity :  0.004   0.037    440
  Dihedral  :  3.689  14.204    359
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  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:  2.73 (0.45), residues: 319
  helix:  2.14 (0.30), residues: 259
  sheet:  None (None), residues: 0
  loop :  0.45 (0.86), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 105 
 TYR   0.015   0.001   TYR A 225 
 PHE   0.028   0.002   PHE A 108 
 TRP   0.013   0.002   TRP A 186 
 HIS   0.003   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 2780)
  covalent geometry    : angle       0.55326 ( 3774)
  hydrogen bonds       : bond        0.04642 (  216)
  hydrogen bonds       : angle       4.58989 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8927 (tm-30)
REVERT: A  188 GLU cc_start: 0.9023 (pt0) cc_final: 0.8404 (pt0)
REVERT: A  244 ASN cc_start: 0.8781 (m-40) cc_final: 0.8496 (m-40)
REVERT: A  411 MET cc_start: 0.8649 (mtm) cc_final: 0.8344 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0779
  time to fit residues: 7.9185
Evaluate side-chains
  68 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0870
   chunk 14 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
A 261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.127609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.110485 restraints weight = 29523.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.114843 restraints weight = 14027.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.117436 restraints weight = 7849.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.119179 restraints weight = 5094.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.120170 restraints weight = 3675.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2780  Z= 0.113
  Angle     :  0.457   3.973   3774  Z= 0.254
  Chirality :  0.035   0.116    427
  Planarity :  0.003   0.029    440
  Dihedral  :  3.515  13.048    359
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  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:  3.42 (0.45), residues: 319
  helix:  2.68 (0.30), residues: 259
  sheet:  None (None), residues: 0
  loop :  0.36 (0.85), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 105 
 TYR   0.007   0.001   TYR L 111 
 PHE   0.018   0.001   PHE A 108 
 TRP   0.010   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 2780)
  covalent geometry    : angle       0.45713 ( 3774)
  hydrogen bonds       : bond        0.04334 (  216)
  hydrogen bonds       : angle       3.90665 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: A  188 GLU cc_start: 0.8924 (pt0) cc_final: 0.8227 (pt0)
REVERT: A  219 ILE cc_start: 0.8044 (mm) cc_final: 0.7604 (tp)
REVERT: A  244 ASN cc_start: 0.8695 (m110) cc_final: 0.8466 (m110)
REVERT: A  411 MET cc_start: 0.8594 (mtm) cc_final: 0.8360 (mtt)
REVERT: A  447 ILE cc_start: 0.8850 (tt) cc_final: 0.8563 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0781
  time to fit residues: 8.3902
Evaluate side-chains
  67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 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 = 0.3857 r_free = 0.3857 target = 0.120372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.103879 restraints weight = 31386.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.107880 restraints weight = 14408.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.110209 restraints weight = 7957.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.111784 restraints weight = 5171.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.112739 restraints weight = 3733.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   2780  Z= 0.309
  Angle     :  0.669   7.397   3774  Z= 0.397
  Chirality :  0.038   0.115    427
  Planarity :  0.005   0.034    440
  Dihedral  :  4.168  16.108    359
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  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:  1.30 (0.44), residues: 319
  helix:  1.15 (0.30), residues: 259
  sheet:  None (None), residues: 0
  loop : -0.03 (0.85), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  39 
 TYR   0.019   0.002   TYR A 225 
 PHE   0.035   0.003   PHE A 112 
 TRP   0.020   0.002   TRP A 284 
 HIS   0.007   0.002   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 2780)
  covalent geometry    : angle       0.66932 ( 3774)
  hydrogen bonds       : bond        0.05172 (  216)
  hydrogen bonds       : angle       5.14501 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.9382 (tm-30) cc_final: 0.8932 (tm-30)
REVERT: A  188 GLU cc_start: 0.9011 (pt0) cc_final: 0.8435 (pt0)
REVERT: A  219 ILE cc_start: 0.8053 (mm) cc_final: 0.7262 (tp)
REVERT: A  411 MET cc_start: 0.8761 (mtm) cc_final: 0.8458 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0809
  time to fit residues: 7.9500
Evaluate side-chains
  64 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0270
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.8842

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.124233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.107634 restraints weight = 30934.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.111782 restraints weight = 14298.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.114320 restraints weight = 7884.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.115890 restraints weight = 5022.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.116875 restraints weight = 3679.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2780  Z= 0.153
  Angle     :  0.494   4.127   3774  Z= 0.286
  Chirality :  0.036   0.117    427
  Planarity :  0.004   0.032    440
  Dihedral  :  3.784  13.848    359
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  2.30 (0.45), residues: 319
  helix:  1.87 (0.30), residues: 259
  sheet:  None (None), residues: 0
  loop :  0.14 (0.87), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  39 
 TYR   0.013   0.001   TYR A 225 
 PHE   0.027   0.002   PHE A 112 
 TRP   0.011   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2780)
  covalent geometry    : angle       0.49380 ( 3774)
  hydrogen bonds       : bond        0.04622 (  216)
  hydrogen bonds       : angle       4.35462 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.8825 (mmm) cc_final: 0.7995 (mmm)
REVERT: A  175 GLN cc_start: 0.9348 (tm-30) cc_final: 0.8948 (tm-30)
REVERT: A  188 GLU cc_start: 0.8908 (pt0) cc_final: 0.8376 (pt0)
REVERT: A  411 MET cc_start: 0.8696 (mtm) cc_final: 0.8438 (mtt)
REVERT: A  421 MET cc_start: 0.7462 (tpt) cc_final: 0.7094 (tmm)
REVERT: A  447 ILE cc_start: 0.8907 (tt) cc_final: 0.8688 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0785
  time to fit residues: 7.8634
Evaluate side-chains
  66 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:    0.4980
   chunk 4 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.3974 r_free = 0.3974 target = 0.126747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.109875 restraints weight = 30459.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.113999 restraints weight = 14332.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.116640 restraints weight = 8122.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.118126 restraints weight = 5230.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.119157 restraints weight = 3857.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2780  Z= 0.110
  Angle     :  0.449   4.159   3774  Z= 0.255
  Chirality :  0.035   0.112    427
  Planarity :  0.003   0.035    440
  Dihedral  :  3.535  14.025    359
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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:  3.14 (0.46), residues: 319
  helix:  2.47 (0.30), residues: 259
  sheet:  None (None), residues: 0
  loop :  0.38 (0.89), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 105 
 TYR   0.008   0.001   TYR A 350 
 PHE   0.027   0.002   PHE A 112 
 TRP   0.008   0.001   TRP A 186 
 HIS   0.002   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 2780)
  covalent geometry    : angle       0.44913 ( 3774)
  hydrogen bonds       : bond        0.04257 (  216)
  hydrogen bonds       : angle       3.90343 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.8733 (mmm) cc_final: 0.7893 (mmm)
REVERT: A  175 GLN cc_start: 0.9388 (tm-30) cc_final: 0.8980 (tm-30)
REVERT: A  188 GLU cc_start: 0.8901 (pt0) cc_final: 0.8364 (pt0)
REVERT: A  411 MET cc_start: 0.8628 (mtm) cc_final: 0.8383 (mtt)
REVERT: A  421 MET cc_start: 0.7294 (tpt) cc_final: 0.6809 (tmm)
REVERT: A  447 ILE cc_start: 0.8812 (tt) cc_final: 0.8570 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0755
  time to fit residues: 7.7076
Evaluate side-chains
  67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.3952 r_free = 0.3952 target = 0.126831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.110061 restraints weight = 30516.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114344 restraints weight = 14300.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.117043 restraints weight = 7970.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.118630 restraints weight = 5053.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.119695 restraints weight = 3650.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6813
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2780  Z= 0.113
  Angle     :  0.447   3.847   3774  Z= 0.251
  Chirality :  0.034   0.109    427
  Planarity :  0.003   0.034    440
  Dihedral  :  3.464  14.295    359
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.22 (0.45), residues: 319
  helix:  2.55 (0.30), residues: 261
  sheet:  None (None), residues: 0
  loop :  0.13 (0.87), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 266 
 TYR   0.010   0.001   TYR A 350 
 PHE   0.028   0.001   PHE A 112 
 TRP   0.007   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 2780)
  covalent geometry    : angle       0.44698 ( 3774)
  hydrogen bonds       : bond        0.04019 (  216)
  hydrogen bonds       : angle       3.78701 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.8721 (mmm) cc_final: 0.7044 (ttt)
REVERT: A  175 GLN cc_start: 0.9378 (tm-30) cc_final: 0.8941 (tm-30)
REVERT: A  188 GLU cc_start: 0.8914 (pt0) cc_final: 0.8336 (pt0)
REVERT: A  411 MET cc_start: 0.8615 (mtm) cc_final: 0.8372 (mtt)
REVERT: A  421 MET cc_start: 0.7186 (tpt) cc_final: 0.6622 (tmm)
REVERT: A  447 ILE cc_start: 0.8792 (tt) cc_final: 0.8493 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0836
  time to fit residues: 8.4370
Evaluate side-chains
  64 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.124674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.108358 restraints weight = 30885.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.112309 restraints weight = 14403.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.114836 restraints weight = 8123.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.116376 restraints weight = 5308.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.117233 restraints weight = 3938.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2780  Z= 0.138
  Angle     :  0.473   4.099   3774  Z= 0.268
  Chirality :  0.035   0.112    427
  Planarity :  0.003   0.033    440
  Dihedral  :  3.497  14.547    359
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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:  3.07 (0.46), residues: 319
  helix:  2.47 (0.30), residues: 260
  sheet:  None (None), residues: 0
  loop :  0.01 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 266 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.026   0.002   PHE A 112 
 TRP   0.010   0.001   TRP A 459 
 HIS   0.002   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2780)
  covalent geometry    : angle       0.47312 ( 3774)
  hydrogen bonds       : bond        0.04048 (  216)
  hydrogen bonds       : angle       3.96831 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.8760 (mmm) cc_final: 0.7961 (mmm)
REVERT: A  175 GLN cc_start: 0.9398 (tm-30) cc_final: 0.8981 (tm-30)
REVERT: A  188 GLU cc_start: 0.8908 (pt0) cc_final: 0.8346 (pt0)
REVERT: A  411 MET cc_start: 0.8758 (mtm) cc_final: 0.8482 (mtt)
REVERT: A  447 ILE cc_start: 0.8794 (tt) cc_final: 0.8551 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0751
  time to fit residues: 7.5630
Evaluate side-chains
  66 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.3976 r_free = 0.3976 target = 0.126910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.110394 restraints weight = 32005.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.114771 restraints weight = 14592.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.117310 restraints weight = 8014.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.118932 restraints weight = 5112.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.119914 restraints weight = 3690.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2780  Z= 0.108
  Angle     :  0.452   3.748   3774  Z= 0.251
  Chirality :  0.035   0.112    427
  Planarity :  0.003   0.034    440
  Dihedral  :  3.412  14.626    359
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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:  3.38 (0.46), residues: 319
  helix:  2.67 (0.30), residues: 260
  sheet:  None (None), residues: 0
  loop :  0.18 (0.89), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 105 
 TYR   0.009   0.001   TYR A 350 
 PHE   0.024   0.001   PHE A 112 
 TRP   0.008   0.001   TRP A 451 
 HIS   0.002   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 2780)
  covalent geometry    : angle       0.45233 ( 3774)
  hydrogen bonds       : bond        0.03922 (  216)
  hydrogen bonds       : angle       3.75486 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 MET cc_start: 0.8408 (mmp) cc_final: 0.7427 (tpp)
REVERT: A  165 MET cc_start: 0.8733 (mmm) cc_final: 0.7933 (mmm)
REVERT: A  175 GLN cc_start: 0.9398 (tm-30) cc_final: 0.8965 (tm-30)
REVERT: A  188 GLU cc_start: 0.8902 (pt0) cc_final: 0.8305 (pt0)
REVERT: A  244 ASN cc_start: 0.8998 (m-40) cc_final: 0.8686 (p0)
REVERT: A  411 MET cc_start: 0.8718 (mtm) cc_final: 0.8426 (mtt)
REVERT: A  447 ILE cc_start: 0.8731 (tt) cc_final: 0.8506 (mt)
REVERT: A  461 LEU cc_start: 0.9023 (mt) cc_final: 0.8780 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0785
  time to fit residues: 8.2252
Evaluate side-chains
  66 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.3950 r_free = 0.3950 target = 0.125121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.108524 restraints weight = 33181.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.112687 restraints weight = 15201.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.115157 restraints weight = 8470.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.116575 restraints weight = 5468.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.117505 restraints weight = 4107.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2780  Z= 0.157
  Angle     :  0.502   4.473   3774  Z= 0.291
  Chirality :  0.036   0.141    427
  Planarity :  0.004   0.032    440
  Dihedral  :  3.520  14.821    359
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  2.95 (0.46), residues: 319
  helix:  2.37 (0.30), residues: 260
  sheet:  None (None), residues: 0
  loop :  0.09 (0.89), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 266 
 TYR   0.013   0.001   TYR A 225 
 PHE   0.028   0.002   PHE A 112 
 TRP   0.015   0.001   TRP A 459 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2780)
  covalent geometry    : angle       0.50230 ( 3774)
  hydrogen bonds       : bond        0.04094 (  216)
  hydrogen bonds       : angle       4.12284 (  642)

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

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

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  638 Ramachandran restraints generated.
    319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 MET cc_start: 0.8485 (mmp) cc_final: 0.7639 (tpp)
REVERT: A  165 MET cc_start: 0.8756 (mmm) cc_final: 0.8026 (mmm)
REVERT: A  175 GLN cc_start: 0.9409 (tm-30) cc_final: 0.8963 (tm-30)
REVERT: A  188 GLU cc_start: 0.8930 (pt0) cc_final: 0.8380 (pt0)
REVERT: A  411 MET cc_start: 0.8776 (mtm) cc_final: 0.8499 (mtt)
REVERT: A  447 ILE cc_start: 0.8786 (tt) cc_final: 0.8568 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0749
  time to fit residues: 7.1600
Evaluate side-chains
  62 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0000
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0670
   overall best weight:    0.4522

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.127973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.111042 restraints weight = 31299.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.115205 restraints weight = 14562.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.117703 restraints weight = 8142.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.119263 restraints weight = 5337.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.120180 restraints weight = 4028.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2780  Z= 0.103
  Angle     :  0.451   4.544   3774  Z= 0.248
  Chirality :  0.035   0.124    427
  Planarity :  0.003   0.035    440
  Dihedral  :  3.399  14.749    359
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  3.52 (0.46), residues: 319
  helix:  2.76 (0.30), residues: 260
  sheet:  None (None), residues: 0
  loop :  0.31 (0.90), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.011   0.001   TYR A 350 
 PHE   0.022   0.001   PHE A 112 
 TRP   0.007   0.001   TRP A 186 
 HIS   0.002   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 2780)
  covalent geometry    : angle       0.45107 ( 3774)
  hydrogen bonds       : bond        0.03853 (  216)
  hydrogen bonds       : angle       3.68029 (  642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1302.71 seconds
wall clock time: 22 minutes 45.08 seconds (1365.08 seconds total)