Starting phenix.real_space_refine
on Fri Aug 22 14:42:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u5x_41935/08_2025/8u5x_41935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u5x_41935/08_2025/8u5x_41935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u5x_41935/08_2025/8u5x_41935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u5x_41935/08_2025/8u5x_41935.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u5x_41935/08_2025/8u5x_41935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u5x_41935/08_2025/8u5x_41935.map"
  }
  resolution = 2.79
  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=   0.072
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      28      5.16       5
     C    2984      2.51       5
     N     688      2.21       5
     O     753      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4453
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4440
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'IAC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.39, per 1000 atoms: 0.31
  Number of scatterers: 4453
  At special positions: 0
  Unit cell: (93.0804, 72.0265, 77.567, 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      28     16.00
     O     753      8.00
     N     688      7.00
     C    2984      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: 0.37
  Conformation dependent library (CDL) restraints added in 194.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1064

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      91.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 62
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 3.961A  pdb=" N   LYS A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   GLY A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 93
    Processing helix  chain 'A' and resid 94 through 98
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.622A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 143
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 162 through 165
    Processing helix  chain 'A' and resid 166 through 196
      removed outlier: 4.328A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 202 through 216
    Processing helix  chain 'A' and resid 217 through 234
    Processing helix  chain 'A' and resid 238 through 251
      removed outlier: 4.205A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 265
      removed outlier: 3.561A  pdb=" N   VAL A 265 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 322
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 4.308A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.609A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 368 through 370
      No H-bonds generated for 'chain 'A' and resid 368 through 370'
    Processing helix  chain 'A' and resid 371 through 404
    Processing helix  chain 'A' and resid 405 through 409
    Processing helix  chain 'A' and resid 411 through 436
    Processing helix  chain 'A' and resid 439 through 474
      removed outlier: 3.556A  pdb=" N   GLY A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ARG A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 503
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
    Processing helix  chain 'A' and resid 516 through 544
    Processing helix  chain 'A' and resid 655 through 683
      removed outlier: 3.688A  pdb=" N   GLY A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 711
      removed outlier: 5.726A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)

    374 hydrogen bonds defined for protein.
    1101 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: 0.66

  Time building geometry restraints manager: 0.51 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: 1306
        1.34 -     1.46: 833
        1.46 -     1.57: 2377
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 4561
  Sorted by residual:
  bond pdb=" C1  IAC A 901 "
       pdb=" C7  IAC A 901 "
    ideal  model  delta    sigma   weight residual
    1.433  1.364  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" C   IAC A 901 "
       pdb=" C1  IAC A 901 "
    ideal  model  delta    sigma   weight residual
    1.414  1.366  0.048 2.00e-02 2.50e+03 5.71e+00
  bond pdb=" C17 IAC A 901 "
       pdb=" C7  IAC A 901 "
    ideal  model  delta    sigma   weight residual
    1.487  1.532 -0.045 2.00e-02 2.50e+03 4.95e+00
  bond pdb=" CA  TRP A 679 "
       pdb=" C   TRP A 679 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.028 1.28e-02 6.10e+03 4.73e+00
  bond pdb=" CB  VAL A 425 "
       pdb=" CG2 VAL A 425 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.63e+00
  ... (remaining 4556 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 6082
        2.70 -     5.40: 109
        5.40 -     8.10: 9
        8.10 -    10.80: 0
       10.80 -    13.50: 2
  Bond angle restraints: 6202
  Sorted by residual:
  angle pdb=" C17 IAC A 901 "
        pdb=" C7  IAC A 901 "
        pdb=" C8  IAC A 901 "
      ideal   model   delta    sigma   weight residual
     127.34  113.84   13.50 3.00e+00 1.11e-01 2.03e+01
  angle pdb=" C1  IAC A 901 "
        pdb=" C7  IAC A 901 "
        pdb=" C17 IAC A 901 "
      ideal   model   delta    sigma   weight residual
     126.92  138.72  -11.80 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" CA  TRP A 679 "
        pdb=" CB  TRP A 679 "
        pdb=" CG  TRP A 679 "
      ideal   model   delta    sigma   weight residual
     113.60  106.51    7.09 1.90e+00 2.77e-01 1.39e+01
  angle pdb=" CA  PHE A 221 "
        pdb=" CB  PHE A 221 "
        pdb=" CG  PHE A 221 "
      ideal   model   delta    sigma   weight residual
     113.80  117.33   -3.53 1.00e+00 1.00e+00 1.25e+01
  angle pdb=" CA  TYR A 451 "
        pdb=" CB  TYR A 451 "
        pdb=" CG  TYR A 451 "
      ideal   model   delta    sigma   weight residual
     113.90  119.97   -6.07 1.80e+00 3.09e-01 1.14e+01
  ... (remaining 6197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 2474
       17.37 -    34.75: 155
       34.75 -    52.12: 21
       52.12 -    69.49: 8
       69.49 -    86.86: 1
  Dihedral angle restraints: 2659
    sinusoidal: 1008
      harmonic: 1651
  Sorted by residual:
  dihedral pdb=" CA  GLN A 654 "
           pdb=" C   GLN A 654 "
           pdb=" N   LEU A 655 "
           pdb=" CA  LEU A 655 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.46  -28.54     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  TYR A 516 "
           pdb=" C   TYR A 516 "
           pdb=" N   GLY A 517 "
           pdb=" CA  GLY A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.17   25.83     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  GLN A 409 "
           pdb=" C   GLN A 409 "
           pdb=" N   LEU A 410 "
           pdb=" CA  LEU A 410 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.19   21.81     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 2656 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 501
       0.043 -    0.087: 189
       0.087 -    0.130: 47
       0.130 -    0.174: 7
       0.174 -    0.217: 2
  Chirality restraints: 746
  Sorted by residual:
  chirality pdb=" CA  PHE A 221 "
            pdb=" N   PHE A 221 "
            pdb=" C   PHE A 221 "
            pdb=" CB  PHE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  THR A 457 "
            pdb=" CA  THR A 457 "
            pdb=" OG1 THR A 457 "
            pdb=" CG2 THR A 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  ILE A  65 "
            pdb=" N   ILE A  65 "
            pdb=" C   ILE A  65 "
            pdb=" CB  ILE A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.60e-01
  ... (remaining 743 not shown)

  Planarity restraints: 747
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 221 "   -0.030 2.00e-02 2.50e+03   2.34e-02 9.59e+00
        pdb=" CG  PHE A 221 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 221 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 221 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 221 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 221 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 221 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 708 "   -0.030 2.00e-02 2.50e+03   2.10e-02 7.72e+00
        pdb=" CG  PHE A 708 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 708 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 708 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 708 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 708 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 708 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 320 "    0.036 2.00e-02 2.50e+03   1.88e-02 7.09e+00
        pdb=" CG  TYR A 320 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 320 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 320 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 320 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 320 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 320 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 320 "    0.014 2.00e-02 2.50e+03
  ... (remaining 744 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 1959
        2.92 -     3.42: 5094
        3.42 -     3.91: 7920
        3.91 -     4.41: 9447
        4.41 -     4.90: 14808
  Nonbonded interactions: 39228
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 359 "
            pdb=" OD2 ASP A 385 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" O   ASN A 682 "
            pdb=" N   GLU A 684 "
     model   vdw
     2.455 3.120
  nonbonded pdb=" O   VAL A 117 "
            pdb=" OG1 THR A 121 "
     model   vdw
     2.459 3.040
  nonbonded pdb=" O   VAL A 340 "
            pdb=" OG1 THR A 344 "
     model   vdw
     2.479 3.040
  nonbonded pdb=" O   ILE A 400 "
            pdb=" OG  SER A 404 "
     model   vdw
     2.498 3.040
  ... (remaining 39223 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     6.080
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.020
  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:7.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
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      :  0.008   0.069   4561  Z= 0.329
  Angle     :  0.875  13.500   6202  Z= 0.471
  Chirality :  0.048   0.217    746
  Planarity :  0.007   0.055    747
  Dihedral  : 12.003  86.862   1595
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  2.86 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.31), residues: 565
  helix: -0.48 (0.21), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.50 (0.56), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  41 
 TYR   0.036   0.004   TYR A 320 
 PHE   0.053   0.004   PHE A 221 
 TRP   0.026   0.004   TRP A 679 
 HIS   0.008   0.004   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00792 ( 4561)
  covalent geometry    : angle       0.87462 ( 6202)
  hydrogen bonds       : bond        0.15998 (  374)
  hydrogen bonds       : angle       7.00831 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 136
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.8207 (tt0) cc_final: 0.6527 (tp30)
REVERT: A   71 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7047 (pptt)
REVERT: A  216 GLN cc_start: 0.8219 (mt0) cc_final: 0.7952 (mt0)
REVERT: A  347 MET cc_start: 0.8699 (tmm) cc_final: 0.8462 (tmm)
REVERT: A  359 TYR cc_start: 0.8855 (t80) cc_final: 0.8083 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 138
  average time/residue: 0.4028
  time to fit residues: 57.9882
Evaluate side-chains
  99 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  447 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 202 ASN
A 412 HIS
A 672 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.135453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.104209 restraints weight = 8329.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.63
r_work: 0.3395 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4561  Z= 0.156
  Angle     :  0.721   8.890   6202  Z= 0.360
  Chirality :  0.043   0.162    746
  Planarity :  0.005   0.040    747
  Dihedral  :  5.660  47.566    604
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.67 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.34), residues: 565
  helix:  1.38 (0.23), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.09 (0.59), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 130 
 TYR   0.012   0.001   TYR A 516 
 PHE   0.030   0.002   PHE A 221 
 TRP   0.016   0.002   TRP A 432 
 HIS   0.006   0.002   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4561)
  covalent geometry    : angle       0.72123 ( 6202)
  hydrogen bonds       : bond        0.05207 (  374)
  hydrogen bonds       : angle       4.96570 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.7554 (tt0) cc_final: 0.5452 (tp30)
REVERT: A   71 LYS cc_start: 0.7302 (mtpt) cc_final: 0.6130 (pmtt)
REVERT: A  193 TRP cc_start: 0.8975 (t60) cc_final: 0.8702 (t60)
REVERT: A  277 VAL cc_start: 0.9136 (t) cc_final: 0.8898 (p)
REVERT: A  295 ARG cc_start: 0.8518 (ttp80) cc_final: 0.7864 (ttt-90)
REVERT: A  299 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8441 (mt-10)
REVERT: A  347 MET cc_start: 0.8567 (tmm) cc_final: 0.8256 (tmm)
REVERT: A  373 LYS cc_start: 0.9347 (mppt) cc_final: 0.8995 (mmpt)
REVERT: A  381 ASN cc_start: 0.7751 (m-40) cc_final: 0.7499 (t0)
REVERT: A  385 ASP cc_start: 0.8483 (m-30) cc_final: 0.8252 (m-30)
REVERT: A  406 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8880 (mttp)
REVERT: A  492 PRO cc_start: 0.8313 (Cg_exo) cc_final: 0.8014 (Cg_endo)
  outliers start: 12
  outliers final: 2
  residues processed: 121
  average time/residue: 0.3789
  time to fit residues: 48.0040
Evaluate side-chains
  100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain A residue  457 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 HIS ** 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 = 0.132330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.100419 restraints weight = 8220.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.61
r_work: 0.3321 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   4561  Z= 0.204
  Angle     :  0.699  10.686   6202  Z= 0.349
  Chirality :  0.045   0.172    746
  Planarity :  0.005   0.039    747
  Dihedral  :  5.011  40.426    602
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.71 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.35), residues: 565
  helix:  1.73 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop :  0.05 (0.60), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  61 
 TYR   0.022   0.002   TYR A 451 
 PHE   0.031   0.002   PHE A 221 
 TRP   0.023   0.003   TRP A 678 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 4561)
  covalent geometry    : angle       0.69923 ( 6202)
  hydrogen bonds       : bond        0.05158 (  374)
  hydrogen bonds       : angle       4.80888 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.7257 (mtpt) cc_final: 0.6791 (mmmt)
REVERT: A  130 ARG cc_start: 0.8570 (ptp90) cc_final: 0.7836 (ptp90)
REVERT: A  146 ASP cc_start: 0.8880 (m-30) cc_final: 0.8663 (m-30)
REVERT: A  159 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8495 (tp-100)
REVERT: A  193 TRP cc_start: 0.8937 (t60) cc_final: 0.8681 (t60)
REVERT: A  277 VAL cc_start: 0.9166 (t) cc_final: 0.8921 (p)
REVERT: A  341 GLU cc_start: 0.8704 (mp0) cc_final: 0.8440 (pm20)
REVERT: A  347 MET cc_start: 0.8650 (tmm) cc_final: 0.8377 (tmm)
REVERT: A  381 ASN cc_start: 0.7775 (m-40) cc_final: 0.7529 (t0)
REVERT: A  385 ASP cc_start: 0.8573 (m-30) cc_final: 0.8287 (m-30)
REVERT: A  406 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8842 (mttp)
REVERT: A  409 GLN cc_start: 0.5820 (OUTLIER) cc_final: 0.5431 (tm-30)
REVERT: A  429 MET cc_start: 0.7709 (tpt) cc_final: 0.7509 (tpt)
REVERT: A  459 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7940 (mp)
  outliers start: 17
  outliers final: 6
  residues processed: 110
  average time/residue: 0.3972
  time to fit residues: 45.6252
Evaluate side-chains
  100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
A 433 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.134924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.103316 restraints weight = 8290.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.66
r_work: 0.3348 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4561  Z= 0.151
  Angle     :  0.698  13.564   6202  Z= 0.340
  Chirality :  0.043   0.165    746
  Planarity :  0.005   0.037    747
  Dihedral  :  4.510  20.190    600
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.76 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.36), residues: 565
  helix:  1.81 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop :  0.16 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  61 
 TYR   0.039   0.002   TYR A 451 
 PHE   0.028   0.002   PHE A 221 
 TRP   0.022   0.002   TRP A 678 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4561)
  covalent geometry    : angle       0.69845 ( 6202)
  hydrogen bonds       : bond        0.04765 (  374)
  hydrogen bonds       : angle       4.62185 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7143 (mtm-85)
REVERT: A   71 LYS cc_start: 0.7031 (mtpt) cc_final: 0.6617 (mmmt)
REVERT: A   99 ASP cc_start: 0.8598 (t0) cc_final: 0.8068 (t70)
REVERT: A  130 ARG cc_start: 0.8570 (ptp90) cc_final: 0.7823 (ptp90)
REVERT: A  146 ASP cc_start: 0.8863 (m-30) cc_final: 0.8586 (m-30)
REVERT: A  159 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8449 (tp-100)
REVERT: A  193 TRP cc_start: 0.8913 (t60) cc_final: 0.8697 (t60)
REVERT: A  203 LYS cc_start: 0.7981 (mmpt) cc_final: 0.7633 (mtmm)
REVERT: A  234 ASP cc_start: 0.8894 (t0) cc_final: 0.8240 (t0)
REVERT: A  236 LYS cc_start: 0.8707 (mttt) cc_final: 0.8289 (mptt)
REVERT: A  246 ASP cc_start: 0.8039 (m-30) cc_final: 0.7817 (m-30)
REVERT: A  277 VAL cc_start: 0.9134 (t) cc_final: 0.8900 (p)
REVERT: A  299 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8563 (mt-10)
REVERT: A  359 TYR cc_start: 0.8767 (t80) cc_final: 0.8552 (t80)
REVERT: A  381 ASN cc_start: 0.7736 (m-40) cc_final: 0.7535 (t0)
REVERT: A  385 ASP cc_start: 0.8511 (m-30) cc_final: 0.8223 (m-30)
REVERT: A  406 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8495 (tppt)
REVERT: A  409 GLN cc_start: 0.5710 (OUTLIER) cc_final: 0.5428 (tm-30)
REVERT: A  459 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8061 (mt)
  outliers start: 9
  outliers final: 3
  residues processed: 115
  average time/residue: 0.3821
  time to fit residues: 45.9058
Evaluate side-chains
  107 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 26 optimal weight:    0.4980
   chunk 41 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.136087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.104700 restraints weight = 8340.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.75
r_work: 0.3401 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4561  Z= 0.139
  Angle     :  0.663  12.372   6202  Z= 0.324
  Chirality :  0.042   0.171    746
  Planarity :  0.005   0.037    747
  Dihedral  :  4.373  19.190    600
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.78 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.36), residues: 565
  helix:  2.01 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop :  0.16 (0.64), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  61 
 TYR   0.047   0.002   TYR A 451 
 PHE   0.028   0.002   PHE A 221 
 TRP   0.021   0.002   TRP A 678 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4561)
  covalent geometry    : angle       0.66300 ( 6202)
  hydrogen bonds       : bond        0.04500 (  374)
  hydrogen bonds       : angle       4.50936 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7212 (mtm-85)
REVERT: A   71 LYS cc_start: 0.7027 (mtpt) cc_final: 0.6639 (mmmt)
REVERT: A   99 ASP cc_start: 0.8564 (t0) cc_final: 0.8116 (t70)
REVERT: A  130 ARG cc_start: 0.8585 (ptp90) cc_final: 0.7813 (ptp90)
REVERT: A  159 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8520 (tp-100)
REVERT: A  193 TRP cc_start: 0.8816 (t60) cc_final: 0.8573 (t60)
REVERT: A  234 ASP cc_start: 0.8869 (t0) cc_final: 0.8263 (t0)
REVERT: A  236 LYS cc_start: 0.8661 (mttt) cc_final: 0.8256 (mptt)
REVERT: A  277 VAL cc_start: 0.9119 (t) cc_final: 0.8879 (p)
REVERT: A  299 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8552 (mt-10)
REVERT: A  359 TYR cc_start: 0.8831 (t80) cc_final: 0.8613 (t80)
REVERT: A  381 ASN cc_start: 0.7785 (m-40) cc_final: 0.7560 (t0)
REVERT: A  385 ASP cc_start: 0.8477 (m-30) cc_final: 0.8192 (m-30)
REVERT: A  396 TRP cc_start: 0.8523 (t-100) cc_final: 0.8254 (t-100)
REVERT: A  410 LEU cc_start: 0.7997 (mm) cc_final: 0.7781 (mm)
REVERT: A  430 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7930 (mmm)
REVERT: A  451 TYR cc_start: 0.6998 (m-10) cc_final: 0.6790 (m-10)
REVERT: A  459 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8099 (mt)
REVERT: A  695 PHE cc_start: 0.8463 (m-80) cc_final: 0.8256 (m-80)
REVERT: A  711 PHE cc_start: 0.8298 (m-80) cc_final: 0.8090 (m-10)
  outliers start: 13
  outliers final: 3
  residues processed: 115
  average time/residue: 0.3908
  time to fit residues: 46.9505
Evaluate side-chains
  103 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 38 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.137089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.105677 restraints weight = 8505.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.77
r_work: 0.3393 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4561  Z= 0.143
  Angle     :  0.685  13.112   6202  Z= 0.332
  Chirality :  0.042   0.190    746
  Planarity :  0.005   0.040    747
  Dihedral  :  4.307  18.949    600
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 20.82 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.36), residues: 565
  helix:  1.96 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop :  0.37 (0.66), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  61 
 TYR   0.015   0.002   TYR A 451 
 PHE   0.039   0.002   PHE A 447 
 TRP   0.023   0.002   TRP A 678 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4561)
  covalent geometry    : angle       0.68463 ( 6202)
  hydrogen bonds       : bond        0.04434 (  374)
  hydrogen bonds       : angle       4.48619 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7147 (mtm-85)
REVERT: A   54 LEU cc_start: 0.9182 (tp) cc_final: 0.8919 (mm)
REVERT: A   61 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8660 (mmm-85)
REVERT: A   71 LYS cc_start: 0.7011 (mtpt) cc_final: 0.6592 (mmmt)
REVERT: A  130 ARG cc_start: 0.8601 (ptp90) cc_final: 0.7884 (ptp90)
REVERT: A  159 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8541 (tp-100)
REVERT: A  203 LYS cc_start: 0.7958 (mmpt) cc_final: 0.7624 (mtmm)
REVERT: A  236 LYS cc_start: 0.8636 (mttt) cc_final: 0.8252 (mptt)
REVERT: A  277 VAL cc_start: 0.9114 (t) cc_final: 0.8881 (p)
REVERT: A  295 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8054 (mtm110)
REVERT: A  299 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8516 (mt-10)
REVERT: A  359 TYR cc_start: 0.8809 (t80) cc_final: 0.8585 (t80)
REVERT: A  381 ASN cc_start: 0.7812 (m-40) cc_final: 0.7562 (t0)
REVERT: A  385 ASP cc_start: 0.8459 (m-30) cc_final: 0.8179 (m-30)
REVERT: A  396 TRP cc_start: 0.8477 (t-100) cc_final: 0.8193 (t-100)
REVERT: A  409 GLN cc_start: 0.5969 (OUTLIER) cc_final: 0.5389 (tm-30)
REVERT: A  430 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7938 (mmm)
REVERT: A  459 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8157 (mt)
REVERT: A  665 LEU cc_start: 0.9289 (mt) cc_final: 0.8941 (pp)
REVERT: A  695 PHE cc_start: 0.8451 (m-80) cc_final: 0.8219 (m-80)
REVERT: A  711 PHE cc_start: 0.8246 (m-80) cc_final: 0.8029 (m-10)
  outliers start: 10
  outliers final: 1
  residues processed: 105
  average time/residue: 0.4346
  time to fit residues: 47.5796
Evaluate side-chains
  98 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    0.1980
   overall best weight:    1.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.136322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.104827 restraints weight = 8338.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.73
r_work: 0.3360 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4561  Z= 0.156
  Angle     :  0.703  12.945   6202  Z= 0.338
  Chirality :  0.045   0.228    746
  Planarity :  0.004   0.041    747
  Dihedral  :  4.253  18.582    600
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.82 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.36), residues: 565
  helix:  2.00 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop :  0.39 (0.65), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  61 
 TYR   0.016   0.002   TYR A 689 
 PHE   0.033   0.002   PHE A 447 
 TRP   0.025   0.002   TRP A 678 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 4561)
  covalent geometry    : angle       0.70313 ( 6202)
  hydrogen bonds       : bond        0.04424 (  374)
  hydrogen bonds       : angle       4.52614 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7165 (mtm-85)
REVERT: A   71 LYS cc_start: 0.6937 (mtpt) cc_final: 0.6536 (mmmt)
REVERT: A  130 ARG cc_start: 0.8612 (ptp90) cc_final: 0.7877 (ptp90)
REVERT: A  193 TRP cc_start: 0.8967 (t60) cc_final: 0.8710 (t60)
REVERT: A  203 LYS cc_start: 0.7888 (mmpt) cc_final: 0.7555 (mtmm)
REVERT: A  236 LYS cc_start: 0.8630 (mttt) cc_final: 0.8232 (mptt)
REVERT: A  277 VAL cc_start: 0.9103 (t) cc_final: 0.8867 (p)
REVERT: A  295 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8043 (mtm110)
REVERT: A  299 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8548 (mt-10)
REVERT: A  359 TYR cc_start: 0.8870 (t80) cc_final: 0.8667 (t80)
REVERT: A  381 ASN cc_start: 0.7812 (m-40) cc_final: 0.7540 (t0)
REVERT: A  396 TRP cc_start: 0.8458 (t-100) cc_final: 0.8174 (t-100)
REVERT: A  406 LYS cc_start: 0.8398 (mttp) cc_final: 0.7846 (tppt)
REVERT: A  430 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8139 (mtm)
REVERT: A  459 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8187 (mp)
REVERT: A  542 MET cc_start: 0.7468 (tmm) cc_final: 0.7251 (tmm)
REVERT: A  665 LEU cc_start: 0.9286 (mt) cc_final: 0.8969 (pp)
  outliers start: 12
  outliers final: 2
  residues processed: 101
  average time/residue: 0.3653
  time to fit residues: 38.5668
Evaluate side-chains
  96 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  471 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 16 optimal weight:   20.0000
   overall best weight:    1.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.135788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.104441 restraints weight = 8351.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.70
r_work: 0.3357 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4561  Z= 0.158
  Angle     :  0.708  11.120   6202  Z= 0.344
  Chirality :  0.046   0.267    746
  Planarity :  0.005   0.041    747
  Dihedral  :  4.264  19.101    600
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 22.04 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.36), residues: 565
  helix:  2.03 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop :  0.27 (0.65), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  61 
 TYR   0.018   0.002   TYR A 407 
 PHE   0.029   0.002   PHE A 447 
 TRP   0.028   0.002   TRP A 678 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4561)
  covalent geometry    : angle       0.70809 ( 6202)
  hydrogen bonds       : bond        0.04459 (  374)
  hydrogen bonds       : angle       4.55569 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7217 (mtm-85)
REVERT: A   71 LYS cc_start: 0.7010 (mtpt) cc_final: 0.6590 (mmmt)
REVERT: A  130 ARG cc_start: 0.8625 (ptp90) cc_final: 0.7908 (ptp90)
REVERT: A  193 TRP cc_start: 0.8849 (t60) cc_final: 0.8513 (t60)
REVERT: A  236 LYS cc_start: 0.8625 (mttt) cc_final: 0.8241 (mptt)
REVERT: A  277 VAL cc_start: 0.9122 (t) cc_final: 0.8888 (p)
REVERT: A  295 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8134 (mtm110)
REVERT: A  299 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8556 (mt-10)
REVERT: A  396 TRP cc_start: 0.8482 (t-100) cc_final: 0.8218 (t-100)
REVERT: A  414 LEU cc_start: 0.8908 (mt) cc_final: 0.8491 (tt)
REVERT: A  430 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7930 (mmm)
REVERT: A  459 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8156 (mp)
REVERT: A  463 LEU cc_start: 0.9291 (mp) cc_final: 0.8731 (mt)
REVERT: A  516 TYR cc_start: 0.7952 (m-80) cc_final: 0.7730 (m-10)
REVERT: A  542 MET cc_start: 0.7450 (tmm) cc_final: 0.7010 (tpt)
REVERT: A  665 LEU cc_start: 0.9318 (mt) cc_final: 0.8990 (pp)
  outliers start: 9
  outliers final: 2
  residues processed: 99
  average time/residue: 0.3821
  time to fit residues: 39.5390
Evaluate side-chains
  90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  471 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS

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 = 0.132961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.101233 restraints weight = 8498.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.70
r_work: 0.3313 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4561  Z= 0.211
  Angle     :  0.745  10.865   6202  Z= 0.364
  Chirality :  0.047   0.298    746
  Planarity :  0.005   0.041    747
  Dihedral  :  4.269  19.089    600
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.43 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.36), residues: 565
  helix:  1.89 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop :  0.62 (0.68), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  61 
 TYR   0.019   0.002   TYR A 451 
 PHE   0.031   0.002   PHE A 221 
 TRP   0.027   0.002   TRP A 678 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 4561)
  covalent geometry    : angle       0.74490 ( 6202)
  hydrogen bonds       : bond        0.04763 (  374)
  hydrogen bonds       : angle       4.71108 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7215 (mtm-85)
REVERT: A   71 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6605 (mmmt)
REVERT: A  130 ARG cc_start: 0.8648 (ptp90) cc_final: 0.7920 (ptp90)
REVERT: A  193 TRP cc_start: 0.8906 (t60) cc_final: 0.8657 (t60)
REVERT: A  203 LYS cc_start: 0.8043 (mmpt) cc_final: 0.7617 (mtmm)
REVERT: A  236 LYS cc_start: 0.8695 (mttt) cc_final: 0.8296 (mptt)
REVERT: A  277 VAL cc_start: 0.9147 (t) cc_final: 0.8895 (p)
REVERT: A  295 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8145 (mtm110)
REVERT: A  299 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8609 (mt-10)
REVERT: A  396 TRP cc_start: 0.8576 (t-100) cc_final: 0.8374 (t-100)
REVERT: A  414 LEU cc_start: 0.8943 (mt) cc_final: 0.8685 (tt)
REVERT: A  430 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8308 (mtt)
REVERT: A  459 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8182 (mp)
REVERT: A  463 LEU cc_start: 0.9293 (mp) cc_final: 0.8687 (mt)
REVERT: A  516 TYR cc_start: 0.8011 (m-80) cc_final: 0.7747 (m-10)
REVERT: A  542 MET cc_start: 0.7472 (tmm) cc_final: 0.7035 (tpt)
REVERT: A  665 LEU cc_start: 0.9287 (mt) cc_final: 0.9035 (pp)
  outliers start: 13
  outliers final: 2
  residues processed: 95
  average time/residue: 0.3561
  time to fit residues: 35.3309
Evaluate side-chains
  91 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 4 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 23 optimal weight:    0.1980
   chunk 3 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.138790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.107729 restraints weight = 8270.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.72
r_work: 0.3425 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.5246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   4561  Z= 0.143
  Angle     :  0.742  11.773   6202  Z= 0.350
  Chirality :  0.046   0.301    746
  Planarity :  0.004   0.041    747
  Dihedral  :  4.180  17.699    600
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 23.67 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.37), residues: 565
  helix:  2.05 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop :  0.71 (0.72), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  61 
 TYR   0.020   0.001   TYR A 451 
 PHE   0.026   0.001   PHE A 221 
 TRP   0.032   0.003   TRP A 678 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4561)
  covalent geometry    : angle       0.74233 ( 6202)
  hydrogen bonds       : bond        0.04325 (  374)
  hydrogen bonds       : angle       4.59186 ( 1101)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7370 (mtm-85)
REVERT: A   54 LEU cc_start: 0.9178 (tp) cc_final: 0.8931 (mm)
REVERT: A   71 LYS cc_start: 0.7010 (mtpt) cc_final: 0.6570 (mmmt)
REVERT: A  130 ARG cc_start: 0.8609 (ptp90) cc_final: 0.7874 (ptp90)
REVERT: A  193 TRP cc_start: 0.8795 (t60) cc_final: 0.8577 (t60)
REVERT: A  203 LYS cc_start: 0.7885 (mmpt) cc_final: 0.7499 (mtmm)
REVERT: A  236 LYS cc_start: 0.8590 (mttt) cc_final: 0.8242 (mptt)
REVERT: A  246 ASP cc_start: 0.7976 (m-30) cc_final: 0.7744 (m-30)
REVERT: A  277 VAL cc_start: 0.9106 (t) cc_final: 0.8877 (p)
REVERT: A  396 TRP cc_start: 0.8409 (t-100) cc_final: 0.8150 (t-100)
REVERT: A  407 TYR cc_start: 0.8090 (p90) cc_final: 0.7848 (p90)
REVERT: A  414 LEU cc_start: 0.8877 (mt) cc_final: 0.8636 (tt)
REVERT: A  430 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7827 (mmm)
REVERT: A  459 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8282 (mp)
REVERT: A  516 TYR cc_start: 0.7835 (m-80) cc_final: 0.7490 (m-10)
REVERT: A  542 MET cc_start: 0.7401 (tmm) cc_final: 0.7029 (tpt)
  outliers start: 4
  outliers final: 0
  residues processed: 93
  average time/residue: 0.3325
  time to fit residues: 32.5239
Evaluate side-chains
  89 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.137699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.106535 restraints weight = 8394.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.76
r_work: 0.3410 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.5404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4561  Z= 0.148
  Angle     :  0.759  12.023   6202  Z= 0.358
  Chirality :  0.047   0.296    746
  Planarity :  0.005   0.041    747
  Dihedral  :  4.170  17.758    600
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 25.92 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.37), residues: 565
  helix:  1.97 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop :  0.50 (0.76), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  61 
 TYR   0.020   0.002   TYR A 451 
 PHE   0.028   0.002   PHE A 221 
 TRP   0.031   0.002   TRP A 678 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4561)
  covalent geometry    : angle       0.75935 ( 6202)
  hydrogen bonds       : bond        0.04391 (  374)
  hydrogen bonds       : angle       4.63923 ( 1101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1413.01 seconds
wall clock time: 24 minutes 58.42 seconds (1498.42 seconds total)