Starting phenix.real_space_refine
on Wed Sep 17 06:19:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zgo_60085/09_2025/8zgo_60085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zgo_60085/09_2025/8zgo_60085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zgo_60085/09_2025/8zgo_60085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zgo_60085/09_2025/8zgo_60085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zgo_60085/09_2025/8zgo_60085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zgo_60085/09_2025/8zgo_60085.cif"
  }
  resolution = 2.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Fe      3      7.16       5
     S      26      5.16       5
     C    3953      2.51       5
     N     948      2.21       5
     O    1049      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5980
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 742, 5860
          Classifications: {'peptide': 742}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 712}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 38
    Chain: "A"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 120
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2}
          Classifications: {'undetermined': 4, 'water': 32}
          Link IDs: {None: 35}
  Time building chain proxies: 1.66, per 1000 atoms: 0.28
  Number of scatterers: 5980
  At special positions: 0
  Unit cell: (76.912, 86.108, 101.992, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      3     26.01
     Ca      1     19.99
     S      26     16.00
     O    1049      8.00
     N     948      7.00
     C    3953      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 365.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 2 sheets defined
      76.7% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 3
      No H-bonds generated for 'chain 'A' and resid 1 through 3'
    Processing helix  chain 'A' and resid 4 through 33
    Processing helix  chain 'A' and resid 51 through 64
      removed outlier: 3.558A  pdb=" N   THR A  64 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 82 through 105
    Processing helix  chain 'A' and resid 112 through 129
      removed outlier: 3.642A  pdb=" N   VAL A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 161
      Proline residue:  A 154  - end of helix
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 173
    Processing helix  chain 'A' and resid 182 through 200
    Processing helix  chain 'A' and resid 226 through 255
      removed outlier: 4.961A  pdb=" N   SER A 252 " --> pdb=" O   MET A 248 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   PHE A 253 " --> pdb=" O   TRP A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 279
    Processing helix  chain 'A' and resid 280 through 305
      removed outlier: 3.534A  pdb=" N   TYR A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR A 305 " --> pdb=" O   THR A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.747A  pdb=" N   TRP A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 359
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 366 through 394
    Processing helix  chain 'A' and resid 398 through 400
      No H-bonds generated for 'chain 'A' and resid 398 through 400'
    Processing helix  chain 'A' and resid 401 through 406
    Processing helix  chain 'A' and resid 416 through 436
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 466 through 471
    Processing helix  chain 'A' and resid 477 through 490
      removed outlier: 3.732A  pdb=" N   VAL A 488 " --> pdb=" O   TRP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 512
    Processing helix  chain 'A' and resid 516 through 536
    Processing helix  chain 'A' and resid 537 through 543
      removed outlier: 3.641A  pdb=" N   LEU A 540 " --> pdb=" O   PRO A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 561
      removed outlier: 3.531A  pdb=" N   ALA A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 3.580A  pdb=" N   VAL A 568 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU A 569 " --> pdb=" O   VAL A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 579
      removed outlier: 3.613A  pdb=" N   HIS A 577 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   SER A 579 " --> pdb=" O   TYR A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 607
      removed outlier: 3.613A  pdb=" N   LEU A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   PHE A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   VAL A 598 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 614
    Processing helix  chain 'A' and resid 617 through 625
      removed outlier: 4.454A  pdb=" N   TYR A 623 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 658
      removed outlier: 3.934A  pdb=" N   ALA A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   PHE A 644 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 686
      removed outlier: 3.728A  pdb=" N   SER A 686 " --> pdb=" O   MET A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
    Processing helix  chain 'A' and resid 702 through 708
    Processing helix  chain 'A' and resid 708 through 713
    Processing helix  chain 'A' and resid 714 through 723
    Processing helix  chain 'A' and resid 723 through 746
      removed outlier: 4.230A  pdb=" N   ALA A 727 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50
      removed outlier: 6.706A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72

    398 hydrogen bonds defined for protein.
    1164 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: 0.94

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.17 -     1.53: 5563
        1.53 -     1.89: 576
        1.89 -     2.24: 7
        2.24 -     2.60: 0
        2.60 -     2.96: 1
  Bond restraints: 6147
  Sorted by residual:
  bond pdb=" C   PRO A 267 "
       pdb=" N   SER A 269 "
    ideal  model  delta    sigma   weight residual
    1.332  2.959 -1.626 1.40e-02 5.10e+03 1.35e+04
  bond pdb=" C   VAL A 568 "
       pdb=" N   LEU A 569 "
    ideal  model  delta    sigma   weight residual
    1.335  1.422 -0.088 1.33e-02 5.65e+03 4.35e+01
  bond pdb=" C   PRO A 219 "
       pdb=" O   PRO A 219 "
    ideal  model  delta    sigma   weight residual
    1.237  1.171  0.066 1.32e-02 5.74e+03 2.52e+01
  bond pdb=" C   GLY A  65 "
       pdb=" N   GLY A  66 "
    ideal  model  delta    sigma   weight residual
    1.326  1.406 -0.079 1.64e-02 3.72e+03 2.34e+01
  bond pdb=" C   PRO A 364 "
       pdb=" O   PRO A 364 "
    ideal  model  delta    sigma   weight residual
    1.234  1.180  0.054 1.14e-02 7.69e+03 2.23e+01
  ... (remaining 6142 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 7852
        2.68 -     5.36: 481
        5.36 -     8.05: 61
        8.05 -    10.73: 13
       10.73 -    13.41: 3
  Bond angle restraints: 8410
  Sorted by residual:
  angle pdb=" CA  PRO A 267 "
        pdb=" N   PRO A 267 "
        pdb=" CD  PRO A 267 "
      ideal   model   delta    sigma   weight residual
     112.00   98.59   13.41 1.40e+00 5.10e-01 9.18e+01
  angle pdb=" O   GLN A  62 "
        pdb=" C   GLN A  62 "
        pdb=" N   THR A  63 "
      ideal   model   delta    sigma   weight residual
     122.12  113.08    9.04 1.06e+00 8.90e-01 7.28e+01
  angle pdb=" CA  GLN A  62 "
        pdb=" C   GLN A  62 "
        pdb=" N   THR A  63 "
      ideal   model   delta    sigma   weight residual
     117.30  126.32   -9.02 1.16e+00 7.43e-01 6.04e+01
  angle pdb=" CA  GLY A  65 "
        pdb=" C   GLY A  65 "
        pdb=" O   GLY A  65 "
      ideal   model   delta    sigma   weight residual
     119.03  110.54    8.49 1.14e+00 7.69e-01 5.55e+01
  angle pdb=" C   GLU A 218 "
        pdb=" CA  GLU A 218 "
        pdb=" CB  GLU A 218 "
      ideal   model   delta    sigma   weight residual
     111.02  122.38  -11.36 1.53e+00 4.27e-01 5.52e+01
  ... (remaining 8405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.23: 2999
       18.23 -    36.47: 293
       36.47 -    54.70: 104
       54.70 -    72.94: 11
       72.94 -    91.17: 8
  Dihedral angle restraints: 3415
    sinusoidal: 1287
      harmonic: 2128
  Sorted by residual:
  dihedral pdb=" CA  PRO A 267 "
           pdb=" C   PRO A 267 "
           pdb=" N   SER A 269 "
           pdb=" CA  SER A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  130.24   49.76     0      5.00e+00 4.00e-02 9.91e+01
  dihedral pdb=" C2C HEM A 801 "
           pdb=" C3C HEM A 801 "
           pdb=" CAC HEM A 801 "
           pdb=" CBC HEM A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -51.48   51.48     2      1.00e+01 1.00e-02 2.94e+01
  dihedral pdb=" C2B HEM A 802 "
           pdb=" C3B HEM A 802 "
           pdb=" CAB HEM A 802 "
           pdb=" CBB HEM A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   44.75  -44.75     2      1.00e+01 1.00e-02 2.38e+01
  ... (remaining 3412 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 720
       0.070 -    0.140: 130
       0.140 -    0.210: 33
       0.210 -    0.280: 14
       0.280 -    0.351: 6
  Chirality restraints: 903
  Sorted by residual:
  chirality pdb=" CB  VAL A 288 "
            pdb=" CA  VAL A 288 "
            pdb=" CG1 VAL A 288 "
            pdb=" CG2 VAL A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CB  VAL A 746 "
            pdb=" CA  VAL A 746 "
            pdb=" CG1 VAL A 746 "
            pdb=" CG2 VAL A 746 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" CA  THR A  63 "
            pdb=" N   THR A  63 "
            pdb=" C   THR A  63 "
            pdb=" CB  THR A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.22    0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 900 not shown)

  Planarity restraints: 1033
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 267 "    0.093 2.00e-02 2.50e+03   1.53e-01 2.34e+02
        pdb=" C   PRO A 267 "   -0.260 2.00e-02 2.50e+03
        pdb=" O   PRO A 267 "    0.125 2.00e-02 2.50e+03
        pdb=" N   SER A 269 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 266 "    0.123 5.00e-02 4.00e+02   1.72e-01 4.74e+01
        pdb=" N   PRO A 267 "   -0.297 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.091 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.083 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 594 "    0.024 2.00e-02 2.50e+03   4.84e-02 2.34e+01
        pdb=" C   LEU A 594 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   LEU A 594 "    0.032 2.00e-02 2.50e+03
        pdb=" N   MET A 595 "    0.028 2.00e-02 2.50e+03
  ... (remaining 1030 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 321
        2.73 -     3.27: 6036
        3.27 -     3.81: 10738
        3.81 -     4.36: 13168
        4.36 -     4.90: 21633
  Nonbonded interactions: 51896
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A 542 "
            pdb="FE    FE A 803 "
     model   vdw
     2.182 2.340
  nonbonded pdb=" OG  SER A 338 "
            pdb=" OH  TYR A 386 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" ND1 HIS A 490 "
            pdb="FE    FE A 803 "
     model   vdw
     2.266 2.340
  nonbonded pdb=" O   GLY A 161 "
            pdb=" O   ASN A 177 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   PHE A 663 "
            pdb=" NE2 GLN A 741 "
     model   vdw
     2.316 3.120
  ... (remaining 51891 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:             2.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.750
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
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      :  0.023   1.626   6149  Z= 1.601
  Angle     :  1.320  13.411   8410  Z= 0.899
  Chirality :  0.070   0.351    903
  Planarity :  0.012   0.172   1033
  Dihedral  : 16.962  91.173   2059
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.23 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.88 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.32), residues: 736
  helix:  0.90 (0.24), residues: 515
  sheet:  None (None), residues: 0
  loop : -0.95 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 724 
 TYR   0.010   0.001   TYR A 375 
 PHE   0.018   0.002   PHE A 639 
 TRP   0.018   0.002   TRP A 342 
 HIS   0.004   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.02289 ( 6147)
  covalent geometry    : angle       1.32004 ( 8410)
  hydrogen bonds       : bond        0.16143 (  398)
  hydrogen bonds       : angle       6.16694 ( 1164)
  Misc. bond           : bond        0.06503 (    2)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.7823 (tttt) cc_final: 0.7604 (tmmt)
REVERT: A  321 GLU cc_start: 0.7857 (tt0) cc_final: 0.7585 (tm-30)
REVERT: A  336 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9179 (mp)
REVERT: A  362 LYS cc_start: 0.8000 (mttt) cc_final: 0.7698 (mtmt)
REVERT: A  594 LEU cc_start: 0.6632 (tm) cc_final: 0.6413 (tp)
REVERT: A  662 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7924 (mm-40)
  outliers start: 18
  outliers final: 8
  residues processed: 62
  average time/residue: 0.6036
  time to fit residues: 39.3163
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  662 GLN
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 272 GLN
A 511 ASN
A 625 GLN
A 628 ASN
A 676 ASN
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.087028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.063386 restraints weight = 8673.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 1.60
r_work: 0.2656 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2554 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9039
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.252   6149  Z= 0.173
  Angle     :  0.651  15.365   8410  Z= 0.313
  Chirality :  0.043   0.132    903
  Planarity :  0.005   0.055   1033
  Dihedral  :  8.767  89.606    832
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.05 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  1.57 (0.32), residues: 738
  helix:  1.77 (0.23), residues: 513
  sheet:  None (None), residues: 0
  loop : -0.64 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 516 
 TYR   0.017   0.002   TYR A 328 
 PHE   0.018   0.002   PHE A 639 
 TRP   0.019   0.002   TRP A 342 
 HIS   0.005   0.002   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6147)
  covalent geometry    : angle       0.65051 ( 8410)
  hydrogen bonds       : bond        0.05678 (  398)
  hydrogen bonds       : angle       4.69240 ( 1164)
  Misc. bond           : bond        0.18388 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8010 (tt0)
REVERT: A  321 GLU cc_start: 0.8300 (tt0) cc_final: 0.8006 (tm-30)
REVERT: A  368 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8021 (ttm170)
REVERT: A  498 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7964 (mt-10)
  outliers start: 13
  outliers final: 4
  residues processed: 56
  average time/residue: 0.6407
  time to fit residues: 37.6079
Evaluate side-chains
  51 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3187 r_free = 0.3187 target = 0.087793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.064168 restraints weight = 8630.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2754 rms_B_bonded: 1.58
r_work: 0.2653 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2550 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.184   6149  Z= 0.126
  Angle     :  0.566  11.772   8410  Z= 0.274
  Chirality :  0.040   0.120    903
  Planarity :  0.004   0.053   1033
  Dihedral  :  7.597  83.733    818
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.22 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  1.87 (0.32), residues: 738
  helix:  2.02 (0.24), residues: 517
  sheet: -1.52 (1.51), residues: 10
  loop : -0.57 (0.43), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 516 
 TYR   0.010   0.001   TYR A 328 
 PHE   0.016   0.001   PHE A 639 
 TRP   0.020   0.001   TRP A 342 
 HIS   0.007   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6147)
  covalent geometry    : angle       0.56637 ( 8410)
  hydrogen bonds       : bond        0.04781 (  398)
  hydrogen bonds       : angle       4.44045 ( 1164)
  Misc. bond           : bond        0.13352 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7897 (tt0)
REVERT: A  321 GLU cc_start: 0.8286 (tt0) cc_final: 0.7884 (tm-30)
REVERT: A  368 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7926 (ttm170)
REVERT: A  498 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7972 (mt-10)
  outliers start: 14
  outliers final: 3
  residues processed: 58
  average time/residue: 0.6059
  time to fit residues: 36.9809
Evaluate side-chains
  49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 37 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0870
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3211 r_free = 0.3211 target = 0.089330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.065816 restraints weight = 8750.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 1.59
r_work: 0.2686 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2583 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.162   6149  Z= 0.112
  Angle     :  0.541  10.684   8410  Z= 0.260
  Chirality :  0.039   0.116    903
  Planarity :  0.004   0.051   1033
  Dihedral  :  7.093  80.870    812
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.39 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.05 (0.32), residues: 738
  helix:  2.09 (0.24), residues: 523
  sheet: -0.97 (1.60), residues: 10
  loop : -0.41 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 516 
 TYR   0.009   0.001   TYR A 328 
 PHE   0.014   0.001   PHE A 639 
 TRP   0.018   0.001   TRP A 342 
 HIS   0.007   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6147)
  covalent geometry    : angle       0.54098 ( 8410)
  hydrogen bonds       : bond        0.04270 (  398)
  hydrogen bonds       : angle       4.31003 ( 1164)
  Misc. bond           : bond        0.11641 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7843 (tt0)
REVERT: A  498 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7967 (mt-10)
  outliers start: 11
  outliers final: 5
  residues processed: 49
  average time/residue: 0.6877
  time to fit residues: 35.4641
Evaluate side-chains
  46 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0670
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3191 r_free = 0.3191 target = 0.088023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.064366 restraints weight = 8879.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 1.60
r_work: 0.2658 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2554 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.189   6149  Z= 0.126
  Angle     :  0.551  11.002   8410  Z= 0.266
  Chirality :  0.040   0.122    903
  Planarity :  0.004   0.050   1033
  Dihedral  :  7.084  80.887    812
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.72 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.13 (0.32), residues: 738
  helix:  2.19 (0.24), residues: 515
  sheet: -0.63 (1.69), residues: 10
  loop : -0.40 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 516 
 TYR   0.011   0.001   TYR A 328 
 PHE   0.017   0.001   PHE A 639 
 TRP   0.017   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6147)
  covalent geometry    : angle       0.55078 ( 8410)
  hydrogen bonds       : bond        0.04650 (  398)
  hydrogen bonds       : angle       4.35736 ( 1164)
  Misc. bond           : bond        0.13632 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7860 (tt0)
REVERT: A  321 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7681 (tt0)
REVERT: A  368 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7934 (ttm170)
REVERT: A  516 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8079 (mmm-85)
  outliers start: 14
  outliers final: 4
  residues processed: 50
  average time/residue: 0.7243
  time to fit residues: 37.8385
Evaluate side-chains
  48 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 58 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0670
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3199 r_free = 0.3199 target = 0.088609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.065008 restraints weight = 8692.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 1.58
r_work: 0.2671 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2568 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.166   6149  Z= 0.119
  Angle     :  0.548  10.584   8410  Z= 0.263
  Chirality :  0.039   0.119    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  7.025  80.370    812
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.88 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.17 (0.32), residues: 738
  helix:  2.20 (0.24), residues: 515
  sheet: -0.50 (1.73), residues: 10
  loop : -0.34 (0.44), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 517 
 TYR   0.010   0.001   TYR A 328 
 PHE   0.016   0.001   PHE A 597 
 TRP   0.017   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6147)
  covalent geometry    : angle       0.54837 ( 8410)
  hydrogen bonds       : bond        0.04442 (  398)
  hydrogen bonds       : angle       4.33313 ( 1164)
  Misc. bond           : bond        0.12037 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7840 (tt0)
REVERT: A  321 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7679 (tt0)
REVERT: A  368 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7931 (ttm170)
  outliers start: 17
  outliers final: 3
  residues processed: 51
  average time/residue: 0.6881
  time to fit residues: 36.7389
Evaluate side-chains
  47 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0870
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3196 r_free = 0.3196 target = 0.088399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.064782 restraints weight = 8705.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 1.59
r_work: 0.2664 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2560 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.175   6149  Z= 0.122
  Angle     :  0.552  10.602   8410  Z= 0.265
  Chirality :  0.039   0.120    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.711  80.553    810
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.89 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.17 (0.32), residues: 738
  helix:  2.14 (0.24), residues: 521
  sheet: -0.47 (1.75), residues: 10
  loop : -0.23 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 655 
 TYR   0.011   0.001   TYR A 328 
 PHE   0.018   0.001   PHE A 597 
 TRP   0.017   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6147)
  covalent geometry    : angle       0.55216 ( 8410)
  hydrogen bonds       : bond        0.04515 (  398)
  hydrogen bonds       : angle       4.33896 ( 1164)
  Misc. bond           : bond        0.12710 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7848 (tt0)
REVERT: A  321 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7669 (tt0)
REVERT: A  368 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7933 (ttm170)
  outliers start: 13
  outliers final: 5
  residues processed: 50
  average time/residue: 0.6813
  time to fit residues: 35.6525
Evaluate side-chains
  47 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   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 741 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 = 0.3160 r_free = 0.3160 target = 0.086175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.062422 restraints weight = 8727.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.2722 rms_B_bonded: 1.59
r_work: 0.2620 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2516 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8974
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.205   6149  Z= 0.161
  Angle     :  0.590  11.515   8410  Z= 0.286
  Chirality :  0.042   0.139    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.882  81.800    810
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.55 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.05 (0.32), residues: 738
  helix:  2.04 (0.23), residues: 521
  sheet: -0.45 (1.77), residues: 10
  loop : -0.27 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 204 
 TYR   0.014   0.001   TYR A 328 
 PHE   0.023   0.001   PHE A 597 
 TRP   0.015   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6147)
  covalent geometry    : angle       0.59024 ( 8410)
  hydrogen bonds       : bond        0.05278 (  398)
  hydrogen bonds       : angle       4.45789 ( 1164)
  Misc. bond           : bond        0.15229 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7922 (tt0)
REVERT: A  321 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7703 (tt0)
REVERT: A  336 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8772 (mp)
REVERT: A  368 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8000 (ttm170)
REVERT: A  434 MET cc_start: 0.9252 (mmm) cc_final: 0.8888 (mmm)
  outliers start: 13
  outliers final: 4
  residues processed: 51
  average time/residue: 0.7271
  time to fit residues: 38.7717
Evaluate side-chains
  50 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3173 r_free = 0.3173 target = 0.086950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.063287 restraints weight = 8692.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.2738 rms_B_bonded: 1.58
r_work: 0.2636 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2533 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.184   6149  Z= 0.139
  Angle     :  0.579  11.072   8410  Z= 0.280
  Chirality :  0.041   0.127    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.812  80.804    810
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.72 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.06 (0.32), residues: 738
  helix:  2.05 (0.23), residues: 521
  sheet: -0.55 (1.73), residues: 10
  loop : -0.26 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 368 
 TYR   0.012   0.001   TYR A 328 
 PHE   0.023   0.001   PHE A 597 
 TRP   0.018   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6147)
  covalent geometry    : angle       0.57892 ( 8410)
  hydrogen bonds       : bond        0.04882 (  398)
  hydrogen bonds       : angle       4.42140 ( 1164)
  Misc. bond           : bond        0.13632 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7900 (tt0)
REVERT: A  321 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7703 (tt0)
REVERT: A  368 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7939 (ttm170)
REVERT: A  434 MET cc_start: 0.9245 (mmm) cc_final: 0.8875 (mmm)
REVERT: A  498 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7978 (mt-10)
  outliers start: 10
  outliers final: 4
  residues processed: 49
  average time/residue: 0.6955
  time to fit residues: 35.6266
Evaluate side-chains
  49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0370
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3185 r_free = 0.3185 target = 0.087740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.064215 restraints weight = 8718.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 1.59
r_work: 0.2656 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.172   6149  Z= 0.124
  Angle     :  0.563  10.500   8410  Z= 0.270
  Chirality :  0.040   0.142    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.720  80.386    810
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.22 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.13 (0.32), residues: 738
  helix:  2.10 (0.23), residues: 521
  sheet: -0.49 (1.74), residues: 10
  loop : -0.24 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 655 
 TYR   0.011   0.001   TYR A 328 
 PHE   0.022   0.001   PHE A 597 
 TRP   0.019   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6147)
  covalent geometry    : angle       0.56325 ( 8410)
  hydrogen bonds       : bond        0.04576 (  398)
  hydrogen bonds       : angle       4.36947 ( 1164)
  Misc. bond           : bond        0.12596 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7871 (tt0)
REVERT: A  321 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7725 (tt0)
REVERT: A  368 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7930 (ttm170)
REVERT: A  434 MET cc_start: 0.9244 (mmm) cc_final: 0.8874 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 45
  average time/residue: 0.6812
  time to fit residues: 32.0445
Evaluate side-chains
  49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0010
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 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 = 0.3194 r_free = 0.3194 target = 0.088300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.064783 restraints weight = 8634.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 1.58
r_work: 0.2666 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2563 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.169   6149  Z= 0.120
  Angle     :  0.560  10.526   8410  Z= 0.269
  Chirality :  0.039   0.118    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.663  80.281    810
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.22 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.11 (0.32), residues: 738
  helix:  2.04 (0.23), residues: 527
  sheet: -0.32 (1.80), residues: 10
  loop : -0.19 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 591 
 TYR   0.010   0.001   TYR A 328 
 PHE   0.021   0.001   PHE A 597 
 TRP   0.020   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6147)
  covalent geometry    : angle       0.56011 ( 8410)
  hydrogen bonds       : bond        0.04442 (  398)
  hydrogen bonds       : angle       4.34413 ( 1164)
  Misc. bond           : bond        0.12284 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2547.96 seconds
wall clock time: 44 minutes 14.95 seconds (2654.95 seconds total)