Starting phenix.real_space_refine
on Wed Sep 17 03:00:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9noy_49621/09_2025/9noy_49621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9noy_49621/09_2025/9noy_49621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9noy_49621/09_2025/9noy_49621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9noy_49621/09_2025/9noy_49621.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9noy_49621/09_2025/9noy_49621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9noy_49621/09_2025/9noy_49621.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      22      5.16       5
     C    1355      2.51       5
     N     315      2.21       5
     O     339      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  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: 2031
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2031
          Classifications: {'peptide': 257}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
          Chain breaks: 1
  Time building chain proxies: 0.97, per 1000 atoms: 0.48
  Number of scatterers: 2031
  At special positions: 0
  Unit cell: (56.787, 51.026, 76.539, 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      22     16.00
     O     339      8.00
     N     315      7.00
     C    1355      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: 0.21
  Conformation dependent library (CDL) restraints added in 94.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  490

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      89.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 563 through 590
    Processing helix  chain 'A' and resid 593 through 600
    Processing helix  chain 'A' and resid 601 through 617
      removed outlier: 3.748A  pdb=" N   PHE A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 622
      removed outlier: 3.661A  pdb=" N   TYR A 621 " --> pdb=" O   VAL A 617 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL A 622 " --> pdb=" O   VAL A 618 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 617 through 622'
    Processing helix  chain 'A' and resid 626 through 636
      removed outlier: 4.270A  pdb=" N   GLN A 634 " --> pdb=" O   CYS A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 660
    Processing helix  chain 'A' and resid 665 through 675
      removed outlier: 3.566A  pdb=" N   TYR A 669 " --> pdb=" O   PHE A 665 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A 670 " --> pdb=" O   PRO A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 699
      removed outlier: 3.799A  pdb=" N   MET A 682 " --> pdb=" O   PRO A 678 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 683 " --> pdb=" O   TYR A 679 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ALA A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 748
      removed outlier: 3.751A  pdb=" N   PHE A 730 " --> pdb=" O   ASN A 726 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN A 731 " --> pdb=" O   SER A 727 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   MET A 748 " --> pdb=" O   SER A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 782
      removed outlier: 4.177A  pdb=" N   SER A 781 " --> pdb=" O   CYS A 777 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA A 782 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 818
      removed outlier: 4.370A  pdb=" N   TYR A 807 " --> pdb=" O   ILE A 803 " (cutoff:3.500A)
      Proline residue:  A 810  - end of helix
    Processing helix  chain 'A' and resid 819 through 822
    Processing helix  chain 'A' and resid 823 through 836

    160 hydrogen bonds defined for protein.
    477 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: 0.31

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 590
        1.34 -     1.46: 536
        1.46 -     1.58: 925
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 2086
  Sorted by residual:
  bond pdb=" CB  ILE A 815 "
       pdb=" CG2 ILE A 815 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 5.99e-01
  bond pdb=" CA  VAL A 618 "
       pdb=" CB  VAL A 618 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 4.49e-01
  bond pdb=" CB  VAL A 569 "
       pdb=" CG1 VAL A 569 "
    ideal  model  delta    sigma   weight residual
    1.521  1.502  0.019 3.30e-02 9.18e+02 3.26e-01
  bond pdb=" CG  GLU A 560 "
       pdb=" CD  GLU A 560 "
    ideal  model  delta    sigma   weight residual
    1.516  1.530 -0.014 2.50e-02 1.60e+03 2.95e-01
  bond pdb=" CG  LEU A 816 "
       pdb=" CD2 LEU A 816 "
    ideal  model  delta    sigma   weight residual
    1.521  1.504  0.017 3.30e-02 9.18e+02 2.64e-01
  ... (remaining 2081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 2746
        1.44 -     2.88: 74
        2.88 -     4.32: 14
        4.32 -     5.76: 6
        5.76 -     7.20: 1
  Bond angle restraints: 2841
  Sorted by residual:
  angle pdb=" C   VAL A 786 "
        pdb=" N   LEU A 787 "
        pdb=" CA  LEU A 787 "
      ideal   model   delta    sigma   weight residual
     121.54  126.04   -4.50 1.91e+00 2.74e-01 5.56e+00
  angle pdb=" CA  LEU A 794 "
        pdb=" CB  LEU A 794 "
        pdb=" CG  LEU A 794 "
      ideal   model   delta    sigma   weight residual
     116.30  123.50   -7.20 3.50e+00 8.16e-02 4.23e+00
  angle pdb=" C   GLU A 563 "
        pdb=" CA  GLU A 563 "
        pdb=" CB  GLU A 563 "
      ideal   model   delta    sigma   weight residual
     109.86  113.32   -3.46 1.80e+00 3.09e-01 3.70e+00
  angle pdb=" C   PHE A 591 "
        pdb=" N   GLN A 592 "
        pdb=" CA  GLN A 592 "
      ideal   model   delta    sigma   weight residual
     122.08  124.47   -2.39 1.47e+00 4.63e-01 2.65e+00
  angle pdb=" C   TYR A 807 "
        pdb=" N   PHE A 808 "
        pdb=" CA  PHE A 808 "
      ideal   model   delta    sigma   weight residual
     122.36  119.78    2.58 1.72e+00 3.38e-01 2.25e+00
  ... (remaining 2836 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.85: 998
       15.85 -    31.71: 161
       31.71 -    47.56: 49
       47.56 -    63.42: 12
       63.42 -    79.27: 2
  Dihedral angle restraints: 1222
    sinusoidal: 461
      harmonic: 761
  Sorted by residual:
  dihedral pdb=" CA  GLU A 563 "
           pdb=" C   GLU A 563 "
           pdb=" N   ALA A 564 "
           pdb=" CA  ALA A 564 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.30  -19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" N   MET A 682 "
           pdb=" CA  MET A 682 "
           pdb=" CB  MET A 682 "
           pdb=" CG  MET A 682 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.41  -58.59     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  ARG A 597 "
           pdb=" CB  ARG A 597 "
           pdb=" CG  ARG A 597 "
           pdb=" CD  ARG A 597 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.99  -57.01     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 1219 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 187
       0.027 -    0.053: 92
       0.053 -    0.080: 38
       0.080 -    0.106: 17
       0.106 -    0.133: 3
  Chirality restraints: 337
  Sorted by residual:
  chirality pdb=" CB  THR A 609 "
            pdb=" CA  THR A 609 "
            pdb=" OG1 THR A 609 "
            pdb=" CG2 THR A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  PRO A 565 "
            pdb=" N   PRO A 565 "
            pdb=" C   PRO A 565 "
            pdb=" CB  PRO A 565 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.44e-01
  chirality pdb=" CA  MET A 661 "
            pdb=" N   MET A 661 "
            pdb=" C   MET A 661 "
            pdb=" CB  MET A 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.08e-01
  ... (remaining 334 not shown)

  Planarity restraints: 341
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 561 "    0.014 2.00e-02 2.50e+03   1.64e-02 6.71e+00
        pdb=" CG  TRP A 561 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 561 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 561 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 561 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 561 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 561 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 561 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 561 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 561 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 564 "   -0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO A 565 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 565 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 565 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 809 "   -0.023 5.00e-02 4.00e+02   3.45e-02 1.90e+00
        pdb=" N   PRO A 810 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 810 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 810 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 338 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.08: 1473
        3.08 -     3.54: 2421
        3.54 -     3.99: 2849
        3.99 -     4.44: 3692
        4.44 -     4.90: 5315
  Nonbonded interactions: 15750
  Sorted by model distance:
  nonbonded pdb=" C   SER A 579 "
            pdb=" OG  SER A 579 "
     model   vdw
     2.625 2.616
  nonbonded pdb=" N   PHE A 591 "
            pdb=" O   PHE A 591 "
     model   vdw
     2.642 2.496
  nonbonded pdb=" O   VAL A 656 "
            pdb=" O   LYS A 660 "
     model   vdw
     2.643 3.040
  nonbonded pdb=" N   TYR A 783 "
            pdb=" O   TYR A 783 "
     model   vdw
     2.649 2.496
  nonbonded pdb=" C   SER A 775 "
            pdb=" OG  SER A 775 "
     model   vdw
     2.655 2.616
  ... (remaining 15745 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.190
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.960
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2086  Z= 0.135
  Angle     :  0.605   7.202   2841  Z= 0.301
  Chirality :  0.040   0.133    337
  Planarity :  0.005   0.047    341
  Dihedral  : 17.430  79.271    732
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 33.33 %
    Favored  : 65.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.53), residues: 253
  helix:  1.66 (0.37), residues: 203
  sheet:  None (None), residues: 0
  loop : -0.27 (0.82), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 597 
 TYR   0.007   0.001   TYR A 834 
 PHE   0.022   0.001   PHE A 684 
 TRP   0.042   0.004   TRP A 561 
 HIS   0.002   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2086)
  covalent geometry    : angle       0.60537 ( 2841)
  hydrogen bonds       : bond        0.14387 (  160)
  hydrogen bonds       : angle       5.63297 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  690 MET cc_start: 0.7373 (ppp) cc_final: 0.6997 (ppp)
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0535
  time to fit residues: 4.3252
Evaluate side-chains
  63 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  688 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0870
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.134691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.117766 restraints weight = 4010.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.121017 restraints weight = 2183.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.123401 restraints weight = 1428.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.125098 restraints weight = 1044.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.126127 restraints weight = 826.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2086  Z= 0.137
  Angle     :  0.585   9.146   2841  Z= 0.288
  Chirality :  0.039   0.122    337
  Planarity :  0.005   0.046    341
  Dihedral  :  5.850  56.564    288
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 31.56 %
    Favored  : 62.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.53), residues: 253
  helix:  2.06 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -0.08 (0.79), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 633 
 TYR   0.010   0.001   TYR A 669 
 PHE   0.016   0.001   PHE A 684 
 TRP   0.018   0.002   TRP A 561 
 HIS   0.001   0.000   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 2086)
  covalent geometry    : angle       0.58470 ( 2841)
  hydrogen bonds       : bond        0.03785 (  160)
  hydrogen bonds       : angle       4.19409 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  563 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: A  657 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8072 (t)
REVERT: A  660 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8314 (ttpt)
REVERT: A  682 MET cc_start: 0.7586 (tmm) cc_final: 0.6802 (tmm)
REVERT: A  690 MET cc_start: 0.7651 (ppp) cc_final: 0.7186 (ppp)
  outliers start: 13
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0482
  time to fit residues: 4.1342
Evaluate side-chains
  67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  660 LYS
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  793 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 654 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.133373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116542 restraints weight = 4016.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.119826 restraints weight = 2170.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.122064 restraints weight = 1417.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.123644 restraints weight = 1049.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.124772 restraints weight = 837.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2086  Z= 0.146
  Angle     :  0.594   9.000   2841  Z= 0.291
  Chirality :  0.039   0.118    337
  Planarity :  0.005   0.043    341
  Dihedral  :  5.713  57.129    286
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 32.00 %
    Favored  : 60.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.53), residues: 253
  helix:  2.09 (0.37), residues: 202
  sheet:  None (None), residues: 0
  loop : -0.30 (0.79), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 633 
 TYR   0.009   0.001   TYR A 621 
 PHE   0.013   0.001   PHE A 745 
 TRP   0.014   0.002   TRP A 561 
 HIS   0.001   0.000   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 2086)
  covalent geometry    : angle       0.59439 ( 2841)
  hydrogen bonds       : bond        0.03520 (  160)
  hydrogen bonds       : angle       4.00772 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  563 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: A  657 CYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8130 (t)
REVERT: A  682 MET cc_start: 0.7481 (tmm) cc_final: 0.6546 (tmm)
REVERT: A  690 MET cc_start: 0.7728 (ppp) cc_final: 0.7279 (ppp)
  outliers start: 16
  outliers final: 10
  residues processed: 71
  average time/residue: 0.0472
  time to fit residues: 4.0368
Evaluate side-chains
  70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  795 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 0 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0870
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.134687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.117906 restraints weight = 3954.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121242 restraints weight = 2138.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.123613 restraints weight = 1406.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.125218 restraints weight = 1027.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.126419 restraints weight = 819.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2086  Z= 0.123
  Angle     :  0.605   7.978   2841  Z= 0.287
  Chirality :  0.038   0.107    337
  Planarity :  0.005   0.041    341
  Dihedral  :  5.603  58.680    286
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 33.78 %
    Favored  : 60.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.54), residues: 253
  helix:  2.14 (0.37), residues: 206
  sheet:  None (None), residues: 0
  loop :  0.08 (0.86), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 674 
 TYR   0.012   0.001   TYR A 621 
 PHE   0.015   0.001   PHE A 684 
 TRP   0.023   0.002   TRP A 561 
 HIS   0.001   0.000   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2086)
  covalent geometry    : angle       0.60471 ( 2841)
  hydrogen bonds       : bond        0.03266 (  160)
  hydrogen bonds       : angle       3.93343 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  621 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6656 (t80)
REVERT: A  657 CYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8087 (t)
REVERT: A  682 MET cc_start: 0.7514 (tmm) cc_final: 0.6522 (tmm)
REVERT: A  690 MET cc_start: 0.7820 (ppp) cc_final: 0.7333 (ppp)
  outliers start: 12
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0494
  time to fit residues: 4.2345
Evaluate side-chains
  67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  832 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.1980
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.133577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.116949 restraints weight = 4045.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.120195 restraints weight = 2166.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.122562 restraints weight = 1414.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.124194 restraints weight = 1039.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.125395 restraints weight = 821.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2086  Z= 0.146
  Angle     :  0.637   8.416   2841  Z= 0.306
  Chirality :  0.040   0.128    337
  Planarity :  0.005   0.053    341
  Dihedral  :  5.729  59.134    286
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 32.44 %
    Favored  : 60.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.54), residues: 253
  helix:  2.06 (0.37), residues: 208
  sheet:  None (None), residues: 0
  loop :  0.10 (0.91), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 633 
 TYR   0.011   0.001   TYR A 621 
 PHE   0.007   0.001   PHE A 637 
 TRP   0.024   0.002   TRP A 561 
 HIS   0.002   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2086)
  covalent geometry    : angle       0.63666 ( 2841)
  hydrogen bonds       : bond        0.03313 (  160)
  hydrogen bonds       : angle       3.85259 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  621 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6635 (t80)
REVERT: A  657 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8100 (t)
REVERT: A  682 MET cc_start: 0.7530 (tmm) cc_final: 0.6570 (tmm)
REVERT: A  690 MET cc_start: 0.7912 (ppp) cc_final: 0.7414 (ppp)
REVERT: A  803 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8602 (tt)
  outliers start: 16
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0548
  time to fit residues: 4.3610
Evaluate side-chains
  67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  832 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.133375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116657 restraints weight = 3970.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.119858 restraints weight = 2140.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.122074 restraints weight = 1399.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.123658 restraints weight = 1041.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.124797 restraints weight = 829.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2086  Z= 0.160
  Angle     :  0.650   8.111   2841  Z= 0.313
  Chirality :  0.039   0.124    337
  Planarity :  0.006   0.056    341
  Dihedral  :  5.974  59.224    286
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  7.56 %
    Allowed  : 32.00 %
    Favored  : 60.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.55), residues: 253
  helix:  2.06 (0.38), residues: 208
  sheet:  None (None), residues: 0
  loop :  0.09 (0.91), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 633 
 TYR   0.015   0.002   TYR A 621 
 PHE   0.007   0.001   PHE A 637 
 TRP   0.026   0.002   TRP A 561 
 HIS   0.001   0.000   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 2086)
  covalent geometry    : angle       0.65000 ( 2841)
  hydrogen bonds       : bond        0.03436 (  160)
  hydrogen bonds       : angle       3.90045 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  621 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.6408 (t80)
REVERT: A  657 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8113 (t)
REVERT: A  682 MET cc_start: 0.7645 (tmm) cc_final: 0.6651 (tmm)
REVERT: A  690 MET cc_start: 0.8021 (ppp) cc_final: 0.7454 (ppp)
REVERT: A  803 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8588 (tt)
  outliers start: 17
  outliers final: 11
  residues processed: 70
  average time/residue: 0.0533
  time to fit residues: 4.4348
Evaluate side-chains
  72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  821 ARG
Chi-restraints excluded: chain A residue  832 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    0.4980
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 654 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.133050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116385 restraints weight = 4037.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.119620 restraints weight = 2178.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121998 restraints weight = 1430.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.123444 restraints weight = 1050.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.124673 restraints weight = 844.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2086  Z= 0.145
  Angle     :  0.641   7.901   2841  Z= 0.309
  Chirality :  0.039   0.137    337
  Planarity :  0.005   0.056    341
  Dihedral  :  5.961  59.751    286
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 34.22 %
    Favored  : 59.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.55), residues: 253
  helix:  2.13 (0.38), residues: 208
  sheet:  None (None), residues: 0
  loop :  0.12 (0.92), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 633 
 TYR   0.016   0.001   TYR A 621 
 PHE   0.016   0.001   PHE A 745 
 TRP   0.029   0.003   TRP A 561 
 HIS   0.002   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2086)
  covalent geometry    : angle       0.64111 ( 2841)
  hydrogen bonds       : bond        0.03329 (  160)
  hydrogen bonds       : angle       3.84999 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  621 TYR cc_start: 0.6761 (OUTLIER) cc_final: 0.6355 (t80)
REVERT: A  682 MET cc_start: 0.7644 (tmm) cc_final: 0.6591 (tmm)
REVERT: A  690 MET cc_start: 0.8071 (ppp) cc_final: 0.7565 (ppp)
REVERT: A  803 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8569 (tt)
  outliers start: 15
  outliers final: 11
  residues processed: 70
  average time/residue: 0.0533
  time to fit residues: 4.4306
Evaluate side-chains
  70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  821 ARG
Chi-restraints excluded: chain A residue  832 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.132935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.115957 restraints weight = 3976.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.119216 restraints weight = 2180.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121435 restraints weight = 1441.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.122772 restraints weight = 1070.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.123946 restraints weight = 881.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2086  Z= 0.159
  Angle     :  0.654   8.375   2841  Z= 0.318
  Chirality :  0.039   0.125    337
  Planarity :  0.006   0.056    341
  Dihedral  :  5.986  59.095    286
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 34.22 %
    Favored  : 59.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.55), residues: 253
  helix:  2.09 (0.38), residues: 207
  sheet:  None (None), residues: 0
  loop : -0.02 (0.90), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 633 
 TYR   0.015   0.001   TYR A 621 
 PHE   0.017   0.001   PHE A 684 
 TRP   0.035   0.003   TRP A 561 
 HIS   0.001   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2086)
  covalent geometry    : angle       0.65377 ( 2841)
  hydrogen bonds       : bond        0.03451 (  160)
  hydrogen bonds       : angle       3.90235 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  606 LEU cc_start: 0.9201 (tp) cc_final: 0.8906 (tp)
REVERT: A  621 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6379 (t80)
REVERT: A  682 MET cc_start: 0.7694 (tmm) cc_final: 0.6493 (tmm)
REVERT: A  685 ILE cc_start: 0.9315 (tp) cc_final: 0.9086 (mt)
REVERT: A  690 MET cc_start: 0.8143 (ppp) cc_final: 0.7620 (ppp)
REVERT: A  780 MET cc_start: 0.8059 (mmm) cc_final: 0.7806 (mmm)
REVERT: A  803 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8587 (tt)
  outliers start: 15
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0535
  time to fit residues: 4.4363
Evaluate side-chains
  70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  821 ARG
Chi-restraints excluded: chain A residue  832 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0270
   chunk 16 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5038

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.133807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.117036 restraints weight = 3965.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.120286 restraints weight = 2150.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.122603 restraints weight = 1417.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.123857 restraints weight = 1045.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125069 restraints weight = 864.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2086  Z= 0.133
  Angle     :  0.640   8.240   2841  Z= 0.308
  Chirality :  0.039   0.128    337
  Planarity :  0.005   0.056    341
  Dihedral  :  5.825  57.371    286
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 35.56 %
    Favored  : 58.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.55), residues: 253
  helix:  2.10 (0.38), residues: 208
  sheet:  None (None), residues: 0
  loop :  0.14 (0.91), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 633 
 TYR   0.016   0.001   TYR A 621 
 PHE   0.013   0.001   PHE A 745 
 TRP   0.037   0.003   TRP A 561 
 HIS   0.001   0.000   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 2086)
  covalent geometry    : angle       0.64008 ( 2841)
  hydrogen bonds       : bond        0.03220 (  160)
  hydrogen bonds       : angle       3.83328 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A  621 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6345 (t80)
REVERT: A  682 MET cc_start: 0.7638 (tmm) cc_final: 0.6602 (tmm)
REVERT: A  685 ILE cc_start: 0.9315 (tp) cc_final: 0.8998 (tp)
REVERT: A  690 MET cc_start: 0.8148 (ppp) cc_final: 0.7658 (ppp)
REVERT: A  803 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8553 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0560
  time to fit residues: 4.2953
Evaluate side-chains
  69 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  821 ARG
Chi-restraints excluded: chain A residue  832 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 11 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 = 0.3781 r_free = 0.3781 target = 0.134253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.117405 restraints weight = 4066.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120690 restraints weight = 2195.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.122870 restraints weight = 1444.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124542 restraints weight = 1081.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.125787 restraints weight = 867.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2086  Z= 0.132
  Angle     :  0.643   8.677   2841  Z= 0.307
  Chirality :  0.039   0.122    337
  Planarity :  0.005   0.056    341
  Dihedral  :  5.738  55.487    286
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 36.89 %
    Favored  : 58.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.55), residues: 253
  helix:  2.15 (0.37), residues: 207
  sheet:  None (None), residues: 0
  loop :  0.08 (0.91), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 633 
 TYR   0.015   0.001   TYR A 621 
 PHE   0.012   0.001   PHE A 745 
 TRP   0.037   0.003   TRP A 561 
 HIS   0.001   0.000   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 2086)
  covalent geometry    : angle       0.64251 ( 2841)
  hydrogen bonds       : bond        0.03234 (  160)
  hydrogen bonds       : angle       3.81677 (  477)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.063 
Fit side-chains
REVERT: A  561 TRP cc_start: 0.6962 (m100) cc_final: 0.6746 (m100)
REVERT: A  621 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6356 (t80)
REVERT: A  667 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7971 (ptt180)
REVERT: A  682 MET cc_start: 0.7642 (tmm) cc_final: 0.6407 (tmm)
REVERT: A  685 ILE cc_start: 0.9301 (tp) cc_final: 0.8981 (tp)
REVERT: A  690 MET cc_start: 0.8169 (ppp) cc_final: 0.7689 (ppp)
REVERT: A  803 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8563 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0589
  time to fit residues: 4.7049
Evaluate side-chains
  70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  821 ARG
Chi-restraints excluded: chain A residue  832 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0470
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.3478

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.135582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.118868 restraints weight = 4058.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.122216 restraints weight = 2197.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.124413 restraints weight = 1438.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.126201 restraints weight = 1075.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.126605 restraints weight = 851.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2086  Z= 0.118
  Angle     :  0.676  12.393   2841  Z= 0.311
  Chirality :  0.038   0.121    337
  Planarity :  0.005   0.056    341
  Dihedral  :  5.596  55.040    286
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 35.11 %
    Favored  : 58.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.55), residues: 253
  helix:  2.19 (0.38), residues: 208
  sheet:  None (None), residues: 0
  loop :  0.21 (0.93), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 633 
 TYR   0.013   0.001   TYR A 621 
 PHE   0.010   0.001   PHE A 745 
 TRP   0.031   0.003   TRP A 561 
 HIS   0.000   0.000   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 2086)
  covalent geometry    : angle       0.67557 ( 2841)
  hydrogen bonds       : bond        0.03042 (  160)
  hydrogen bonds       : angle       3.74182 (  477)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 718.98 seconds
wall clock time: 12 minutes 58.64 seconds (778.64 seconds total)