Starting phenix.real_space_refine
on Wed Sep 17 08:15:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nfk_49368/09_2025/9nfk_49368_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nfk_49368/09_2025/9nfk_49368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nfk_49368/09_2025/9nfk_49368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nfk_49368/09_2025/9nfk_49368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nfk_49368/09_2025/9nfk_49368_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nfk_49368/09_2025/9nfk_49368_neut.cif"
  }
  resolution = 3.99
  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=   0.001 sd=   0.042
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      46      5.16       5
     C    4498      2.51       5
     N    1163      2.21       5
     O    1268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 6975
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 898, 6975
          Classifications: {'peptide': 898}
          Link IDs: {'PTRANS': 23, 'TRANS': 874}
          Chain breaks: 3
  Time building chain proxies: 1.81, per 1000 atoms: 0.26
  Number of scatterers: 6975
  At special positions: 0
  Unit cell: (71.06, 99.11, 138.38, 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      46     16.00
     O    1268      8.00
     N    1163      7.00
     C    4498      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: 0.67
  Conformation dependent library (CDL) restraints added in 418.8 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1662

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 3 sheets defined
      81.0% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 52
      removed outlier: 3.765A  pdb=" N   PHE A  52 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 96
      Proline residue:  A  78  - end of helix
      removed outlier: 4.101A  pdb=" N   MET A  96 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 170
    Processing helix  chain 'A' and resid 171 through 178
      removed outlier: 3.654A  pdb=" N   PHE A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 200
      removed outlier: 4.011A  pdb=" N   VAL A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASP A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 222
    Processing helix  chain 'A' and resid 223 through 272
      removed outlier: 4.075A  pdb=" N   LEU A 228 " --> pdb=" O   TRP A 224 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.645A  pdb=" N   VAL A 247 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 280
    Processing helix  chain 'A' and resid 281 through 336
      removed outlier: 3.819A  pdb=" N   GLU A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 360
    Processing helix  chain 'A' and resid 360 through 383
    Processing helix  chain 'A' and resid 444 through 453
      removed outlier: 3.725A  pdb=" N   THR A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'A' and resid 495 through 502
    Processing helix  chain 'A' and resid 508 through 519
      removed outlier: 3.513A  pdb=" N   ALA A 519 " --> pdb=" O   ALA A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
      removed outlier: 3.946A  pdb=" N   ASP A 523 " --> pdb=" O   ASN A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 534
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 544 through 558
    Processing helix  chain 'A' and resid 574 through 589
    Processing helix  chain 'A' and resid 600 through 607
      removed outlier: 3.509A  pdb=" N   ILE A 604 " --> pdb=" O   ARG A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 631
      removed outlier: 3.669A  pdb=" N   LEU A 627 " --> pdb=" O   THR A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 640
      removed outlier: 3.620A  pdb=" N   THR A 636 " --> pdb=" O   GLY A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 721
    Processing helix  chain 'A' and resid 725 through 759
      removed outlier: 3.848A  pdb=" N   GLN A 743 " --> pdb=" O   ASN A 739 " (cutoff:3.500A)
      Proline residue:  A 744  - end of helix
      removed outlier: 3.610A  pdb=" N   GLU A 759 " --> pdb=" O   ALA A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 816
    Processing helix  chain 'A' and resid 817 through 826
      removed outlier: 3.782A  pdb=" N   ASN A 823 " --> pdb=" O   TRP A 820 " (cutoff:3.500A)
      Proline residue:  A 824  - end of helix
    Processing helix  chain 'A' and resid 827 through 871
      removed outlier: 3.650A  pdb=" N   MET A 850 " --> pdb=" O   THR A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 888
      removed outlier: 3.704A  pdb=" N   LEU A 876 " --> pdb=" O   TRP A 872 " (cutoff:3.500A)
      Proline residue:  A 883  - end of helix
    Processing helix  chain 'A' and resid 889 through 895
      removed outlier: 3.530A  pdb=" N   MET A 893 " --> pdb=" O   GLY A 889 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLN A 894 " --> pdb=" O   SER A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 920
    Processing helix  chain 'A' and resid 920 through 928
    Processing helix  chain 'A' and resid 929 through 984
      removed outlier: 4.156A  pdb=" N   VAL A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      Proline residue:  A 944  - end of helix
      removed outlier: 3.657A  pdb=" N   ILE A 966 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   TYR A 967 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 1006
      removed outlier: 3.762A  pdb=" N   GLY A1006 " --> pdb=" O   ALA A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1031
    Processing sheet with id=AA1, first strand: chain 'A' and resid 427 through 429
      removed outlier: 3.951A  pdb=" N   ILE A 409 " --> pdb=" O   GLU A 460 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLU A 460 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438
      removed outlier: 3.981A  pdb=" N   GLU A 620 " --> pdb=" O   GLY A 612 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 482 through 485

    569 hydrogen bonds defined for protein.
    1674 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: 1.22

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2232
        1.34 -     1.46: 1616
        1.46 -     1.58: 3174
        1.58 -     1.70: 0
        1.70 -     1.81: 86
  Bond restraints: 7108
  Sorted by residual:
  bond pdb=" CA  LYS A 396 "
       pdb=" CB  LYS A 396 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.18e+00
  bond pdb=" CA  GLY A  74 "
       pdb=" C   GLY A  74 "
    ideal  model  delta    sigma   weight residual
    1.514  1.501  0.013 1.41e-02 5.03e+03 8.76e-01
  bond pdb=" CB  MET A 885 "
       pdb=" CG  MET A 885 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.68e-01
  bond pdb=" CB  PHE A 347 "
       pdb=" CG  PHE A 347 "
    ideal  model  delta    sigma   weight residual
    1.502  1.481  0.021 2.30e-02 1.89e+03 8.18e-01
  bond pdb=" CB  VAL A 349 "
       pdb=" CG2 VAL A 349 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.14e-01
  ... (remaining 7103 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 9353
        1.47 -     2.94: 199
        2.94 -     4.40: 38
        4.40 -     5.87: 7
        5.87 -     7.34: 1
  Bond angle restraints: 9598
  Sorted by residual:
  angle pdb=" CA  MET A1029 "
        pdb=" CB  MET A1029 "
        pdb=" CG  MET A1029 "
      ideal   model   delta    sigma   weight residual
     114.10  119.10   -5.00 2.00e+00 2.50e-01 6.26e+00
  angle pdb=" CB  MET A 885 "
        pdb=" CG  MET A 885 "
        pdb=" SD  MET A 885 "
      ideal   model   delta    sigma   weight residual
     112.70  120.04   -7.34 3.00e+00 1.11e-01 5.98e+00
  angle pdb=" CA  ILE A 551 "
        pdb=" CB  ILE A 551 "
        pdb=" CG1 ILE A 551 "
      ideal   model   delta    sigma   weight residual
     110.40  114.00   -3.60 1.70e+00 3.46e-01 4.49e+00
  angle pdb=" CA  MET A 885 "
        pdb=" CB  MET A 885 "
        pdb=" CG  MET A 885 "
      ideal   model   delta    sigma   weight residual
     114.10  118.33   -4.23 2.00e+00 2.50e-01 4.48e+00
  angle pdb=" C   PHE A 216 "
        pdb=" N   ILE A 217 "
        pdb=" CA  ILE A 217 "
      ideal   model   delta    sigma   weight residual
     120.46  117.63    2.83 1.37e+00 5.33e-01 4.26e+00
  ... (remaining 9593 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 3642
       17.84 -    35.69: 465
       35.69 -    53.53: 97
       53.53 -    71.38: 24
       71.38 -    89.22: 9
  Dihedral angle restraints: 4237
    sinusoidal: 1653
      harmonic: 2584
  Sorted by residual:
  dihedral pdb=" CA  ASN A 761 "
           pdb=" C   ASN A 761 "
           pdb=" N   GLN A 762 "
           pdb=" CA  GLN A 762 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.19  -21.81     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  ALA A 232 "
           pdb=" C   ALA A 232 "
           pdb=" N   VAL A 233 "
           pdb=" CA  VAL A 233 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.53   16.47     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASN A 423 "
           pdb=" C   ASN A 423 "
           pdb=" N   ASN A 424 "
           pdb=" CA  ASN A 424 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.04   15.96     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 4234 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 869
       0.041 -    0.081: 185
       0.081 -    0.122: 42
       0.122 -    0.163: 4
       0.163 -    0.204: 1
  Chirality restraints: 1101
  Sorted by residual:
  chirality pdb=" CB  VAL A 581 "
            pdb=" CA  VAL A 581 "
            pdb=" CG1 VAL A 581 "
            pdb=" CG2 VAL A 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  THR A 958 "
            pdb=" CA  THR A 958 "
            pdb=" OG1 THR A 958 "
            pdb=" CG2 THR A 958 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  VAL A 463 "
            pdb=" N   VAL A 463 "
            pdb=" C   VAL A 463 "
            pdb=" CB  VAL A 463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 1098 not shown)

  Planarity restraints: 1212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 743 "   -0.026 5.00e-02 4.00e+02   3.92e-02 2.45e+00
        pdb=" N   PRO A 744 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 744 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 744 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 186 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.80e+00
        pdb=" C   ARG A 186 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ARG A 186 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 187 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 875 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.33e+00
        pdb=" C   THR A 875 "    0.020 2.00e-02 2.50e+03
        pdb=" O   THR A 875 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU A 876 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1209 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 101
        2.56 -     3.14: 6737
        3.14 -     3.73: 11901
        3.73 -     4.31: 14985
        4.31 -     4.90: 24450
  Nonbonded interactions: 58174
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 871 "
            pdb=" OG1 THR A 875 "
     model   vdw
     1.971 3.040
  nonbonded pdb=" O   PRO A 397 "
            pdb=" OH  TYR A 477 "
     model   vdw
     1.989 3.040
  nonbonded pdb=" NH1 ARG A 454 "
            pdb=" O   ILE A 470 "
     model   vdw
     2.009 3.120
  nonbonded pdb=" O   VAL A 842 "
            pdb=" OG1 THR A 846 "
     model   vdw
     2.025 3.040
  nonbonded pdb=" O   TYR A 945 "
            pdb=" OG  SER A 948 "
     model   vdw
     2.033 3.040
  ... (remaining 58169 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:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.460
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7108  Z= 0.187
  Angle     :  0.566   7.338   9598  Z= 0.316
  Chirality :  0.037   0.204   1101
  Planarity :  0.004   0.039   1212
  Dihedral  : 16.991  89.223   2575
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.49 %
    Favored  : 78.14 %
  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:  1.45 (0.28), residues: 890
  helix:  1.66 (0.19), residues: 664
  sheet: -0.57 (0.99), residues: 28
  loop : -1.14 (0.48), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 550 
 TYR   0.011   0.002   TYR A 413 
 PHE   0.015   0.002   PHE A 164 
 TRP   0.012   0.001   TRP A 872 
 HIS   0.006   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7108)
  covalent geometry    : angle       0.56581 ( 9598)
  hydrogen bonds       : bond        0.11061 (  569)
  hydrogen bonds       : angle       5.39017 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ILE cc_start: 0.8961 (mm) cc_final: 0.8734 (mm)
REVERT: A  293 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8657 (mm)
REVERT: A  317 MET cc_start: 0.8679 (mmm) cc_final: 0.8385 (mmm)
REVERT: A  398 ASP cc_start: 0.9238 (p0) cc_final: 0.8887 (p0)
REVERT: A  422 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5317 (tp)
REVERT: A  480 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7835 (mm-30)
REVERT: A  640 MET cc_start: 0.4325 (ppp) cc_final: 0.3669 (ppp)
REVERT: A  741 MET cc_start: 0.8531 (tmm) cc_final: 0.8156 (tmm)
REVERT: A  779 ILE cc_start: 0.8839 (mm) cc_final: 0.8203 (mm)
REVERT: A  783 THR cc_start: 0.7563 (m) cc_final: 0.6957 (p)
REVERT: A  813 MET cc_start: 0.6125 (mtt) cc_final: 0.5712 (mtt)
REVERT: A  814 MET cc_start: 0.6812 (mmm) cc_final: 0.6577 (mmp)
REVERT: A  843 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7948 (tm-30)
REVERT: A  857 ILE cc_start: 0.8474 (tp) cc_final: 0.8198 (pt)
REVERT: A  893 MET cc_start: 0.6514 (ppp) cc_final: 0.5674 (mmt)
REVERT: A 1027 MET cc_start: 0.8813 (ttp) cc_final: 0.8275 (ppp)
  outliers start: 25
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0748
  time to fit residues: 16.5476
Evaluate side-chains
  153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 GLN
A 453 GLN
A 499 ASN
A 614 HIS
A 949 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.131801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.114919 restraints weight = 23071.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.117485 restraints weight = 14362.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.119211 restraints weight = 9992.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.120512 restraints weight = 7578.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.121366 restraints weight = 6108.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7108  Z= 0.154
  Angle     :  0.608   7.231   9598  Z= 0.325
  Chirality :  0.042   0.238   1101
  Planarity :  0.004   0.038   1212
  Dihedral  :  7.757  88.158   1002
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 16.33 %
    Favored  : 79.35 %
  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:  1.54 (0.28), residues: 890
  helix:  1.73 (0.19), residues: 671
  sheet: -0.65 (0.95), residues: 28
  loop : -1.25 (0.49), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 454 
 TYR   0.025   0.002   TYR A 259 
 PHE   0.014   0.001   PHE A 613 
 TRP   0.009   0.001   TRP A 979 
 HIS   0.003   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7108)
  covalent geometry    : angle       0.60843 ( 9598)
  hydrogen bonds       : bond        0.04664 (  569)
  hydrogen bonds       : angle       4.64300 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.9199 (mt) cc_final: 0.8954 (mt)
REVERT: A  133 MET cc_start: 0.8010 (tpp) cc_final: 0.7634 (tpp)
REVERT: A  248 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7198 (tp)
REVERT: A  293 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8565 (mm)
REVERT: A  316 LEU cc_start: 0.9612 (tt) cc_final: 0.9276 (pp)
REVERT: A  348 PHE cc_start: 0.8692 (m-80) cc_final: 0.8333 (m-80)
REVERT: A  398 ASP cc_start: 0.9067 (p0) cc_final: 0.8743 (p0)
REVERT: A  425 MET cc_start: 0.5821 (mtp) cc_final: 0.5477 (mtp)
REVERT: A  480 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7845 (mm-30)
REVERT: A  526 MET cc_start: 0.2079 (OUTLIER) cc_final: 0.1532 (pmm)
REVERT: A  640 MET cc_start: 0.4759 (ppp) cc_final: 0.4334 (ppp)
REVERT: A  779 ILE cc_start: 0.8860 (mm) cc_final: 0.8354 (mm)
REVERT: A  783 THR cc_start: 0.7420 (m) cc_final: 0.6847 (p)
REVERT: A  813 MET cc_start: 0.5861 (mtt) cc_final: 0.5574 (mtt)
REVERT: A  843 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7943 (tm-30)
REVERT: A  893 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5724 (mmt)
REVERT: A  903 ASP cc_start: 0.5520 (OUTLIER) cc_final: 0.3565 (p0)
REVERT: A 1020 MET cc_start: 0.7993 (ppp) cc_final: 0.7789 (ppp)
REVERT: A 1027 MET cc_start: 0.8739 (ttp) cc_final: 0.8225 (ppp)
  outliers start: 32
  outliers final: 14
  residues processed: 166
  average time/residue: 0.0676
  time to fit residues: 15.9882
Evaluate side-chains
  150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  893 MET
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   chunk 29 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0980
   chunk 34 optimal weight:    8.9990
   chunk 75 optimal weight:    0.6980
   chunk 76 optimal weight:    0.1980
   chunk 87 optimal weight:    0.0770
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0010
   overall best weight:    0.1944

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 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 = 0.4171 r_free = 0.4171 target = 0.134102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.117361 restraints weight = 22736.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.119953 restraints weight = 14065.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.121821 restraints weight = 9721.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.123121 restraints weight = 7290.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.124056 restraints weight = 5840.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
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      :  0.003   0.040   7108  Z= 0.135
  Angle     :  0.595   8.288   9598  Z= 0.316
  Chirality :  0.041   0.232   1101
  Planarity :  0.003   0.034   1212
  Dihedral  :  7.028  82.564    986
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 16.60 %
    Favored  : 79.22 %
  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:  1.53 (0.28), residues: 890
  helix:  1.72 (0.19), residues: 670
  sheet: -0.46 (1.02), residues: 27
  loop : -1.26 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.033   0.002   TYR A 259 
 PHE   0.019   0.001   PHE A 613 
 TRP   0.007   0.001   TRP A 979 
 HIS   0.003   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7108)
  covalent geometry    : angle       0.59517 ( 9598)
  hydrogen bonds       : bond        0.04294 (  569)
  hydrogen bonds       : angle       4.48484 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.9114 (mt) cc_final: 0.8827 (mt)
REVERT: A  133 MET cc_start: 0.7951 (tpp) cc_final: 0.7585 (tpp)
REVERT: A  293 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8557 (mm)
REVERT: A  480 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7777 (mm-30)
REVERT: A  526 MET cc_start: 0.1991 (OUTLIER) cc_final: 0.1427 (pmm)
REVERT: A  640 MET cc_start: 0.5117 (ppp) cc_final: 0.4655 (ppp)
REVERT: A  779 ILE cc_start: 0.8764 (mm) cc_final: 0.8375 (mm)
REVERT: A  783 THR cc_start: 0.7184 (m) cc_final: 0.6510 (p)
REVERT: A  813 MET cc_start: 0.5693 (mtt) cc_final: 0.5310 (mtt)
REVERT: A  843 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7761 (tm-30)
REVERT: A  893 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5786 (mmt)
REVERT: A  903 ASP cc_start: 0.5348 (OUTLIER) cc_final: 0.4769 (p0)
REVERT: A  905 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8807 (mmtm)
REVERT: A  929 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7133 (mpt180)
REVERT: A  954 VAL cc_start: 0.9422 (t) cc_final: 0.9103 (p)
REVERT: A  976 PHE cc_start: 0.6277 (t80) cc_final: 0.6011 (t80)
REVERT: A 1026 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6503 (mpp)
REVERT: A 1027 MET cc_start: 0.8771 (ttp) cc_final: 0.8246 (ppp)
  outliers start: 31
  outliers final: 13
  residues processed: 161
  average time/residue: 0.0678
  time to fit residues: 15.5816
Evaluate side-chains
  144 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  893 MET
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1026 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   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 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.133437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.116150 restraints weight = 23324.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.118799 restraints weight = 14585.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.120622 restraints weight = 10133.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.121953 restraints weight = 7660.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.122907 restraints weight = 6153.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7108  Z= 0.146
  Angle     :  0.617   9.028   9598  Z= 0.324
  Chirality :  0.042   0.261   1101
  Planarity :  0.003   0.030   1212
  Dihedral  :  6.604  77.619    983
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 18.35 %
    Favored  : 76.92 %
  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:  1.44 (0.28), residues: 890
  helix:  1.64 (0.19), residues: 671
  sheet: -0.60 (1.01), residues: 27
  loop : -1.22 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 550 
 TYR   0.020   0.001   TYR A 477 
 PHE   0.013   0.001   PHE A 788 
 TRP   0.010   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7108)
  covalent geometry    : angle       0.61680 ( 9598)
  hydrogen bonds       : bond        0.04288 (  569)
  hydrogen bonds       : angle       4.51134 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.9144 (mt) cc_final: 0.8847 (mt)
REVERT: A  133 MET cc_start: 0.8049 (tpp) cc_final: 0.7654 (tpp)
REVERT: A  168 MET cc_start: 0.8036 (mmp) cc_final: 0.7175 (mmp)
REVERT: A  425 MET cc_start: 0.5309 (mtp) cc_final: 0.4981 (mtt)
REVERT: A  480 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7810 (mm-30)
REVERT: A  526 MET cc_start: 0.2986 (mpp) cc_final: 0.1449 (tpp)
REVERT: A  640 MET cc_start: 0.5091 (ppp) cc_final: 0.4665 (ppp)
REVERT: A  708 GLU cc_start: 0.5089 (OUTLIER) cc_final: 0.4367 (mp0)
REVERT: A  779 ILE cc_start: 0.8589 (mm) cc_final: 0.8161 (mm)
REVERT: A  783 THR cc_start: 0.7228 (m) cc_final: 0.6627 (p)
REVERT: A  786 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8734 (t)
REVERT: A  794 PHE cc_start: 0.7991 (m-80) cc_final: 0.7467 (m-80)
REVERT: A  843 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8009 (tm-30)
REVERT: A  893 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.5681 (mmt)
REVERT: A  903 ASP cc_start: 0.5485 (OUTLIER) cc_final: 0.4472 (p0)
REVERT: A  905 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8800 (mmtm)
REVERT: A  954 VAL cc_start: 0.9372 (t) cc_final: 0.9014 (p)
REVERT: A  961 PHE cc_start: 0.7364 (t80) cc_final: 0.6851 (t80)
REVERT: A  976 PHE cc_start: 0.6347 (t80) cc_final: 0.6070 (t80)
REVERT: A  999 LEU cc_start: 0.8238 (mt) cc_final: 0.7944 (mt)
REVERT: A 1003 MET cc_start: 0.7821 (mpp) cc_final: 0.7274 (mpp)
REVERT: A 1026 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6571 (mpp)
REVERT: A 1027 MET cc_start: 0.8836 (ttp) cc_final: 0.8374 (ppp)
  outliers start: 35
  outliers final: 19
  residues processed: 150
  average time/residue: 0.0657
  time to fit residues: 13.9613
Evaluate side-chains
  145 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  786 THR
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  893 MET
Chi-restraints excluded: chain A residue  894 GLN
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1026 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 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 = 0.4151 r_free = 0.4151 target = 0.132550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.115479 restraints weight = 23325.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.118073 restraints weight = 14434.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.119937 restraints weight = 10039.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.121269 restraints weight = 7576.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.122079 restraints weight = 6066.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7108  Z= 0.151
  Angle     :  0.600   9.120   9598  Z= 0.316
  Chirality :  0.042   0.254   1101
  Planarity :  0.003   0.026   1212
  Dihedral  :  6.267  76.552    981
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 19.70 %
    Favored  : 75.84 %
  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:  1.47 (0.28), residues: 890
  helix:  1.69 (0.19), residues: 670
  sheet: -0.92 (0.98), residues: 27
  loop : -1.24 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 550 
 TYR   0.021   0.001   TYR A 477 
 PHE   0.022   0.002   PHE A 347 
 TRP   0.006   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7108)
  covalent geometry    : angle       0.60035 ( 9598)
  hydrogen bonds       : bond        0.04248 (  569)
  hydrogen bonds       : angle       4.45917 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.8093 (tpp) cc_final: 0.7683 (tpp)
REVERT: A  168 MET cc_start: 0.8040 (mmp) cc_final: 0.7575 (mmp)
REVERT: A  348 PHE cc_start: 0.8474 (m-80) cc_final: 0.8141 (m-80)
REVERT: A  422 LEU cc_start: 0.6758 (mt) cc_final: 0.6530 (mt)
REVERT: A  480 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7846 (mm-30)
REVERT: A  526 MET cc_start: 0.3011 (OUTLIER) cc_final: 0.2658 (mpp)
REVERT: A  640 MET cc_start: 0.5091 (ppp) cc_final: 0.4685 (ppp)
REVERT: A  708 GLU cc_start: 0.4410 (OUTLIER) cc_final: 0.3439 (mp0)
REVERT: A  779 ILE cc_start: 0.8653 (mm) cc_final: 0.8168 (mm)
REVERT: A  783 THR cc_start: 0.7285 (m) cc_final: 0.6836 (p)
REVERT: A  787 MET cc_start: 0.8712 (mmm) cc_final: 0.8344 (mmm)
REVERT: A  814 MET cc_start: 0.4978 (mmp) cc_final: 0.4697 (mmm)
REVERT: A  843 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8110 (tm-30)
REVERT: A  893 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.5678 (mmt)
REVERT: A  954 VAL cc_start: 0.9400 (t) cc_final: 0.9031 (p)
REVERT: A  961 PHE cc_start: 0.7393 (t80) cc_final: 0.6863 (t80)
REVERT: A  976 PHE cc_start: 0.6517 (t80) cc_final: 0.6263 (t80)
REVERT: A  999 LEU cc_start: 0.8623 (mt) cc_final: 0.8011 (mt)
REVERT: A 1003 MET cc_start: 0.7917 (mpp) cc_final: 0.7592 (mpp)
REVERT: A 1026 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6621 (mpp)
REVERT: A 1027 MET cc_start: 0.8855 (ttp) cc_final: 0.8428 (ppp)
  outliers start: 33
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0695
  time to fit residues: 14.5256
Evaluate side-chains
  145 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  893 MET
Chi-restraints excluded: chain A residue  894 GLN
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1026 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 71 optimal weight:    0.2980
   chunk 87 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   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 207 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 = 0.4164 r_free = 0.4164 target = 0.133458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.116428 restraints weight = 23200.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.119036 restraints weight = 14524.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.120853 restraints weight = 10124.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.122017 restraints weight = 7629.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.123062 restraints weight = 6193.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7108  Z= 0.133
  Angle     :  0.590   9.414   9598  Z= 0.307
  Chirality :  0.041   0.252   1101
  Planarity :  0.003   0.025   1212
  Dihedral  :  6.163  76.966    981
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 21.19 %
    Favored  : 74.36 %
  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:  1.60 (0.28), residues: 890
  helix:  1.79 (0.19), residues: 671
  sheet: -1.08 (0.97), residues: 27
  loop : -1.19 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 975 
 TYR   0.018   0.001   TYR A 477 
 PHE   0.019   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 872 
 HIS   0.002   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7108)
  covalent geometry    : angle       0.58997 ( 9598)
  hydrogen bonds       : bond        0.04100 (  569)
  hydrogen bonds       : angle       4.35266 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.8157 (tpp) cc_final: 0.7685 (tpp)
REVERT: A  168 MET cc_start: 0.8044 (mmp) cc_final: 0.7606 (mmp)
REVERT: A  348 PHE cc_start: 0.8218 (m-80) cc_final: 0.7940 (m-80)
REVERT: A  422 LEU cc_start: 0.6826 (mt) cc_final: 0.6581 (mt)
REVERT: A  480 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7808 (mm-30)
REVERT: A  526 MET cc_start: 0.2964 (OUTLIER) cc_final: 0.1424 (tpp)
REVERT: A  640 MET cc_start: 0.5180 (ppp) cc_final: 0.4835 (ppp)
REVERT: A  708 GLU cc_start: 0.4373 (OUTLIER) cc_final: 0.3420 (mp0)
REVERT: A  779 ILE cc_start: 0.8631 (mm) cc_final: 0.8189 (mm)
REVERT: A  783 THR cc_start: 0.7325 (m) cc_final: 0.6738 (p)
REVERT: A  786 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8449 (t)
REVERT: A  787 MET cc_start: 0.8653 (mmm) cc_final: 0.8360 (mmm)
REVERT: A  794 PHE cc_start: 0.8094 (m-80) cc_final: 0.7591 (m-80)
REVERT: A  814 MET cc_start: 0.5434 (mmp) cc_final: 0.5156 (mmm)
REVERT: A  843 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8212 (tm-30)
REVERT: A  893 MET cc_start: 0.6362 (ppp) cc_final: 0.5575 (mmt)
REVERT: A  903 ASP cc_start: 0.5533 (OUTLIER) cc_final: 0.4397 (p0)
REVERT: A  954 VAL cc_start: 0.9338 (t) cc_final: 0.8986 (p)
REVERT: A  961 PHE cc_start: 0.7333 (t80) cc_final: 0.6965 (t80)
REVERT: A  965 MET cc_start: 0.7736 (mmp) cc_final: 0.7126 (mmp)
REVERT: A  999 LEU cc_start: 0.8665 (mt) cc_final: 0.8058 (mt)
REVERT: A 1026 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6600 (mpp)
REVERT: A 1027 MET cc_start: 0.8770 (ttp) cc_final: 0.8479 (ptp)
  outliers start: 33
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0673
  time to fit residues: 14.5765
Evaluate side-chains
  139 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  786 THR
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  894 GLN
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1026 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0030
   chunk 63 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0470
   chunk 75 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.4688

-------------------------------------------------------------------------------
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 = 0.4174 r_free = 0.4174 target = 0.134268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.117180 restraints weight = 23059.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.119801 restraints weight = 14409.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.121604 restraints weight = 10056.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.122914 restraints weight = 7626.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.123838 restraints weight = 6145.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7108  Z= 0.131
  Angle     :  0.617  10.896   9598  Z= 0.315
  Chirality :  0.042   0.261   1101
  Planarity :  0.003   0.024   1212
  Dihedral  :  6.076  76.933    980
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 22.67 %
    Favored  : 73.41 %
  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:  1.63 (0.28), residues: 890
  helix:  1.80 (0.19), residues: 671
  sheet: -0.93 (0.94), residues: 27
  loop : -1.18 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 975 
 TYR   0.017   0.001   TYR A 477 
 PHE   0.020   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 872 
 HIS   0.002   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7108)
  covalent geometry    : angle       0.61723 ( 9598)
  hydrogen bonds       : bond        0.04099 (  569)
  hydrogen bonds       : angle       4.38351 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 MET cc_start: 0.8314 (mmp) cc_final: 0.7978 (mmp)
REVERT: A  348 PHE cc_start: 0.8270 (m-80) cc_final: 0.7914 (m-80)
REVERT: A  422 LEU cc_start: 0.6719 (mt) cc_final: 0.6430 (mt)
REVERT: A  480 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7833 (mm-30)
REVERT: A  522 TYR cc_start: 0.6772 (t80) cc_final: 0.6359 (t80)
REVERT: A  526 MET cc_start: 0.2962 (OUTLIER) cc_final: 0.1412 (tpp)
REVERT: A  640 MET cc_start: 0.5111 (ppp) cc_final: 0.4752 (ppp)
REVERT: A  708 GLU cc_start: 0.4582 (OUTLIER) cc_final: 0.3918 (mp0)
REVERT: A  779 ILE cc_start: 0.8678 (mm) cc_final: 0.8405 (mm)
REVERT: A  783 THR cc_start: 0.7308 (m) cc_final: 0.6749 (p)
REVERT: A  786 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8693 (t)
REVERT: A  787 MET cc_start: 0.8688 (mmm) cc_final: 0.8473 (mmm)
REVERT: A  814 MET cc_start: 0.5194 (mmp) cc_final: 0.4924 (mmm)
REVERT: A  843 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8244 (tm-30)
REVERT: A  857 ILE cc_start: 0.8470 (tp) cc_final: 0.8046 (pt)
REVERT: A  903 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.4391 (p0)
REVERT: A  954 VAL cc_start: 0.9324 (t) cc_final: 0.8964 (p)
REVERT: A  961 PHE cc_start: 0.7599 (t80) cc_final: 0.6912 (t80)
REVERT: A  965 MET cc_start: 0.7669 (mmp) cc_final: 0.7157 (mmp)
REVERT: A 1003 MET cc_start: 0.7741 (mpp) cc_final: 0.7534 (mpp)
REVERT: A 1026 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6570 (mpp)
REVERT: A 1027 MET cc_start: 0.8809 (ttp) cc_final: 0.8410 (ppp)
  outliers start: 29
  outliers final: 18
  residues processed: 147
  average time/residue: 0.0679
  time to fit residues: 14.2012
Evaluate side-chains
  140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  786 THR
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  894 GLN
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1026 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.133723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.116333 restraints weight = 23682.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.118956 restraints weight = 14929.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.120780 restraints weight = 10483.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.122034 restraints weight = 8003.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.123008 restraints weight = 6516.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7108  Z= 0.144
  Angle     :  0.664  10.886   9598  Z= 0.334
  Chirality :  0.043   0.259   1101
  Planarity :  0.003   0.026   1212
  Dihedral  :  6.085  76.367    980
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.56 %
    Favored  : 71.93 %
  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:  1.61 (0.28), residues: 890
  helix:  1.79 (0.19), residues: 671
  sheet: -0.19 (1.03), residues: 22
  loop : -1.31 (0.45), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 550 
 TYR   0.018   0.001   TYR A 477 
 PHE   0.028   0.002   PHE A  84 
 TRP   0.007   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7108)
  covalent geometry    : angle       0.66393 ( 9598)
  hydrogen bonds       : bond        0.04122 (  569)
  hydrogen bonds       : angle       4.39696 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.8184 (tpp) cc_final: 0.7815 (tpp)
REVERT: A  348 PHE cc_start: 0.8191 (m-80) cc_final: 0.7962 (m-80)
REVERT: A  422 LEU cc_start: 0.6782 (mt) cc_final: 0.6456 (mt)
REVERT: A  480 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7833 (mm-30)
REVERT: A  522 TYR cc_start: 0.6701 (t80) cc_final: 0.6294 (t80)
REVERT: A  526 MET cc_start: 0.2920 (OUTLIER) cc_final: 0.1353 (tpp)
REVERT: A  548 LYS cc_start: 0.6558 (ptpt) cc_final: 0.6314 (ptpp)
REVERT: A  640 MET cc_start: 0.5098 (ppp) cc_final: 0.4753 (ppp)
REVERT: A  708 GLU cc_start: 0.4607 (OUTLIER) cc_final: 0.3907 (mp0)
REVERT: A  779 ILE cc_start: 0.8451 (mm) cc_final: 0.7948 (mm)
REVERT: A  783 THR cc_start: 0.7481 (m) cc_final: 0.6881 (p)
REVERT: A  786 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8401 (t)
REVERT: A  787 MET cc_start: 0.8654 (mmm) cc_final: 0.8302 (mmm)
REVERT: A  814 MET cc_start: 0.5432 (mmp) cc_final: 0.5114 (mmm)
REVERT: A  843 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7929 (tm-30)
REVERT: A  857 ILE cc_start: 0.8850 (tp) cc_final: 0.8523 (pt)
REVERT: A  903 ASP cc_start: 0.5625 (OUTLIER) cc_final: 0.4436 (p0)
REVERT: A  954 VAL cc_start: 0.9299 (t) cc_final: 0.8920 (p)
REVERT: A  961 PHE cc_start: 0.7547 (t80) cc_final: 0.7050 (t80)
REVERT: A 1003 MET cc_start: 0.7918 (mpp) cc_final: 0.7605 (mpp)
REVERT: A 1026 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6502 (mpp)
REVERT: A 1027 MET cc_start: 0.8757 (ttp) cc_final: 0.8540 (ptp)
  outliers start: 26
  outliers final: 17
  residues processed: 142
  average time/residue: 0.0664
  time to fit residues: 13.3271
Evaluate side-chains
  145 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  786 THR
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  894 GLN
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1026 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 35 optimal weight:    0.0170
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0870
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.134764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.117566 restraints weight = 23182.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.120136 restraints weight = 14577.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.121970 restraints weight = 10255.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.123264 restraints weight = 7810.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.124183 restraints weight = 6332.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7108  Z= 0.134
  Angle     :  0.673  11.503   9598  Z= 0.334
  Chirality :  0.043   0.259   1101
  Planarity :  0.003   0.026   1212
  Dihedral  :  5.969  75.949    978
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.43 %
    Favored  : 72.06 %
  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:  1.61 (0.28), residues: 890
  helix:  1.79 (0.19), residues: 671
  sheet:  0.01 (1.03), residues: 22
  loop : -1.33 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 274 
 TYR   0.017   0.001   TYR A 477 
 PHE   0.023   0.001   PHE A  84 
 TRP   0.006   0.001   TRP A 872 
 HIS   0.002   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7108)
  covalent geometry    : angle       0.67327 ( 9598)
  hydrogen bonds       : bond        0.04068 (  569)
  hydrogen bonds       : angle       4.36213 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.8162 (tpp) cc_final: 0.7718 (tpp)
REVERT: A  136 VAL cc_start: 0.9378 (m) cc_final: 0.9141 (p)
REVERT: A  168 MET cc_start: 0.8312 (mmp) cc_final: 0.8011 (mmp)
REVERT: A  348 PHE cc_start: 0.8234 (m-80) cc_final: 0.7973 (m-80)
REVERT: A  422 LEU cc_start: 0.6734 (mt) cc_final: 0.6432 (mt)
REVERT: A  480 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7785 (mm-30)
REVERT: A  481 MET cc_start: 0.7821 (mtp) cc_final: 0.7228 (tpp)
REVERT: A  522 TYR cc_start: 0.6596 (t80) cc_final: 0.6242 (t80)
REVERT: A  526 MET cc_start: 0.3057 (OUTLIER) cc_final: 0.1651 (tpp)
REVERT: A  640 MET cc_start: 0.5065 (ppp) cc_final: 0.4735 (ppp)
REVERT: A  708 GLU cc_start: 0.4549 (OUTLIER) cc_final: 0.3905 (mp0)
REVERT: A  745 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7380 (tm)
REVERT: A  779 ILE cc_start: 0.8567 (mm) cc_final: 0.8313 (mm)
REVERT: A  783 THR cc_start: 0.7462 (m) cc_final: 0.6868 (p)
REVERT: A  786 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8357 (t)
REVERT: A  787 MET cc_start: 0.8668 (mmm) cc_final: 0.8300 (mmm)
REVERT: A  814 MET cc_start: 0.5310 (mmp) cc_final: 0.5027 (mmm)
REVERT: A  843 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7951 (tm-30)
REVERT: A  857 ILE cc_start: 0.8912 (tp) cc_final: 0.8443 (pt)
REVERT: A  903 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.4432 (p0)
REVERT: A  954 VAL cc_start: 0.9268 (t) cc_final: 0.8883 (p)
REVERT: A  961 PHE cc_start: 0.7425 (t80) cc_final: 0.6919 (t80)
REVERT: A 1003 MET cc_start: 0.7899 (mpp) cc_final: 0.7517 (mpp)
REVERT: A 1026 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6518 (mpp)
REVERT: A 1027 MET cc_start: 0.8727 (ttp) cc_final: 0.8164 (ppp)
  outliers start: 26
  outliers final: 18
  residues processed: 147
  average time/residue: 0.0671
  time to fit residues: 14.0435
Evaluate side-chains
  147 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  786 THR
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  894 GLN
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1026 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 ASN
** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.131679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.114301 restraints weight = 23405.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.116810 restraints weight = 14847.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.118579 restraints weight = 10526.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.119820 restraints weight = 8110.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.120724 restraints weight = 6622.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7108  Z= 0.198
  Angle     :  0.738  11.798   9598  Z= 0.374
  Chirality :  0.045   0.270   1101
  Planarity :  0.004   0.028   1212
  Dihedral  :  6.136  75.210    978
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.16 %
    Favored  : 72.47 %
  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:  1.43 (0.28), residues: 890
  helix:  1.63 (0.19), residues: 672
  sheet: -0.64 (0.90), residues: 28
  loop : -1.22 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 849 
 TYR   0.021   0.002   TYR A 477 
 PHE   0.030   0.002   PHE A 821 
 TRP   0.011   0.001   TRP A 872 
 HIS   0.004   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7108)
  covalent geometry    : angle       0.73841 ( 9598)
  hydrogen bonds       : bond        0.04462 (  569)
  hydrogen bonds       : angle       4.51019 ( 1674)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.8216 (tpp) cc_final: 0.7559 (tpp)
REVERT: A  136 VAL cc_start: 0.9453 (m) cc_final: 0.9189 (p)
REVERT: A  413 TYR cc_start: 0.5882 (m-80) cc_final: 0.5659 (m-80)
REVERT: A  480 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7881 (mm-30)
REVERT: A  522 TYR cc_start: 0.6707 (t80) cc_final: 0.6335 (t80)
REVERT: A  526 MET cc_start: 0.3072 (OUTLIER) cc_final: 0.1660 (tpp)
REVERT: A  548 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6471 (ptpp)
REVERT: A  640 MET cc_start: 0.4982 (ppp) cc_final: 0.4617 (ppp)
REVERT: A  708 GLU cc_start: 0.4034 (OUTLIER) cc_final: 0.3666 (pm20)
REVERT: A  779 ILE cc_start: 0.8593 (mm) cc_final: 0.8050 (mm)
REVERT: A  783 THR cc_start: 0.7673 (m) cc_final: 0.7031 (p)
REVERT: A  786 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8484 (t)
REVERT: A  787 MET cc_start: 0.8729 (mmm) cc_final: 0.8312 (mmm)
REVERT: A  843 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7977 (tm-30)
REVERT: A  857 ILE cc_start: 0.8880 (tp) cc_final: 0.8515 (pt)
REVERT: A  903 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.4608 (p0)
REVERT: A  954 VAL cc_start: 0.9375 (t) cc_final: 0.8985 (p)
REVERT: A  961 PHE cc_start: 0.7490 (t80) cc_final: 0.7045 (t80)
REVERT: A 1003 MET cc_start: 0.8000 (mpp) cc_final: 0.7605 (mpp)
REVERT: A 1027 MET cc_start: 0.8925 (ttp) cc_final: 0.8579 (ptp)
  outliers start: 25
  outliers final: 17
  residues processed: 143
  average time/residue: 0.0663
  time to fit residues: 13.4876
Evaluate side-chains
  147 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  548 LYS
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  751 SER
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  786 THR
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  903 ASP
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  933 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 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 = 0.4134 r_free = 0.4134 target = 0.131389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.114397 restraints weight = 22827.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.116934 restraints weight = 14321.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.118741 restraints weight = 10033.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.120045 restraints weight = 7612.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.120969 restraints weight = 6127.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7108  Z= 0.173
  Angle     :  0.730  11.952   9598  Z= 0.367
  Chirality :  0.044   0.267   1101
  Planarity :  0.003   0.022   1212
  Dihedral  :  6.177  75.785    978
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 24.83 %
    Favored  : 71.93 %
  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:  1.32 (0.28), residues: 890
  helix:  1.56 (0.19), residues: 672
  sheet: -0.13 (1.03), residues: 22
  loop : -1.38 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 274 
 TYR   0.019   0.002   TYR A 477 
 PHE   0.032   0.002   PHE A  84 
 TRP   0.013   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7108)
  covalent geometry    : angle       0.72963 ( 9598)
  hydrogen bonds       : bond        0.04441 (  569)
  hydrogen bonds       : angle       4.53306 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1187.64 seconds
wall clock time: 21 minutes 19.96 seconds (1279.96 seconds total)