Starting phenix.real_space_refine
on Fri Jul 25 04:01:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nfk_49368/07_2025/9nfk_49368_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nfk_49368/07_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_49368/07_2025/9nfk_49368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nfk_49368/07_2025/9nfk_49368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nfk_49368/07_2025/9nfk_49368_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nfk_49368/07_2025/9nfk_49368_neut.cif"
  }
  resolution = 3.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.42, per 1000 atoms: 0.63
  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: 1.86
  Conformation dependent library (CDL) restraints added in 997.8 milliseconds
  

  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: 0.69
  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: 2.18

  Time building geometry restraints manager: 2.20 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:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.240
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.010
-------------------------------------------------------------------------------
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 : 17.57
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.012   0.001   TRP A 872 
 HIS   0.006   0.001   HIS A 624 
 PHE   0.015   0.002   PHE A 164 
 TYR   0.011   0.002   TYR A 413 
 ARG   0.004   0.001   ARG A 550 

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

*********************** 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  : 0.738 
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: A  206 ILE cc_start: 0.8961 (mm) cc_final: 0.8733 (mm)
REVERT: A  293 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8658 (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: 0.8876 (p0)
REVERT: A  422 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5311 (tp)
REVERT: A  640 MET cc_start: 0.4325 (ppp) cc_final: 0.3672 (ppp)
REVERT: A  741 MET cc_start: 0.8531 (tmm) cc_final: 0.8157 (tmm)
REVERT: A  779 ILE cc_start: 0.8839 (mm) cc_final: 0.8202 (mm)
REVERT: A  783 THR cc_start: 0.7563 (m) cc_final: 0.6958 (p)
REVERT: A  813 MET cc_start: 0.6125 (mtt) cc_final: 0.5691 (mtt)
REVERT: A  814 MET cc_start: 0.6812 (mmm) cc_final: 0.6576 (mmp)
REVERT: A  843 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7950 (tm-30)
REVERT: A  857 ILE cc_start: 0.8474 (tp) cc_final: 0.8199 (pt)
REVERT: A  893 MET cc_start: 0.6514 (ppp) cc_final: 0.5669 (mmt)
REVERT: A 1027 MET cc_start: 0.8813 (ttp) cc_final: 0.8612 (ptp)
  outliers start: 25
  outliers final: 17
  residues processed: 158
  average time/residue: 0.1631
  time to fit residues: 35.6734
Evaluate side-chains
  154 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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 75 optimal weight:    0.0040
   chunk 67 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0470
   overall best weight:    0.9892

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 453 GLN
A 474 ASN
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 = 0.4126 r_free = 0.4126 target = 0.130986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.114350 restraints weight = 22889.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.116864 restraints weight = 14211.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.118623 restraints weight = 9901.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7108  Z= 0.165
  Angle     :  0.611   7.422   9598  Z= 0.327
  Chirality :  0.042   0.239   1101
  Planarity :  0.004   0.038   1212
  Dihedral  :  7.808  87.975   1002
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.28), residues: 890
  helix:  1.68 (0.19), residues: 670
  sheet: -0.65 (0.96), residues: 28
  loop : -1.26 (0.49), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 979 
 HIS   0.003   0.001   HIS A 953 
 PHE   0.014   0.002   PHE A 613 
 TYR   0.024   0.002   TYR A 259 
 ARG   0.005   0.000   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04746 (  569)
  hydrogen bonds       : angle       4.69289 ( 1674)
  covalent geometry    : bond        0.00346 ( 7108)
  covalent geometry    : angle       0.61092 ( 9598)

*********************** 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
  177 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.9197 (mt) cc_final: 0.8949 (mt)
REVERT: A  133 MET cc_start: 0.8033 (tpp) cc_final: 0.7652 (tpp)
REVERT: A  293 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (mm)
REVERT: A  316 LEU cc_start: 0.9617 (tt) cc_final: 0.9281 (pp)
REVERT: A  348 PHE cc_start: 0.8680 (m-80) cc_final: 0.8344 (m-80)
REVERT: A  398 ASP cc_start: 0.9095 (p0) cc_final: 0.8768 (p0)
REVERT: A  480 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: A  640 MET cc_start: 0.4319 (ppp) cc_final: 0.4050 (ppp)
REVERT: A  779 ILE cc_start: 0.8740 (mm) cc_final: 0.8202 (mm)
REVERT: A  783 THR cc_start: 0.7480 (m) cc_final: 0.6899 (p)
REVERT: A  813 MET cc_start: 0.6074 (mtt) cc_final: 0.5681 (mtt)
REVERT: A  814 MET cc_start: 0.6666 (mmm) cc_final: 0.6272 (mmp)
REVERT: A  843 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8012 (tm-30)
REVERT: A  893 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5800 (mmt)
REVERT: A  903 ASP cc_start: 0.5690 (OUTLIER) cc_final: 0.4568 (p0)
REVERT: A  975 ARG cc_start: 0.7982 (ptt180) cc_final: 0.7728 (ptt90)
REVERT: A 1020 MET cc_start: 0.8050 (ppp) cc_final: 0.7831 (ppp)
  outliers start: 32
  outliers final: 16
  residues processed: 166
  average time/residue: 0.1586
  time to fit residues: 36.9261
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  : 0.702 
-------------------------------------------------------------------------------
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  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  558 VAL
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 63 optimal weight:    0.1980
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0570
   chunk 13 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.0102

-------------------------------------------------------------------------------
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 ** 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 = 0.4139 r_free = 0.4139 target = 0.131658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.114568 restraints weight = 22969.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.117098 restraints weight = 14263.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.118932 restraints weight = 9924.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7108  Z= 0.157
  Angle     :  0.606   8.597   9598  Z= 0.322
  Chirality :  0.042   0.243   1101
  Planarity :  0.004   0.035   1212
  Dihedral  :  7.192  82.110    986
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.95 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.28), residues: 890
  helix:  1.57 (0.19), residues: 670
  sheet: -0.62 (0.95), residues: 28
  loop : -1.22 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 979 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.018   0.002   PHE A 613 
 TYR   0.032   0.002   TYR A 259 
 ARG   0.004   0.000   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04500 (  569)
  hydrogen bonds       : angle       4.62150 ( 1674)
  covalent geometry    : bond        0.00334 ( 7108)
  covalent geometry    : angle       0.60559 ( 9598)

*********************** 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
  171 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.9206 (mt) cc_final: 0.8953 (mt)
REVERT: A  133 MET cc_start: 0.7986 (tpp) cc_final: 0.7623 (tpp)
REVERT: A  293 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8578 (mm)
REVERT: A  398 ASP cc_start: 0.8949 (p0) cc_final: 0.8656 (p0)
REVERT: A  480 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7875 (mm-30)
REVERT: A  526 MET cc_start: 0.1596 (pmm) cc_final: 0.1298 (pmm)
REVERT: A  628 MET cc_start: 0.3604 (mmm) cc_final: 0.3202 (mmm)
REVERT: A  640 MET cc_start: 0.4957 (ppp) cc_final: 0.4591 (ppp)
REVERT: A  779 ILE cc_start: 0.8702 (mm) cc_final: 0.8272 (mm)
REVERT: A  783 THR cc_start: 0.7363 (m) cc_final: 0.6670 (p)
REVERT: A  814 MET cc_start: 0.6673 (mmm) cc_final: 0.6458 (mmm)
REVERT: A  893 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5800 (mmt)
REVERT: A  929 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6424 (mpt180)
REVERT: A  954 VAL cc_start: 0.9178 (t) cc_final: 0.8814 (p)
REVERT: A  999 LEU cc_start: 0.8425 (mt) cc_final: 0.7574 (mt)
REVERT: A 1026 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6568 (mpp)
REVERT: A 1027 MET cc_start: 0.8151 (ptp) cc_final: 0.7305 (ppp)
  outliers start: 30
  outliers final: 17
  residues processed: 159
  average time/residue: 0.1625
  time to fit residues: 35.7372
Evaluate side-chains
  149 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
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  211 THR
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  421 ILE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  741 MET
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  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 69 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 ** 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 = 0.4159 r_free = 0.4159 target = 0.133124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.116042 restraints weight = 23138.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.118631 restraints weight = 14371.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.120480 restraints weight = 9967.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2339

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= 0.143
  Angle     :  0.622   9.729   9598  Z= 0.325
  Chirality :  0.042   0.241   1101
  Planarity :  0.003   0.030   1212
  Dihedral  :  6.722  76.703    983
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.35 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.28), residues: 890
  helix:  1.53 (0.19), residues: 670
  sheet: -0.79 (0.96), residues: 27
  loop : -1.18 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 327 
 HIS   0.002   0.001   HIS A 953 
 PHE   0.052   0.002   PHE A 348 
 TYR   0.019   0.001   TYR A 477 
 ARG   0.002   0.000   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04411 (  569)
  hydrogen bonds       : angle       4.53073 ( 1674)
  covalent geometry    : bond        0.00303 ( 7108)
  covalent geometry    : angle       0.62243 ( 9598)

*********************** 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
  163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.7982 (tpp) cc_final: 0.7611 (tpp)
REVERT: A  348 PHE cc_start: 0.8696 (m-80) cc_final: 0.8358 (m-80)
REVERT: A  480 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7796 (mm-30)
REVERT: A  526 MET cc_start: 0.0822 (pmm) cc_final: 0.0498 (pmm)
REVERT: A  543 MET cc_start: 0.5277 (tpt) cc_final: 0.4646 (tpt)
REVERT: A  548 LYS cc_start: 0.7191 (mttp) cc_final: 0.6124 (tptt)
REVERT: A  640 MET cc_start: 0.5140 (ppp) cc_final: 0.4696 (ppp)
REVERT: A  779 ILE cc_start: 0.8798 (mm) cc_final: 0.8332 (mm)
REVERT: A  783 THR cc_start: 0.7309 (m) cc_final: 0.6688 (p)
REVERT: A  814 MET cc_start: 0.6344 (mmm) cc_final: 0.6028 (mmm)
REVERT: A  843 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8045 (tm-30)
REVERT: A  893 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5765 (mmt)
REVERT: A  903 ASP cc_start: 0.5590 (OUTLIER) cc_final: 0.5076 (p0)
REVERT: A  905 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8824 (mmtm)
REVERT: A  929 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7064 (mpt180)
REVERT: A  954 VAL cc_start: 0.9408 (t) cc_final: 0.9037 (p)
REVERT: A 1003 MET cc_start: 0.7872 (mpp) cc_final: 0.7274 (mpp)
REVERT: A 1020 MET cc_start: 0.7903 (ppp) cc_final: 0.7680 (ppp)
REVERT: A 1026 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6472 (mpp)
REVERT: A 1027 MET cc_start: 0.9009 (ptp) cc_final: 0.8185 (ppp)
  outliers start: 30
  outliers final: 16
  residues processed: 152
  average time/residue: 0.1631
  time to fit residues: 34.5125
Evaluate side-chains
  150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   79 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  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  601 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  719 MET
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  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 54 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0060
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.9598

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 GLN
A 582 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.132602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.115316 restraints weight = 23043.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.117817 restraints weight = 14446.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.119658 restraints weight = 10171.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.2502

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= 0.150
  Angle     :  0.629  10.654   9598  Z= 0.323
  Chirality :  0.041   0.249   1101
  Planarity :  0.003   0.025   1212
  Dihedral  :  6.331  77.134    981
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 18.49 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.28), residues: 890
  helix:  1.53 (0.19), residues: 670
  sheet: -0.99 (0.92), residues: 27
  loop : -1.16 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.031   0.001   PHE A 348 
 TYR   0.020   0.001   TYR A 477 
 ARG   0.003   0.000   ARG A 975 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  569)
  hydrogen bonds       : angle       4.47679 ( 1674)
  covalent geometry    : bond        0.00318 ( 7108)
  covalent geometry    : angle       0.62869 ( 9598)

*********************** 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
  165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.831 
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: A   80 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7375 (ptt)
REVERT: A  133 MET cc_start: 0.8001 (tpp) cc_final: 0.7652 (tpp)
REVERT: A  168 MET cc_start: 0.7945 (mmp) cc_final: 0.7220 (mmp)
REVERT: A  422 LEU cc_start: 0.6933 (mt) cc_final: 0.6612 (mt)
REVERT: A  480 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7812 (mm-30)
REVERT: A  526 MET cc_start: 0.0809 (pmm) cc_final: 0.0479 (pmm)
REVERT: A  640 MET cc_start: 0.5107 (ppp) cc_final: 0.4690 (ppp)
REVERT: A  708 GLU cc_start: 0.3951 (OUTLIER) cc_final: 0.3703 (pm20)
REVERT: A  779 ILE cc_start: 0.8664 (mm) cc_final: 0.8221 (mm)
REVERT: A  783 THR cc_start: 0.7302 (m) cc_final: 0.6777 (p)
REVERT: A  787 MET cc_start: 0.8695 (mmm) cc_final: 0.8357 (mmm)
REVERT: A  814 MET cc_start: 0.5782 (mmm) cc_final: 0.5341 (mmm)
REVERT: A  843 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8031 (tm-30)
REVERT: A  893 MET cc_start: 0.6518 (ppp) cc_final: 0.5736 (mmt)
REVERT: A  903 ASP cc_start: 0.5557 (OUTLIER) cc_final: 0.4844 (p0)
REVERT: A  954 VAL cc_start: 0.9374 (t) cc_final: 0.9012 (p)
REVERT: A  961 PHE cc_start: 0.7361 (t80) cc_final: 0.6783 (t80)
REVERT: A  965 MET cc_start: 0.7794 (mmp) cc_final: 0.7254 (mmp)
REVERT: A 1003 MET cc_start: 0.7978 (mpp) cc_final: 0.7685 (mpp)
REVERT: A 1026 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6476 (mpp)
REVERT: A 1027 MET cc_start: 0.9040 (ptp) cc_final: 0.8218 (ppp)
  outliers start: 32
  outliers final: 20
  residues processed: 153
  average time/residue: 0.1701
  time to fit residues: 36.3697
Evaluate side-chains
  159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue   87 MET
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  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  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  789 LEU
Chi-restraints excluded: chain A residue  803 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0770
   chunk 55 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0870
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.5716

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.134109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.116765 restraints weight = 23153.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.119388 restraints weight = 14521.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.121214 restraints weight = 10144.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7108  Z= 0.133
  Angle     :  0.612   9.722   9598  Z= 0.313
  Chirality :  0.040   0.259   1101
  Planarity :  0.003   0.026   1212
  Dihedral  :  6.133  76.476    979
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 19.57 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.28), residues: 890
  helix:  1.58 (0.19), residues: 671
  sheet: -1.08 (0.90), residues: 27
  loop : -1.18 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A1024 
 PHE   0.025   0.001   PHE A 348 
 TYR   0.018   0.001   TYR A 477 
 ARG   0.003   0.000   ARG A 975 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04184 (  569)
  hydrogen bonds       : angle       4.36799 ( 1674)
  covalent geometry    : bond        0.00279 ( 7108)
  covalent geometry    : angle       0.61250 ( 9598)

*********************** 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
  166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7408 (ptt)
REVERT: A  133 MET cc_start: 0.7984 (tpp) cc_final: 0.7671 (tpp)
REVERT: A  168 MET cc_start: 0.8124 (mmp) cc_final: 0.7217 (mmp)
REVERT: A  422 LEU cc_start: 0.6930 (mt) cc_final: 0.6601 (mt)
REVERT: A  480 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7789 (mm-30)
REVERT: A  526 MET cc_start: 0.0994 (pmm) cc_final: 0.0748 (pmm)
REVERT: A  640 MET cc_start: 0.5039 (ppp) cc_final: 0.4648 (ppp)
REVERT: A  779 ILE cc_start: 0.8610 (mm) cc_final: 0.8319 (mm)
REVERT: A  783 THR cc_start: 0.7237 (m) cc_final: 0.6744 (p)
REVERT: A  786 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8427 (t)
REVERT: A  787 MET cc_start: 0.8631 (mmm) cc_final: 0.8325 (mmm)
REVERT: A  794 PHE cc_start: 0.8054 (m-80) cc_final: 0.7565 (m-80)
REVERT: A  814 MET cc_start: 0.5634 (mmm) cc_final: 0.5154 (mmm)
REVERT: A  843 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8097 (tm-30)
REVERT: A  893 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5894 (mmt)
REVERT: A  903 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.4454 (p0)
REVERT: A  954 VAL cc_start: 0.9313 (t) cc_final: 0.8952 (p)
REVERT: A  961 PHE cc_start: 0.7357 (t80) cc_final: 0.6781 (t80)
REVERT: A  965 MET cc_start: 0.7901 (mmp) cc_final: 0.7285 (mmp)
REVERT: A 1003 MET cc_start: 0.7931 (mpp) cc_final: 0.7624 (mtt)
REVERT: A 1020 MET cc_start: 0.8037 (ppp) cc_final: 0.7696 (ppp)
REVERT: A 1026 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6446 (mpp)
REVERT: A 1027 MET cc_start: 0.9016 (ptp) cc_final: 0.8226 (ppp)
  outliers start: 35
  outliers final: 18
  residues processed: 157
  average time/residue: 0.1652
  time to fit residues: 36.0953
Evaluate side-chains
  149 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  170 GLN
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  250 ASN
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  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  803 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1024 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.131086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.113902 restraints weight = 22790.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.116392 restraints weight = 14306.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.118171 restraints weight = 10051.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7108  Z= 0.187
  Angle     :  0.667  10.439   9598  Z= 0.344
  Chirality :  0.042   0.252   1101
  Planarity :  0.004   0.025   1212
  Dihedral  :  6.222  76.177    978
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 21.59 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.28), residues: 890
  helix:  1.56 (0.19), residues: 670
  sheet: -0.95 (0.91), residues: 27
  loop : -1.23 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 872 
 HIS   0.004   0.001   HIS A 375 
 PHE   0.027   0.002   PHE A 524 
 TYR   0.022   0.002   TYR A 477 
 ARG   0.009   0.001   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04476 (  569)
  hydrogen bonds       : angle       4.53797 ( 1674)
  covalent geometry    : bond        0.00394 ( 7108)
  covalent geometry    : angle       0.66659 ( 9598)

*********************** 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
  162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7338 (ptt)
REVERT: A  133 MET cc_start: 0.8094 (tpp) cc_final: 0.7732 (tpp)
REVERT: A  357 MET cc_start: 0.6474 (mmt) cc_final: 0.5749 (tpp)
REVERT: A  422 LEU cc_start: 0.6935 (mt) cc_final: 0.6664 (mt)
REVERT: A  480 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7868 (mm-30)
REVERT: A  526 MET cc_start: 0.0923 (pmm) cc_final: 0.0656 (pmm)
REVERT: A  601 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8128 (pp)
REVERT: A  640 MET cc_start: 0.5093 (ppp) cc_final: 0.4706 (ppp)
REVERT: A  779 ILE cc_start: 0.8591 (mm) cc_final: 0.8019 (mm)
REVERT: A  783 THR cc_start: 0.7639 (m) cc_final: 0.7019 (p)
REVERT: A  786 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8531 (t)
REVERT: A  787 MET cc_start: 0.8700 (mmm) cc_final: 0.8327 (mmm)
REVERT: A  814 MET cc_start: 0.6453 (mmm) cc_final: 0.6006 (mmm)
REVERT: A  843 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8122 (tm-30)
REVERT: A  853 LEU cc_start: 0.9232 (tp) cc_final: 0.8987 (tp)
REVERT: A  857 ILE cc_start: 0.8530 (tp) cc_final: 0.8140 (pt)
REVERT: A  893 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.5905 (mmt)
REVERT: A  903 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.4354 (p0)
REVERT: A  954 VAL cc_start: 0.9399 (t) cc_final: 0.9017 (p)
REVERT: A  961 PHE cc_start: 0.7510 (t80) cc_final: 0.7004 (t80)
REVERT: A 1024 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.7051 (m170)
REVERT: A 1026 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6653 (mpp)
REVERT: A 1027 MET cc_start: 0.9038 (ptp) cc_final: 0.8082 (ppp)
  outliers start: 32
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1634
  time to fit residues: 34.3929
Evaluate side-chains
  151 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  210 SER
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  250 ASN
Chi-restraints excluded: chain A residue  425 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  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  803 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 1024 HIS
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 56 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4153 r_free = 0.4153 target = 0.132455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.115221 restraints weight = 23142.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.117802 restraints weight = 14414.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.119575 restraints weight = 10072.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7108  Z= 0.148
  Angle     :  0.667  10.955   9598  Z= 0.337
  Chirality :  0.042   0.263   1101
  Planarity :  0.003   0.025   1212
  Dihedral  :  6.150  76.018    978
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 23.21 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.28), residues: 890
  helix:  1.55 (0.19), residues: 671
  sheet: -0.78 (0.93), residues: 27
  loop : -1.22 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.016   0.001   PHE A 348 
 TYR   0.018   0.002   TYR A 477 
 ARG   0.003   0.000   ARG A 975 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04314 (  569)
  hydrogen bonds       : angle       4.48883 ( 1674)
  covalent geometry    : bond        0.00313 ( 7108)
  covalent geometry    : angle       0.66665 ( 9598)

*********************** 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
  161 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7395 (ptt)
REVERT: A  133 MET cc_start: 0.8042 (tpp) cc_final: 0.7700 (tpp)
REVERT: A  422 LEU cc_start: 0.6943 (mt) cc_final: 0.6651 (mt)
REVERT: A  480 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7836 (mm-30)
REVERT: A  526 MET cc_start: 0.0982 (pmm) cc_final: 0.0709 (pmm)
REVERT: A  601 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8277 (pp)
REVERT: A  640 MET cc_start: 0.5070 (ppp) cc_final: 0.4708 (ppp)
REVERT: A  745 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7355 (tm)
REVERT: A  779 ILE cc_start: 0.8525 (mm) cc_final: 0.8006 (mm)
REVERT: A  783 THR cc_start: 0.7606 (m) cc_final: 0.6961 (p)
REVERT: A  786 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8481 (t)
REVERT: A  787 MET cc_start: 0.8700 (mmm) cc_final: 0.8293 (mmm)
REVERT: A  794 PHE cc_start: 0.8069 (m-80) cc_final: 0.7549 (m-80)
REVERT: A  814 MET cc_start: 0.5658 (mmm) cc_final: 0.5153 (mmm)
REVERT: A  843 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8076 (tm-30)
REVERT: A  857 ILE cc_start: 0.8510 (tp) cc_final: 0.8100 (pt)
REVERT: A  893 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.5851 (mmt)
REVERT: A  903 ASP cc_start: 0.5801 (OUTLIER) cc_final: 0.4561 (p0)
REVERT: A  954 VAL cc_start: 0.9350 (t) cc_final: 0.8986 (p)
REVERT: A  961 PHE cc_start: 0.7470 (t80) cc_final: 0.6847 (t80)
REVERT: A  965 MET cc_start: 0.7929 (mmp) cc_final: 0.7348 (mmp)
REVERT: A  999 LEU cc_start: 0.8359 (mt) cc_final: 0.7635 (mt)
REVERT: A 1026 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6446 (mpp)
REVERT: A 1027 MET cc_start: 0.8987 (ptp) cc_final: 0.8213 (ppp)
  outliers start: 27
  outliers final: 18
  residues processed: 152
  average time/residue: 0.1748
  time to fit residues: 36.9217
Evaluate side-chains
  150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  170 GLN
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  250 ASN
Chi-restraints excluded: chain A residue  425 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  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  803 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  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 44 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   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 = 0.132305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.114948 restraints weight = 23453.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.117543 restraints weight = 14628.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.119384 restraints weight = 10229.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7108  Z= 0.155
  Angle     :  0.678  11.195   9598  Z= 0.342
  Chirality :  0.042   0.265   1101
  Planarity :  0.003   0.025   1212
  Dihedral  :  6.153  76.255    978
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 22.94 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.28), residues: 890
  helix:  1.55 (0.19), residues: 671
  sheet: -0.67 (0.95), residues: 27
  loop : -1.21 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.015   0.001   PHE A 348 
 TYR   0.019   0.002   TYR A 477 
 ARG   0.004   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  569)
  hydrogen bonds       : angle       4.52172 ( 1674)
  covalent geometry    : bond        0.00329 ( 7108)
  covalent geometry    : angle       0.67772 ( 9598)

*********************** 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
  159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7450 (ptt)
REVERT: A  130 TYR cc_start: 0.7004 (m-80) cc_final: 0.6685 (m-80)
REVERT: A  133 MET cc_start: 0.8060 (tpp) cc_final: 0.7705 (tpp)
REVERT: A  168 MET cc_start: 0.7919 (mmp) cc_final: 0.7648 (mmp)
REVERT: A  348 PHE cc_start: 0.8917 (m-80) cc_final: 0.8473 (m-80)
REVERT: A  413 TYR cc_start: 0.5533 (m-80) cc_final: 0.5232 (m-80)
REVERT: A  422 LEU cc_start: 0.6998 (mt) cc_final: 0.6656 (mt)
REVERT: A  480 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7840 (mm-30)
REVERT: A  526 MET cc_start: 0.2228 (pmm) cc_final: 0.1871 (pmm)
REVERT: A  601 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8286 (pp)
REVERT: A  640 MET cc_start: 0.5205 (ppp) cc_final: 0.4888 (ppp)
REVERT: A  726 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.6003 (t60)
REVERT: A  745 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7359 (tm)
REVERT: A  779 ILE cc_start: 0.8545 (mm) cc_final: 0.8022 (mm)
REVERT: A  783 THR cc_start: 0.7660 (m) cc_final: 0.7012 (p)
REVERT: A  786 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8469 (t)
REVERT: A  787 MET cc_start: 0.8742 (mmm) cc_final: 0.8315 (mmm)
REVERT: A  794 PHE cc_start: 0.8075 (m-80) cc_final: 0.7536 (m-80)
REVERT: A  814 MET cc_start: 0.5628 (mmm) cc_final: 0.5110 (mmm)
REVERT: A  843 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8023 (tm-30)
REVERT: A  853 LEU cc_start: 0.9461 (tp) cc_final: 0.9257 (tp)
REVERT: A  857 ILE cc_start: 0.8461 (tp) cc_final: 0.8160 (pt)
REVERT: A  893 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.5806 (mmt)
REVERT: A  903 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.4606 (p0)
REVERT: A  954 VAL cc_start: 0.9358 (t) cc_final: 0.8984 (p)
REVERT: A  961 PHE cc_start: 0.7479 (t80) cc_final: 0.6847 (t80)
REVERT: A  965 MET cc_start: 0.7921 (mmp) cc_final: 0.7358 (mmp)
REVERT: A 1026 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6688 (mpp)
REVERT: A 1027 MET cc_start: 0.9035 (ptp) cc_final: 0.8237 (ppp)
  outliers start: 30
  outliers final: 19
  residues processed: 150
  average time/residue: 0.1612
  time to fit residues: 33.6589
Evaluate side-chains
  155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  170 GLN
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  250 ASN
Chi-restraints excluded: chain A residue  425 MET
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  719 MET
Chi-restraints excluded: chain A residue  726 TRP
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  803 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  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 18 optimal weight:    0.9990
   chunk 88 optimal weight:    8.9990
   chunk 27 optimal weight:    0.5980
   chunk 55 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0000
   overall best weight:    0.6584

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.133917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.116184 restraints weight = 23609.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.118724 restraints weight = 14926.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.120554 restraints weight = 10563.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.3299

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= 0.140
  Angle     :  0.680  11.994   9598  Z= 0.339
  Chirality :  0.042   0.274   1101
  Planarity :  0.003   0.026   1212
  Dihedral  :  6.059  75.152    978
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.48 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.28), residues: 890
  helix:  1.59 (0.19), residues: 673
  sheet:  0.20 (1.04), residues: 22
  loop : -1.35 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 872 
 HIS   0.002   0.001   HIS A 953 
 PHE   0.017   0.001   PHE A 348 
 TYR   0.017   0.001   TYR A 477 
 ARG   0.004   0.000   ARG A 975 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04202 (  569)
  hydrogen bonds       : angle       4.47778 ( 1674)
  covalent geometry    : bond        0.00294 ( 7108)
  covalent geometry    : angle       0.67978 ( 9598)

********************** 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: 26
    poor density    : 125
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7310 (ptt)
REVERT: A  133 MET cc_start: 0.8118 (tpp) cc_final: 0.7827 (tpp)
REVERT: A  168 MET cc_start: 0.7956 (mmp) cc_final: 0.7678 (mmp)
REVERT: A  357 MET cc_start: 0.6275 (mmt) cc_final: 0.5993 (mmt)
REVERT: A  413 TYR cc_start: 0.5674 (m-80) cc_final: 0.5449 (m-80)
REVERT: A  480 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7812 (mm-30)
REVERT: A  526 MET cc_start: 0.1481 (pmm) cc_final: 0.1096 (pmm)
REVERT: A  548 LYS cc_start: 0.7167 (mttt) cc_final: 0.6459 (mptt)
REVERT: A  601 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8283 (pp)
REVERT: A  640 MET cc_start: 0.5127 (ppp) cc_final: 0.4802 (ppp)
REVERT: A  745 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7229 (tm)
REVERT: A  779 ILE cc_start: 0.8417 (mm) cc_final: 0.7947 (mm)
REVERT: A  783 THR cc_start: 0.7646 (m) cc_final: 0.7008 (p)
REVERT: A  786 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8424 (t)
REVERT: A  787 MET cc_start: 0.8722 (mmm) cc_final: 0.8326 (mmm)
REVERT: A  814 MET cc_start: 0.5518 (mmm) cc_final: 0.4995 (mmm)
REVERT: A  843 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8005 (tm-30)
REVERT: A  857 ILE cc_start: 0.8438 (tp) cc_final: 0.8129 (pt)
REVERT: A  893 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.5747 (mmt)
REVERT: A  903 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.4577 (p0)
REVERT: A  954 VAL cc_start: 0.9281 (t) cc_final: 0.8915 (p)
REVERT: A  961 PHE cc_start: 0.7394 (t80) cc_final: 0.6996 (t80)
REVERT: A  965 MET cc_start: 0.7815 (mmp) cc_final: 0.7475 (mmp)
REVERT: A 1026 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6440 (mpp)
REVERT: A 1027 MET cc_start: 0.8989 (ptp) cc_final: 0.8199 (ppp)
  outliers start: 26
  outliers final: 15
  residues processed: 143
  average time/residue: 0.1588
  time to fit residues: 31.4162
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  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  170 GLN
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  250 ASN
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  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  803 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0470
   chunk 87 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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 = 0.4170 r_free = 0.4170 target = 0.133577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.116115 restraints weight = 23486.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.118687 restraints weight = 14869.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.120510 restraints weight = 10485.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7108  Z= 0.144
  Angle     :  0.689  11.687   9598  Z= 0.346
  Chirality :  0.043   0.273   1101
  Planarity :  0.003   0.027   1212
  Dihedral  :  6.041  75.701    978
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 24.43 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.28), residues: 890
  helix:  1.59 (0.20), residues: 672
  sheet: -0.66 (0.86), residues: 32
  loop : -1.23 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 872 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.018   0.001   TYR A 477 
 ARG   0.003   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04268 (  569)
  hydrogen bonds       : angle       4.54846 ( 1674)
  covalent geometry    : bond        0.00305 ( 7108)
  covalent geometry    : angle       0.68879 ( 9598)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2295.07 seconds
wall clock time: 40 minutes 37.88 seconds (2437.88 seconds total)