Starting phenix.real_space_refine
on Tue Mar 11 22:24:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zox_14849/03_2025/7zox_14849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zox_14849/03_2025/7zox_14849.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zox_14849/03_2025/7zox_14849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zox_14849/03_2025/7zox_14849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zox_14849/03_2025/7zox_14849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zox_14849/03_2025/7zox_14849.cif"
  }
  resolution = 4.4
  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=   0.000 sd=   0.002
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      41      5.16       5
     C    4277      2.51       5
     N    1179      2.21       5
     O    1275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6772
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 607, 4923
          Classifications: {'peptide': 607}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 586}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 965
          Classifications: {'peptide': 125}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 122}
    Chain: "C"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 884
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
  Time building chain proxies: 3.97, per 1000 atoms: 0.59
  Number of scatterers: 6772
  At special positions: 0
  Unit cell: (115.926, 115.092, 125.934, 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      41     16.00
     O    1275      8.00
     N    1179      7.00
     C    4277      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  96 " distance=2.04

  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: 1.48
  Conformation dependent library (CDL) restraints added in 849.1 milliseconds
  

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      53.1% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 197
    Processing helix  chain 'A' and resid 204 through 212
      removed outlier: 3.631A  pdb=" N   LEU A 208 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 233
      removed outlier: 3.962A  pdb=" N   ASP A 223 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 248
    Processing helix  chain 'A' and resid 248 through 275
    Processing helix  chain 'A' and resid 290 through 300
      removed outlier: 3.725A  pdb=" N   ARG A 295 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 329
    Processing helix  chain 'A' and resid 331 through 342
      removed outlier: 3.964A  pdb=" N   ALA A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.891A  pdb=" N   ASN A 351 " --> pdb=" O   GLY A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 380
    Processing helix  chain 'A' and resid 385 through 397
      removed outlier: 3.600A  pdb=" N   ARG A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 420
    Processing helix  chain 'A' and resid 437 through 449
    Processing helix  chain 'A' and resid 452 through 457
      removed outlier: 4.306A  pdb=" N   VAL A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASN A 457 " --> pdb=" O   HIS A 453 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 452 through 457'
    Processing helix  chain 'A' and resid 459 through 470
      removed outlier: 3.581A  pdb=" N   THR A 470 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 481
      removed outlier: 3.754A  pdb=" N   PHE A 479 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 500
    Processing helix  chain 'A' and resid 528 through 538
    Processing helix  chain 'A' and resid 544 through 553
      removed outlier: 3.840A  pdb=" N   ALA A 548 " --> pdb=" O   ASP A 544 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN A 550 " --> pdb=" O   ARG A 546 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TYR A 551 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 556
      No H-bonds generated for 'chain 'A' and resid 554 through 556'
    Processing helix  chain 'A' and resid 565 through 578
      removed outlier: 4.349A  pdb=" N   GLU A 573 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ILE A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 603
      removed outlier: 3.913A  pdb=" N   PHE A 602 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 620
    Processing helix  chain 'A' and resid 622 through 633
    Processing helix  chain 'A' and resid 635 through 648
      removed outlier: 3.700A  pdb=" N   LYS A 645 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A 646 " --> pdb=" O   LEU A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 653
      removed outlier: 4.217A  pdb=" N   SER A 652 " --> pdb=" O   PRO A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 678
    Processing helix  chain 'A' and resid 683 through 706
      removed outlier: 4.051A  pdb=" N   THR A 689 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 717
      removed outlier: 3.502A  pdb=" N   SER A 711 " --> pdb=" O   HIS A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 735
      removed outlier: 3.841A  pdb=" N   PHE A 735 " --> pdb=" O   ARG A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 764
      removed outlier: 3.572A  pdb=" N   ASN A 745 " --> pdb=" O   GLU A 741 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   SER A 747 " --> pdb=" O   ARG A 743 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   GLU A 748 " --> pdb=" O   HIS A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 798
    Processing helix  chain 'A' and resid 805 through 820
      removed outlier: 3.527A  pdb=" N   ASN A 809 " --> pdb=" O   SER A 805 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 93
      removed outlier: 3.510A  pdb=" N   THR B  93 " --> pdb=" O   PRO B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 114
      removed outlier: 3.520A  pdb=" N   ASP B 113 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 76
      No H-bonds generated for 'chain 'C' and resid 74 through 76'
    Processing helix  chain 'C' and resid 101 through 107
      removed outlier: 3.968A  pdb=" N   ALA C 107 " --> pdb=" O   ALA C 103 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA2, first strand: chain 'A' and resid 514 through 515
    Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9
    Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 15
      removed outlier: 5.729A  pdb=" N   ARG B  40 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   PHE B  49 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 8
      removed outlier: 3.546A  pdb=" N   SER C  26 " --> pdb=" O   GLN C   4 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL C   6 " --> pdb=" O   VAL C  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 13
      removed outlier: 3.759A  pdb=" N   THR C 120 " --> pdb=" O   GLY C  11 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ARG C  39 " --> pdb=" O   TRP C  48 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   TRP C  48 " --> pdb=" O   ARG C  39 " (cutoff:3.500A)

    353 hydrogen bonds defined for protein.
    999 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: 2.04

  Time building geometry restraints manager: 1.80 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: 2252
        1.34 -     1.46: 1333
        1.46 -     1.58: 3240
        1.58 -     1.69: 0
        1.69 -     1.81: 68
  Bond restraints: 6893
  Sorted by residual:
  bond pdb=" CA  HIS A 744 "
       pdb=" C   HIS A 744 "
    ideal  model  delta    sigma   weight residual
    1.522  1.492  0.030 1.72e-02 3.38e+03 3.04e+00
  bond pdb=" C   VAL A 650 "
       pdb=" O   VAL A 650 "
    ideal  model  delta    sigma   weight residual
    1.241  1.223  0.018 1.19e-02 7.06e+03 2.29e+00
  bond pdb=" CA  ARG A 246 "
       pdb=" C   ARG A 246 "
    ideal  model  delta    sigma   weight residual
    1.522  1.498  0.023 1.72e-02 3.38e+03 1.82e+00
  bond pdb=" C   LEU A 364 "
       pdb=" N   SER A 365 "
    ideal  model  delta    sigma   weight residual
    1.330  1.312  0.018 1.47e-02 4.63e+03 1.56e+00
  bond pdb=" CA  ASP A 399 "
       pdb=" C   ASP A 399 "
    ideal  model  delta    sigma   weight residual
    1.532  1.522  0.011 9.60e-03 1.09e+04 1.29e+00
  ... (remaining 6888 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 8680
        1.33 -     2.66: 528
        2.66 -     3.98: 72
        3.98 -     5.31: 16
        5.31 -     6.64: 6
  Bond angle restraints: 9302
  Sorted by residual:
  angle pdb=" N   SER C  31 "
        pdb=" CA  SER C  31 "
        pdb=" C   SER C  31 "
      ideal   model   delta    sigma   weight residual
     114.75  109.42    5.33 1.26e+00 6.30e-01 1.79e+01
  angle pdb=" N   ASP B  32 "
        pdb=" CA  ASP B  32 "
        pdb=" C   ASP B  32 "
      ideal   model   delta    sigma   weight residual
     114.56  109.41    5.15 1.27e+00 6.20e-01 1.64e+01
  angle pdb=" N   ASN A 737 "
        pdb=" CA  ASN A 737 "
        pdb=" C   ASN A 737 "
      ideal   model   delta    sigma   weight residual
     114.09  107.96    6.13 1.55e+00 4.16e-01 1.56e+01
  angle pdb=" C   ASN A 528 "
        pdb=" N   PHE A 529 "
        pdb=" CA  PHE A 529 "
      ideal   model   delta    sigma   weight residual
     120.82  125.40   -4.58 1.50e+00 4.44e-01 9.34e+00
  angle pdb=" C   GLY A 450 "
        pdb=" N   GLU A 451 "
        pdb=" CA  GLU A 451 "
      ideal   model   delta    sigma   weight residual
     121.54  127.30   -5.76 1.91e+00 2.74e-01 9.10e+00
  ... (remaining 9297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 3683
       17.28 -    34.57: 386
       34.57 -    51.85: 68
       51.85 -    69.13: 22
       69.13 -    86.41: 16
  Dihedral angle restraints: 4175
    sinusoidal: 1696
      harmonic: 2479
  Sorted by residual:
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  96 "
           pdb=" CB  CYS C  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   21.47   71.53     1      1.00e+01 1.00e-02 6.56e+01
  dihedral pdb=" CA  GLU A 451 "
           pdb=" C   GLU A 451 "
           pdb=" N   SER A 452 "
           pdb=" CA  SER A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.53   25.47     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  PHE A 735 "
           pdb=" C   PHE A 735 "
           pdb=" N   ARG A 736 "
           pdb=" CA  ARG A 736 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.55  -21.45     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 547
       0.026 -    0.051: 285
       0.051 -    0.077: 127
       0.077 -    0.102: 53
       0.102 -    0.128: 17
  Chirality restraints: 1029
  Sorted by residual:
  chirality pdb=" CA  VAL C  38 "
            pdb=" N   VAL C  38 "
            pdb=" C   VAL C  38 "
            pdb=" CB  VAL C  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  HIS A 492 "
            pdb=" N   HIS A 492 "
            pdb=" C   HIS A 492 "
            pdb=" CB  HIS A 492 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  ILE A 314 "
            pdb=" N   ILE A 314 "
            pdb=" C   ILE A 314 "
            pdb=" CB  ILE A 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  ... (remaining 1026 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 656 "   -0.046 5.00e-02 4.00e+02   6.94e-02 7.70e+00
        pdb=" N   PRO A 657 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 657 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 657 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  42 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.74e+00
        pdb=" N   PRO B  43 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B  43 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  43 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 721 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO A 722 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 722 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 722 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1119
        2.75 -     3.29: 7223
        3.29 -     3.83: 11255
        3.83 -     4.36: 13389
        4.36 -     4.90: 22056
  Nonbonded interactions: 55042
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 482 "
            pdb=" OD2 ASP B 101 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   GLN A 653 "
            pdb=" NH1 ARG A 661 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   ASP A 781 "
            pdb=" OG  SER A 784 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG  SER A 724 "
            pdb=" OD1 ASP A 726 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ASN C  53 "
            pdb=" NH1 ARG C  72 "
     model   vdw
     2.240 3.120
  ... (remaining 55037 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.00 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:             0.710
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.110
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
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      :  0.005   0.047   6893  Z= 0.305
  Angle     :  0.722   6.641   9302  Z= 0.450
  Chirality :  0.040   0.128   1029
  Planarity :  0.005   0.069   1206
  Dihedral  : 15.618  86.413   2574
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.48 %
    Favored  : 95.38 %
  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: -4.40 (0.22), residues: 836
  helix: -2.76 (0.19), residues: 402
  sheet: -2.88 (0.48), residues: 91
  loop : -2.94 (0.27), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 416 
 HIS   0.007   0.001   HIS A 492 
 PHE   0.023   0.002   PHE A 552 
 TYR   0.018   0.002   TYR A 192 
 ARG   0.003   0.000   ARG A 377 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 MET cc_start: 0.8106 (mtm) cc_final: 0.7871 (mtm)
REVERT: A  293 LEU cc_start: 0.9347 (tp) cc_final: 0.8919 (mt)
REVERT: A  320 TRP cc_start: 0.8141 (m100) cc_final: 0.7277 (m100)
REVERT: A  344 HIS cc_start: 0.8570 (p-80) cc_final: 0.8367 (p-80)
REVERT: A  349 PHE cc_start: 0.8816 (t80) cc_final: 0.8503 (t80)
REVERT: A  504 LEU cc_start: 0.8302 (mt) cc_final: 0.8038 (mt)
REVERT: A  602 PHE cc_start: 0.8199 (p90) cc_final: 0.7702 (p90)
REVERT: A  641 GLU cc_start: 0.8709 (pt0) cc_final: 0.8196 (pt0)
REVERT: A  667 MET cc_start: 0.8558 (tpt) cc_final: 0.8259 (tpp)
REVERT: A  697 ILE cc_start: 0.8972 (mt) cc_final: 0.8745 (mt)
REVERT: A  702 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8518 (tp30)
REVERT: A  703 TYR cc_start: 0.8899 (t80) cc_final: 0.8051 (t80)
REVERT: A  707 HIS cc_start: 0.7666 (m90) cc_final: 0.5965 (m-70)
REVERT: A  716 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8584 (mm-30)
REVERT: A  754 MET cc_start: 0.8998 (tpt) cc_final: 0.8721 (tpt)
REVERT: A  803 ARG cc_start: 0.8778 (mmt180) cc_final: 0.7858 (tpt170)
REVERT: B   32 ASP cc_start: 0.7800 (p0) cc_final: 0.7589 (p0)
REVERT: B   38 TRP cc_start: 0.7008 (m100) cc_final: 0.6805 (m100)
REVERT: B   55 LYS cc_start: 0.8107 (ptmm) cc_final: 0.7701 (ttpp)
REVERT: B   85 MET cc_start: 0.8464 (mtm) cc_final: 0.8091 (mtm)
REVERT: C   82 GLN cc_start: 0.7548 (tp40) cc_final: 0.6900 (tp40)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2286
  time to fit residues: 56.5634
Evaluate side-chains
  143 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0970
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 252 GLN
A 292 ASN
A 337 GLN
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 453 HIS
A 457 ASN
A 745 ASN
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
B  79 ASN
C  77 ASN
C 115 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.075826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.056567 restraints weight = 25103.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.058371 restraints weight = 15645.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.059586 restraints weight = 11311.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6893  Z= 0.180
  Angle     :  0.573   5.903   9302  Z= 0.308
  Chirality :  0.040   0.142   1029
  Planarity :  0.004   0.050   1206
  Dihedral  :  4.996  22.919    938
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.29 (0.27), residues: 836
  helix: -0.61 (0.24), residues: 416
  sheet: -2.53 (0.49), residues: 96
  loop : -2.30 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  37 
 HIS   0.003   0.001   HIS A 492 
 PHE   0.019   0.001   PHE A 796 
 TYR   0.028   0.002   TYR A 262 
 ARG   0.007   0.001   ARG C  67 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LEU cc_start: 0.9288 (tp) cc_final: 0.8850 (mt)
REVERT: A  320 TRP cc_start: 0.8349 (m100) cc_final: 0.7108 (m100)
REVERT: A  344 HIS cc_start: 0.8413 (p-80) cc_final: 0.8119 (p-80)
REVERT: A  349 PHE cc_start: 0.8610 (t80) cc_final: 0.8374 (t80)
REVERT: A  392 TYR cc_start: 0.8334 (m-80) cc_final: 0.8064 (m-10)
REVERT: A  484 GLU cc_start: 0.8251 (pp20) cc_final: 0.8021 (tm-30)
REVERT: A  504 LEU cc_start: 0.8264 (mt) cc_final: 0.8061 (mt)
REVERT: A  602 PHE cc_start: 0.8112 (p90) cc_final: 0.7395 (p90)
REVERT: A  641 GLU cc_start: 0.8603 (pt0) cc_final: 0.8089 (pt0)
REVERT: A  667 MET cc_start: 0.8552 (tpt) cc_final: 0.8061 (tpp)
REVERT: A  697 ILE cc_start: 0.8953 (mt) cc_final: 0.8706 (mt)
REVERT: A  702 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8809 (tp30)
REVERT: A  707 HIS cc_start: 0.7568 (m90) cc_final: 0.6374 (m-70)
REVERT: A  754 MET cc_start: 0.8959 (tpt) cc_final: 0.8497 (tpt)
REVERT: A  755 ASN cc_start: 0.9058 (m110) cc_final: 0.8775 (m110)
REVERT: A  803 ARG cc_start: 0.8560 (mmt180) cc_final: 0.7745 (tpt170)
REVERT: B   15 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7919 (mm-40)
REVERT: B   55 LYS cc_start: 0.8048 (ptmm) cc_final: 0.7835 (ttpp)
REVERT: B  124 THR cc_start: 0.8732 (m) cc_final: 0.8378 (p)
REVERT: C   35 MET cc_start: 0.8733 (mmm) cc_final: 0.8226 (mmm)
REVERT: C   67 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7523 (mtp-110)
REVERT: C   79 LEU cc_start: 0.8417 (tp) cc_final: 0.7612 (tp)
REVERT: C   90 ASP cc_start: 0.7811 (p0) cc_final: 0.7358 (p0)
REVERT: C   96 CYS cc_start: 0.5882 (t) cc_final: 0.3285 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2075
  time to fit residues: 51.4033
Evaluate side-chains
  146 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 GLN
A 725 GLN
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.075626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.056105 restraints weight = 25351.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.057799 restraints weight = 16262.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.058913 restraints weight = 11998.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6893  Z= 0.245
  Angle     :  0.606   6.979   9302  Z= 0.321
  Chirality :  0.042   0.182   1029
  Planarity :  0.005   0.080   1206
  Dihedral  :  4.953  21.699    938
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  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: -1.65 (0.28), residues: 836
  helix: -0.06 (0.25), residues: 422
  sheet: -2.01 (0.55), residues: 91
  loop : -2.14 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP C  37 
 HIS   0.007   0.001   HIS A 492 
 PHE   0.022   0.002   PHE A 552 
 TYR   0.018   0.002   TYR A 192 
 ARG   0.010   0.001   ARG A 661 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LEU cc_start: 0.9289 (tp) cc_final: 0.8804 (mt)
REVERT: A  344 HIS cc_start: 0.8403 (p-80) cc_final: 0.8123 (p-80)
REVERT: A  392 TYR cc_start: 0.8446 (m-80) cc_final: 0.8210 (m-10)
REVERT: A  484 GLU cc_start: 0.8286 (pp20) cc_final: 0.8001 (tm-30)
REVERT: A  570 CYS cc_start: 0.7546 (m) cc_final: 0.7302 (m)
REVERT: A  602 PHE cc_start: 0.8206 (p90) cc_final: 0.7364 (p90)
REVERT: A  618 GLU cc_start: 0.8583 (pp20) cc_final: 0.8113 (pp20)
REVERT: A  641 GLU cc_start: 0.8565 (pt0) cc_final: 0.7990 (pt0)
REVERT: A  667 MET cc_start: 0.8462 (tpt) cc_final: 0.7995 (tpp)
REVERT: A  697 ILE cc_start: 0.9010 (mt) cc_final: 0.8760 (mt)
REVERT: A  702 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8676 (tp30)
REVERT: A  707 HIS cc_start: 0.7426 (m90) cc_final: 0.5844 (m170)
REVERT: A  755 ASN cc_start: 0.9078 (m110) cc_final: 0.8739 (m110)
REVERT: A  803 ARG cc_start: 0.8440 (mmt180) cc_final: 0.7735 (tpt170)
REVERT: B   32 ASP cc_start: 0.7462 (p0) cc_final: 0.6998 (p0)
REVERT: B   98 CYS cc_start: 0.7787 (t) cc_final: 0.7131 (t)
REVERT: B  124 THR cc_start: 0.8796 (m) cc_final: 0.8472 (p)
REVERT: C   67 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7300 (mtp-110)
REVERT: C   79 LEU cc_start: 0.8231 (tp) cc_final: 0.7805 (tp)
REVERT: C   95 TYR cc_start: 0.8375 (m-80) cc_final: 0.7989 (m-80)
REVERT: C   96 CYS cc_start: 0.5596 (t) cc_final: 0.4438 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1971
  time to fit residues: 47.3715
Evaluate side-chains
  145 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0770
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 48 optimal weight:    0.5980
   chunk 73 optimal weight:   30.0000
   chunk 52 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.5342

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

Flipped N/Q/H residues before XYZ refinement:
A 193 ASN
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 814 GLN
B  79 ASN
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.075728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.055991 restraints weight = 25339.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.057789 restraints weight = 15520.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.058995 restraints weight = 11109.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6893  Z= 0.219
  Angle     :  0.578   5.854   9302  Z= 0.308
  Chirality :  0.040   0.132   1029
  Planarity :  0.005   0.060   1206
  Dihedral  :  4.777  22.762    938
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.94 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.28 (0.29), residues: 836
  helix:  0.22 (0.26), residues: 422
  sheet: -1.78 (0.55), residues: 91
  loop : -1.96 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C  37 
 HIS   0.004   0.001   HIS A 492 
 PHE   0.019   0.001   PHE A 552 
 TYR   0.017   0.002   TYR A 192 
 ARG   0.007   0.001   ARG C  20 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LEU cc_start: 0.9008 (tp) cc_final: 0.8766 (mt)
REVERT: A  392 TYR cc_start: 0.8481 (m-80) cc_final: 0.8225 (m-10)
REVERT: A  484 GLU cc_start: 0.8373 (pp20) cc_final: 0.7973 (tm-30)
REVERT: A  570 CYS cc_start: 0.7804 (m) cc_final: 0.7393 (m)
REVERT: A  602 PHE cc_start: 0.8192 (p90) cc_final: 0.7250 (p90)
REVERT: A  618 GLU cc_start: 0.8630 (pp20) cc_final: 0.8157 (pp20)
REVERT: A  641 GLU cc_start: 0.8656 (pt0) cc_final: 0.8081 (pt0)
REVERT: A  667 MET cc_start: 0.8474 (tpt) cc_final: 0.8031 (tpp)
REVERT: A  697 ILE cc_start: 0.9001 (mt) cc_final: 0.8770 (mt)
REVERT: A  702 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8786 (tp30)
REVERT: A  755 ASN cc_start: 0.9090 (m110) cc_final: 0.8741 (m110)
REVERT: B   82 TYR cc_start: 0.6271 (m-10) cc_final: 0.5583 (m-10)
REVERT: B   85 MET cc_start: 0.8685 (mtt) cc_final: 0.8086 (mtm)
REVERT: B  124 THR cc_start: 0.8802 (m) cc_final: 0.8519 (p)
REVERT: C   30 PHE cc_start: 0.8719 (t80) cc_final: 0.8262 (t80)
REVERT: C   35 MET cc_start: 0.8736 (mmm) cc_final: 0.8239 (mmm)
REVERT: C   67 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7475 (mtp-110)
REVERT: C   79 LEU cc_start: 0.8186 (tp) cc_final: 0.7806 (tp)
REVERT: C   90 ASP cc_start: 0.7380 (p0) cc_final: 0.6900 (p0)
REVERT: C   94 TYR cc_start: 0.7762 (m-80) cc_final: 0.7172 (m-80)
REVERT: C   96 CYS cc_start: 0.5571 (t) cc_final: 0.4808 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1982
  time to fit residues: 46.5769
Evaluate side-chains
  140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0870
   chunk 44 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 343 GLN
A 489 HIS
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.077900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.058073 restraints weight = 24936.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.059729 restraints weight = 16043.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.060951 restraints weight = 11856.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6893  Z= 0.155
  Angle     :  0.551   6.460   9302  Z= 0.289
  Chirality :  0.040   0.131   1029
  Planarity :  0.004   0.045   1206
  Dihedral  :  4.530  22.045    938
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  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: -1.05 (0.29), residues: 836
  helix:  0.39 (0.26), residues: 425
  sheet: -1.60 (0.56), residues: 89
  loop : -1.87 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  37 
 HIS   0.002   0.001   HIS A 492 
 PHE   0.017   0.001   PHE A 552 
 TYR   0.015   0.001   TYR A 192 
 ARG   0.006   0.000   ARG C  20 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LEU cc_start: 0.8969 (tp) cc_final: 0.8757 (mt)
REVERT: A  392 TYR cc_start: 0.8425 (m-80) cc_final: 0.8153 (m-10)
REVERT: A  484 GLU cc_start: 0.8348 (pp20) cc_final: 0.7861 (tm-30)
REVERT: A  570 CYS cc_start: 0.7729 (m) cc_final: 0.7075 (m)
REVERT: A  602 PHE cc_start: 0.8050 (p90) cc_final: 0.7087 (p90)
REVERT: A  618 GLU cc_start: 0.8570 (pp20) cc_final: 0.8070 (pp20)
REVERT: A  641 GLU cc_start: 0.8627 (pt0) cc_final: 0.8126 (pt0)
REVERT: A  667 MET cc_start: 0.8342 (tpt) cc_final: 0.7922 (tpp)
REVERT: A  697 ILE cc_start: 0.8980 (mt) cc_final: 0.8740 (mt)
REVERT: A  702 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8796 (tp30)
REVERT: A  754 MET cc_start: 0.8944 (tpt) cc_final: 0.8513 (tpt)
REVERT: A  755 ASN cc_start: 0.9060 (m110) cc_final: 0.8699 (m110)
REVERT: A  814 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8668 (tm-30)
REVERT: B   32 ASP cc_start: 0.7255 (p0) cc_final: 0.6882 (p0)
REVERT: B   38 TRP cc_start: 0.7524 (m100) cc_final: 0.6891 (m100)
REVERT: B   85 MET cc_start: 0.8751 (mtt) cc_final: 0.8543 (mtm)
REVERT: B   98 CYS cc_start: 0.7925 (t) cc_final: 0.6101 (t)
REVERT: B  107 LEU cc_start: 0.8491 (mp) cc_final: 0.8276 (mp)
REVERT: B  124 THR cc_start: 0.8721 (m) cc_final: 0.8473 (p)
REVERT: C   30 PHE cc_start: 0.8724 (t80) cc_final: 0.8206 (t80)
REVERT: C   53 ASN cc_start: 0.7475 (m110) cc_final: 0.7272 (m-40)
REVERT: C   79 LEU cc_start: 0.7918 (tp) cc_final: 0.7590 (tp)
REVERT: C   95 TYR cc_start: 0.8190 (m-80) cc_final: 0.7896 (m-10)
REVERT: C   96 CYS cc_start: 0.4902 (t) cc_final: 0.3415 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1896
  time to fit residues: 47.5224
Evaluate side-chains
  147 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 78 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 4 optimal weight:    0.4980
   chunk 39 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
C  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.077742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.059666 restraints weight = 25238.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.060020 restraints weight = 16350.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.060809 restraints weight = 13630.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6893  Z= 0.160
  Angle     :  0.560   7.763   9302  Z= 0.294
  Chirality :  0.040   0.128   1029
  Planarity :  0.004   0.037   1206
  Dihedral  :  4.417  21.205    938
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  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: -0.82 (0.29), residues: 836
  helix:  0.60 (0.26), residues: 421
  sheet: -1.67 (0.56), residues: 89
  loop : -1.69 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C  37 
 HIS   0.002   0.001   HIS A 492 
 PHE   0.021   0.001   PHE A 349 
 TYR   0.015   0.001   TYR A 192 
 ARG   0.005   0.000   ARG A 594 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LEU cc_start: 0.8957 (tp) cc_final: 0.8741 (mt)
REVERT: A  392 TYR cc_start: 0.8372 (m-80) cc_final: 0.8114 (m-10)
REVERT: A  484 GLU cc_start: 0.8356 (pp20) cc_final: 0.7802 (tm-30)
REVERT: A  570 CYS cc_start: 0.7782 (m) cc_final: 0.6894 (m)
REVERT: A  618 GLU cc_start: 0.8552 (pp20) cc_final: 0.8069 (pp20)
REVERT: A  641 GLU cc_start: 0.8546 (pt0) cc_final: 0.8070 (pt0)
REVERT: A  667 MET cc_start: 0.8133 (tpt) cc_final: 0.7763 (tpp)
REVERT: A  697 ILE cc_start: 0.8977 (mt) cc_final: 0.8668 (mt)
REVERT: A  702 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8165 (tp30)
REVERT: A  707 HIS cc_start: 0.7367 (m90) cc_final: 0.5181 (m170)
REVERT: A  746 LEU cc_start: 0.9282 (mt) cc_final: 0.9044 (mt)
REVERT: A  755 ASN cc_start: 0.9023 (m110) cc_final: 0.8647 (m110)
REVERT: A  814 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8626 (tm-30)
REVERT: B  107 LEU cc_start: 0.8447 (mp) cc_final: 0.8214 (mp)
REVERT: B  124 THR cc_start: 0.8745 (m) cc_final: 0.8527 (p)
REVERT: C   30 PHE cc_start: 0.8675 (t80) cc_final: 0.8203 (t80)
REVERT: C   35 MET cc_start: 0.8726 (mmm) cc_final: 0.8162 (mmm)
REVERT: C   79 LEU cc_start: 0.8120 (tp) cc_final: 0.7756 (tp)
REVERT: C   96 CYS cc_start: 0.5256 (t) cc_final: 0.4364 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1928
  time to fit residues: 45.9156
Evaluate side-chains
  142 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 62 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0970
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.078233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.058310 restraints weight = 24964.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.059680 restraints weight = 16229.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.060965 restraints weight = 12539.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6893  Z= 0.157
  Angle     :  0.565   7.055   9302  Z= 0.297
  Chirality :  0.040   0.141   1029
  Planarity :  0.004   0.036   1206
  Dihedral  :  4.317  20.492    938
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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: -0.69 (0.29), residues: 836
  helix:  0.64 (0.26), residues: 427
  sheet: -1.50 (0.58), residues: 84
  loop : -1.61 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP C  37 
 HIS   0.002   0.000   HIS A 492 
 PHE   0.021   0.001   PHE A 712 
 TYR   0.014   0.001   TYR A 192 
 ARG   0.005   0.000   ARG C  20 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.756 
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  293 LEU cc_start: 0.8957 (tp) cc_final: 0.8724 (mt)
REVERT: A  392 TYR cc_start: 0.8444 (m-80) cc_final: 0.8162 (m-10)
REVERT: A  394 ILE cc_start: 0.9432 (pt) cc_final: 0.9217 (pt)
REVERT: A  570 CYS cc_start: 0.7689 (m) cc_final: 0.6869 (m)
REVERT: A  602 PHE cc_start: 0.8084 (p90) cc_final: 0.7127 (p90)
REVERT: A  618 GLU cc_start: 0.8599 (pp20) cc_final: 0.8049 (pp20)
REVERT: A  638 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7763 (tptt)
REVERT: A  641 GLU cc_start: 0.8511 (pt0) cc_final: 0.7997 (pt0)
REVERT: A  667 MET cc_start: 0.8278 (tpt) cc_final: 0.7876 (tpp)
REVERT: A  697 ILE cc_start: 0.8905 (mt) cc_final: 0.8673 (mt)
REVERT: A  702 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8264 (tp30)
REVERT: A  707 HIS cc_start: 0.7520 (m90) cc_final: 0.5159 (m170)
REVERT: A  742 ILE cc_start: 0.8044 (mm) cc_final: 0.7761 (mm)
REVERT: A  755 ASN cc_start: 0.9112 (m110) cc_final: 0.8723 (m110)
REVERT: A  804 MET cc_start: 0.4975 (ptm) cc_final: 0.4652 (ppp)
REVERT: A  814 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8663 (tm-30)
REVERT: B   32 ASP cc_start: 0.7374 (p0) cc_final: 0.7147 (p0)
REVERT: B  107 LEU cc_start: 0.8385 (mp) cc_final: 0.8176 (mp)
REVERT: B  124 THR cc_start: 0.8703 (m) cc_final: 0.8500 (p)
REVERT: C    5 LEU cc_start: 0.7738 (mm) cc_final: 0.7434 (mt)
REVERT: C   30 PHE cc_start: 0.8698 (t80) cc_final: 0.8086 (t80)
REVERT: C   35 MET cc_start: 0.8723 (mmm) cc_final: 0.8127 (mmm)
REVERT: C   37 TRP cc_start: 0.5376 (m100) cc_final: 0.5063 (m100)
REVERT: C   79 LEU cc_start: 0.8156 (tp) cc_final: 0.7629 (tp)
REVERT: C   85 ARG cc_start: 0.7544 (tmm160) cc_final: 0.7248 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2012
  time to fit residues: 47.8607
Evaluate side-chains
  141 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.076829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.057155 restraints weight = 25345.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.058796 restraints weight = 16394.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.059864 restraints weight = 12160.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6893  Z= 0.225
  Angle     :  0.615   6.877   9302  Z= 0.324
  Chirality :  0.042   0.130   1029
  Planarity :  0.004   0.035   1206
  Dihedral  :  4.563  21.018    938
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  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: -0.76 (0.29), residues: 836
  helix:  0.57 (0.26), residues: 427
  sheet: -1.55 (0.56), residues: 89
  loop : -1.61 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C  37 
 HIS   0.010   0.001   HIS A 358 
 PHE   0.022   0.002   PHE A 552 
 TYR   0.021   0.002   TYR A 630 
 ARG   0.004   0.000   ARG C  20 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LEU cc_start: 0.8970 (tp) cc_final: 0.8725 (mt)
REVERT: A  392 TYR cc_start: 0.8447 (m-80) cc_final: 0.8154 (m-10)
REVERT: A  504 LEU cc_start: 0.8190 (mt) cc_final: 0.7968 (mt)
REVERT: A  570 CYS cc_start: 0.7713 (m) cc_final: 0.7088 (m)
REVERT: A  602 PHE cc_start: 0.8103 (p90) cc_final: 0.7126 (p90)
REVERT: A  618 GLU cc_start: 0.8594 (pp20) cc_final: 0.8109 (pp20)
REVERT: A  641 GLU cc_start: 0.8548 (pt0) cc_final: 0.8096 (pt0)
REVERT: A  667 MET cc_start: 0.8324 (tpt) cc_final: 0.7932 (tpp)
REVERT: A  697 ILE cc_start: 0.8939 (mt) cc_final: 0.8673 (mt)
REVERT: A  702 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8817 (mm-30)
REVERT: A  710 LEU cc_start: 0.8539 (mp) cc_final: 0.8283 (mp)
REVERT: A  746 LEU cc_start: 0.9323 (mt) cc_final: 0.9100 (mt)
REVERT: A  755 ASN cc_start: 0.9123 (m110) cc_final: 0.8751 (m110)
REVERT: A  803 ARG cc_start: 0.8149 (mmt180) cc_final: 0.7418 (tpt170)
REVERT: A  814 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8689 (tm-30)
REVERT: A  819 MET cc_start: 0.8076 (ptp) cc_final: 0.7856 (ptm)
REVERT: B   38 TRP cc_start: 0.7588 (m100) cc_final: 0.6898 (m100)
REVERT: B   98 CYS cc_start: 0.7823 (t) cc_final: 0.5655 (t)
REVERT: B  107 LEU cc_start: 0.8541 (mp) cc_final: 0.8294 (mp)
REVERT: C    5 LEU cc_start: 0.7814 (mm) cc_final: 0.7478 (mt)
REVERT: C   30 PHE cc_start: 0.8687 (t80) cc_final: 0.8131 (t80)
REVERT: C   35 MET cc_start: 0.8694 (mmm) cc_final: 0.8061 (mmm)
REVERT: C   37 TRP cc_start: 0.5508 (m100) cc_final: 0.4910 (m100)
REVERT: C   79 LEU cc_start: 0.8186 (tp) cc_final: 0.7542 (tp)
REVERT: C   85 ARG cc_start: 0.7531 (tmm160) cc_final: 0.7213 (ptm-80)
REVERT: C   96 CYS cc_start: 0.5196 (t) cc_final: 0.4643 (t)
REVERT: C  106 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7554 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2126
  time to fit residues: 48.6080
Evaluate side-chains
  137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0980
   chunk 40 optimal weight:    0.4980
   chunk 70 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0770
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.3338

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN
A 358 HIS
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
C  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.078901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.059133 restraints weight = 25058.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.060875 restraints weight = 16266.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.061980 restraints weight = 12012.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6893  Z= 0.154
  Angle     :  0.595   7.498   9302  Z= 0.310
  Chirality :  0.040   0.140   1029
  Planarity :  0.004   0.036   1206
  Dihedral  :  4.331  21.066    938
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -0.55 (0.29), residues: 836
  helix:  0.70 (0.26), residues: 427
  sheet: -1.44 (0.52), residues: 94
  loop : -1.44 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP C  37 
 HIS   0.010   0.001   HIS A 358 
 PHE   0.026   0.001   PHE A 712 
 TYR   0.022   0.001   TYR A 761 
 ARG   0.005   0.000   ARG C  20 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.725 
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  251 MET cc_start: 0.8585 (tpp) cc_final: 0.7957 (tpp)
REVERT: A  293 LEU cc_start: 0.8930 (tp) cc_final: 0.8706 (mt)
REVERT: A  392 TYR cc_start: 0.8474 (m-80) cc_final: 0.8201 (m-10)
REVERT: A  570 CYS cc_start: 0.7590 (m) cc_final: 0.6985 (m)
REVERT: A  602 PHE cc_start: 0.8057 (p90) cc_final: 0.7057 (p90)
REVERT: A  618 GLU cc_start: 0.8609 (pp20) cc_final: 0.8090 (pp20)
REVERT: A  641 GLU cc_start: 0.8498 (pt0) cc_final: 0.8044 (pt0)
REVERT: A  667 MET cc_start: 0.8264 (tpt) cc_final: 0.7877 (tpp)
REVERT: A  697 ILE cc_start: 0.8906 (mt) cc_final: 0.8670 (mt)
REVERT: A  746 LEU cc_start: 0.9310 (mt) cc_final: 0.9064 (mt)
REVERT: A  755 ASN cc_start: 0.9081 (m110) cc_final: 0.8771 (m110)
REVERT: A  804 MET cc_start: 0.5058 (ptm) cc_final: 0.4666 (ppp)
REVERT: B   38 TRP cc_start: 0.7550 (m100) cc_final: 0.7055 (m100)
REVERT: B   48 GLU cc_start: 0.5827 (mt-10) cc_final: 0.5576 (mt-10)
REVERT: B   98 CYS cc_start: 0.7943 (t) cc_final: 0.6124 (t)
REVERT: B  107 LEU cc_start: 0.8467 (mp) cc_final: 0.8176 (mp)
REVERT: C    5 LEU cc_start: 0.7790 (mm) cc_final: 0.7310 (mt)
REVERT: C   30 PHE cc_start: 0.8701 (t80) cc_final: 0.8207 (t80)
REVERT: C   37 TRP cc_start: 0.5528 (m100) cc_final: 0.5293 (m100)
REVERT: C   74 ASN cc_start: 0.7495 (m-40) cc_final: 0.7154 (m-40)
REVERT: C   79 LEU cc_start: 0.8201 (tp) cc_final: 0.7520 (tp)
REVERT: C   85 ARG cc_start: 0.7500 (tmm160) cc_final: 0.7118 (ptm-80)
REVERT: C   96 CYS cc_start: 0.5341 (t) cc_final: 0.4531 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2160
  time to fit residues: 52.2294
Evaluate side-chains
  139 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0770
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 193 ASN
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 343 GLN
A 358 HIS
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 GLN
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.079007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.059054 restraints weight = 25303.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.060821 restraints weight = 16009.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.062063 restraints weight = 11715.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.4272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6893  Z= 0.156
  Angle     :  0.587   7.130   9302  Z= 0.307
  Chirality :  0.040   0.137   1029
  Planarity :  0.004   0.035   1206
  Dihedral  :  4.318  20.371    938
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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: -0.47 (0.29), residues: 836
  helix:  0.70 (0.26), residues: 429
  sheet: -1.27 (0.53), residues: 94
  loop : -1.35 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C  37 
 HIS   0.008   0.001   HIS A 358 
 PHE   0.025   0.002   PHE A 349 
 TYR   0.017   0.001   TYR C  80 
 ARG   0.004   0.000   ARG C  20 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.726 
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  293 LEU cc_start: 0.8947 (tp) cc_final: 0.8707 (mt)
REVERT: A  392 TYR cc_start: 0.8483 (m-80) cc_final: 0.8213 (m-10)
REVERT: A  570 CYS cc_start: 0.7784 (m) cc_final: 0.7013 (m)
REVERT: A  602 PHE cc_start: 0.8116 (p90) cc_final: 0.7024 (p90)
REVERT: A  618 GLU cc_start: 0.8583 (pp20) cc_final: 0.8103 (pp20)
REVERT: A  641 GLU cc_start: 0.8486 (pt0) cc_final: 0.8052 (pt0)
REVERT: A  667 MET cc_start: 0.8361 (tpt) cc_final: 0.7951 (tpp)
REVERT: A  707 HIS cc_start: 0.7064 (m90) cc_final: 0.6327 (m170)
REVERT: A  743 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7909 (mtt-85)
REVERT: A  746 LEU cc_start: 0.9317 (mt) cc_final: 0.9069 (mt)
REVERT: A  755 ASN cc_start: 0.9061 (m110) cc_final: 0.8781 (m110)
REVERT: A  803 ARG cc_start: 0.7899 (mmt180) cc_final: 0.7053 (tpt170)
REVERT: B   85 MET cc_start: 0.8486 (mtt) cc_final: 0.8281 (mtm)
REVERT: C    5 LEU cc_start: 0.7766 (mm) cc_final: 0.7285 (mt)
REVERT: C   30 PHE cc_start: 0.8701 (t80) cc_final: 0.8220 (t80)
REVERT: C   74 ASN cc_start: 0.7640 (m-40) cc_final: 0.7201 (m-40)
REVERT: C   79 LEU cc_start: 0.8222 (tp) cc_final: 0.7452 (tp)
REVERT: C   85 ARG cc_start: 0.7605 (tmm160) cc_final: 0.7283 (ptm-80)
REVERT: C   96 CYS cc_start: 0.5352 (t) cc_final: 0.4448 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2043
  time to fit residues: 46.8050
Evaluate side-chains
  141 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 358 HIS
** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN
C  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.079189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.059018 restraints weight = 25438.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.060774 restraints weight = 16182.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.061993 restraints weight = 11925.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6893  Z= 0.162
  Angle     :  0.608   7.907   9302  Z= 0.313
  Chirality :  0.040   0.137   1029
  Planarity :  0.004   0.034   1206
  Dihedral  :  4.307  20.416    938
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -0.34 (0.29), residues: 836
  helix:  0.81 (0.26), residues: 429
  sheet: -1.16 (0.54), residues: 94
  loop : -1.31 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP C  37 
 HIS   0.009   0.001   HIS A 358 
 PHE   0.027   0.001   PHE A 712 
 TYR   0.014   0.001   TYR A 761 
 ARG   0.004   0.000   ARG C  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2753.62 seconds
wall clock time: 48 minutes 17.58 seconds (2897.58 seconds total)