Starting phenix.real_space_refine
on Tue Mar  3 15:48:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zox_14849/03_2026/7zox_14849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zox_14849/03_2026/7zox_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_2026/7zox_14849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zox_14849/03_2026/7zox_14849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zox_14849/03_2026/7zox_14849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zox_14849/03_2026/7zox_14849.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.37, per 1000 atoms: 0.20
  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: 0.82
  Conformation dependent library (CDL) restraints added in 247.2 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: 0.14
  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: 0.89

  Time building geometry restraints manager: 0.98 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:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.960
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.600
-------------------------------------------------------------------------------
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   6894  Z= 0.228
  Angle     :  0.722   6.641   9304  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 : 17.06
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 377 
 TYR   0.018   0.002   TYR A 192 
 PHE   0.023   0.002   PHE A 552 
 TRP   0.011   0.002   TRP A 416 
 HIS   0.007   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 6893)
  covalent geometry    : angle       0.72172 ( 9302)
  SS BOND              : bond        0.00531 (    1)
  SS BOND              : angle       1.72317 (    2)
  hydrogen bonds       : bond        0.13820 (  353)
  hydrogen bonds       : angle       6.73920 (  999)

*********************** 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  : 0.246 
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: 0.8105 (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: 0.8142 (m100) cc_final: 0.7277 (m100)
REVERT: A  344 HIS cc_start: 0.8571 (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: 0.8260 (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: 0.8106 (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: 0.0959
  time to fit residues: 23.9785
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  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 403 ASN
A 725 GLN
A 745 ASN
A 814 GLN
B  46 GLN
B  79 ASN
C  53 ASN
C  77 ASN
C 115 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.074118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.054419 restraints weight = 25722.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.056125 restraints weight = 16182.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.057211 restraints weight = 11868.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.058076 restraints weight = 9628.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.058534 restraints weight = 8257.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6894  Z= 0.200
  Angle     :  0.635   6.758   9304  Z= 0.338
  Chirality :  0.042   0.132   1029
  Planarity :  0.005   0.056   1206
  Dihedral  :  5.381  23.349    938
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.93 %
    Favored  : 92.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.26), residues: 836
  helix: -1.00 (0.23), residues: 421
  sheet: -2.59 (0.50), residues: 96
  loop : -2.52 (0.30), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  67 
 TYR   0.026   0.002   TYR A 262 
 PHE   0.017   0.002   PHE A 796 
 TRP   0.018   0.002   TRP C  37 
 HIS   0.006   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6893)
  covalent geometry    : angle       0.63408 ( 9302)
  SS BOND              : bond        0.00609 (    1)
  SS BOND              : angle       2.28698 (    2)
  hydrogen bonds       : bond        0.04234 (  353)
  hydrogen bonds       : angle       5.46377 (  999)

*********************** 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
  181 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.204 
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: 0.9338 (tp) cc_final: 0.8859 (mt)
REVERT: A  320 TRP cc_start: 0.8355 (m100) cc_final: 0.7121 (m100)
REVERT: A  344 HIS cc_start: 0.8421 (p-80) cc_final: 0.8121 (p-80)
REVERT: A  349 PHE cc_start: 0.8600 (t80) cc_final: 0.8353 (t80)
REVERT: A  392 TYR cc_start: 0.8341 (m-80) cc_final: 0.8019 (m-10)
REVERT: A  484 GLU cc_start: 0.8283 (pp20) cc_final: 0.8064 (tm-30)
REVERT: A  504 LEU cc_start: 0.8298 (mt) cc_final: 0.8079 (mt)
REVERT: A  602 PHE cc_start: 0.8126 (p90) cc_final: 0.7418 (p90)
REVERT: A  641 GLU cc_start: 0.8594 (pt0) cc_final: 0.8079 (pt0)
REVERT: A  667 MET cc_start: 0.8588 (tpt) cc_final: 0.8117 (tpp)
REVERT: A  702 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8818 (tp30)
REVERT: A  707 HIS cc_start: 0.7488 (m90) cc_final: 0.6427 (m-70)
REVERT: A  716 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8760 (mm-30)
REVERT: A  754 MET cc_start: 0.8979 (tpt) cc_final: 0.8425 (tpt)
REVERT: B   15 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7918 (mm-40)
REVERT: B   55 LYS cc_start: 0.8057 (ptmm) cc_final: 0.7745 (ttpp)
REVERT: B   98 CYS cc_start: 0.7677 (t) cc_final: 0.6977 (t)
REVERT: C   67 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7362 (mtp-110)
REVERT: C   79 LEU cc_start: 0.8388 (tp) cc_final: 0.7683 (tp)
REVERT: C   90 ASP cc_start: 0.7843 (p0) cc_final: 0.7416 (p0)
REVERT: C   96 CYS cc_start: 0.5734 (t) cc_final: 0.3043 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 181
  average time/residue: 0.0805
  time to fit residues: 19.1567
Evaluate side-chains
  141 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 457 ASN
** 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 = 0.3253 r_free = 0.3253 target = 0.073990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.054830 restraints weight = 25276.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.056589 restraints weight = 15486.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.057796 restraints weight = 11128.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.058544 restraints weight = 8825.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.059129 restraints weight = 7609.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6894  Z= 0.212
  Angle     :  0.646   8.433   9304  Z= 0.343
  Chirality :  0.042   0.131   1029
  Planarity :  0.005   0.052   1206
  Dihedral  :  5.302  23.672    938
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.28), residues: 836
  helix: -0.39 (0.25), residues: 421
  sheet: -2.22 (0.53), residues: 96
  loop : -2.26 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  72 
 TYR   0.030   0.002   TYR A 317 
 PHE   0.022   0.002   PHE A 552 
 TRP   0.036   0.002   TRP C  37 
 HIS   0.009   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 6893)
  covalent geometry    : angle       0.64474 ( 9302)
  SS BOND              : bond        0.01773 (    1)
  SS BOND              : angle       2.93171 (    2)
  hydrogen bonds       : bond        0.04172 (  353)
  hydrogen bonds       : angle       5.27180 (  999)

*********************** 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
  185 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.259 
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: 0.9041 (tp) cc_final: 0.8801 (mt)
REVERT: A  320 TRP cc_start: 0.8319 (m100) cc_final: 0.7123 (m100)
REVERT: A  344 HIS cc_start: 0.8430 (p-80) cc_final: 0.8122 (p-80)
REVERT: A  349 PHE cc_start: 0.8640 (t80) cc_final: 0.8408 (t80)
REVERT: A  392 TYR cc_start: 0.8371 (m-80) cc_final: 0.7933 (m-10)
REVERT: A  484 GLU cc_start: 0.8378 (pp20) cc_final: 0.8092 (tm-30)
REVERT: A  504 LEU cc_start: 0.8357 (mt) cc_final: 0.8146 (mt)
REVERT: A  602 PHE cc_start: 0.8091 (p90) cc_final: 0.7253 (p90)
REVERT: A  641 GLU cc_start: 0.8619 (pt0) cc_final: 0.8068 (pt0)
REVERT: A  667 MET cc_start: 0.8612 (tpt) cc_final: 0.8151 (tpp)
REVERT: A  702 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8737 (tp30)
REVERT: A  707 HIS cc_start: 0.7604 (m90) cc_final: 0.5936 (m170)
REVERT: A  755 ASN cc_start: 0.9090 (m110) cc_final: 0.8851 (m110)
REVERT: A  803 ARG cc_start: 0.8627 (mmt180) cc_final: 0.7862 (tpt170)
REVERT: A  814 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8618 (tm-30)
REVERT: B   32 ASP cc_start: 0.7542 (p0) cc_final: 0.7031 (p0)
REVERT: B   82 TYR cc_start: 0.6589 (m-10) cc_final: 0.6105 (m-10)
REVERT: C   35 MET cc_start: 0.8686 (mmm) cc_final: 0.8094 (mmm)
REVERT: C   67 ARG cc_start: 0.7631 (mtm110) cc_final: 0.7336 (mtp-110)
REVERT: C   79 LEU cc_start: 0.8255 (tp) cc_final: 0.7846 (tp)
REVERT: C   82 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7515 (tp-100)
REVERT: C   95 TYR cc_start: 0.8354 (m-80) cc_final: 0.7998 (m-80)
REVERT: C   96 CYS cc_start: 0.5697 (t) cc_final: 0.4509 (t)
REVERT: C   99 MET cc_start: 0.8086 (tmm) cc_final: 0.7865 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0859
  time to fit residues: 20.7524
Evaluate side-chains
  135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 73 optimal weight:   30.0000
   chunk 27 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 453 HIS
A 814 GLN
B  79 ASN
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.076824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.057444 restraints weight = 25347.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.059103 restraints weight = 16586.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.060218 restraints weight = 12352.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.061016 restraints weight = 10081.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.061515 restraints weight = 8737.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6894  Z= 0.129
  Angle     :  0.565   5.960   9304  Z= 0.301
  Chirality :  0.040   0.127   1029
  Planarity :  0.004   0.047   1206
  Dihedral  :  4.871  22.274    938
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.29), residues: 836
  helix:  0.17 (0.26), residues: 423
  sheet: -1.81 (0.54), residues: 91
  loop : -2.03 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  20 
 TYR   0.021   0.002   TYR A 317 
 PHE   0.018   0.001   PHE A 552 
 TRP   0.013   0.001   TRP C  37 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6893)
  covalent geometry    : angle       0.56363 ( 9302)
  SS BOND              : bond        0.00450 (    1)
  SS BOND              : angle       2.36078 (    2)
  hydrogen bonds       : bond        0.03501 (  353)
  hydrogen bonds       : angle       4.80530 (  999)

*********************** 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
  187 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.197 
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: 0.8962 (tp) cc_final: 0.8757 (mt)
REVERT: A  484 GLU cc_start: 0.8305 (pp20) cc_final: 0.7873 (tm-30)
REVERT: A  570 CYS cc_start: 0.7622 (m) cc_final: 0.7152 (m)
REVERT: A  641 GLU cc_start: 0.8495 (pt0) cc_final: 0.8035 (pt0)
REVERT: A  667 MET cc_start: 0.8407 (tpt) cc_final: 0.7969 (tpp)
REVERT: A  697 ILE cc_start: 0.8938 (mt) cc_final: 0.8690 (mt)
REVERT: A  702 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8361 (tp30)
REVERT: A  707 HIS cc_start: 0.7457 (m90) cc_final: 0.5807 (m-70)
REVERT: A  755 ASN cc_start: 0.9022 (m110) cc_final: 0.8707 (m110)
REVERT: A  803 ARG cc_start: 0.8491 (mmt180) cc_final: 0.7830 (tpt170)
REVERT: A  814 GLN cc_start: 0.8967 (tm130) cc_final: 0.8661 (tm-30)
REVERT: B   32 ASP cc_start: 0.7352 (p0) cc_final: 0.7125 (p0)
REVERT: B   38 TRP cc_start: 0.7465 (m100) cc_final: 0.6787 (m100)
REVERT: B   98 CYS cc_start: 0.7816 (t) cc_final: 0.5959 (t)
REVERT: B  124 THR cc_start: 0.8678 (m) cc_final: 0.8366 (p)
REVERT: C   35 MET cc_start: 0.8631 (mmm) cc_final: 0.8065 (mmm)
REVERT: C   67 ARG cc_start: 0.7506 (mtm110) cc_final: 0.7278 (mtp-110)
REVERT: C   79 LEU cc_start: 0.7739 (tp) cc_final: 0.7504 (tp)
REVERT: C   95 TYR cc_start: 0.8376 (m-80) cc_final: 0.8091 (m-80)
REVERT: C   96 CYS cc_start: 0.4721 (t) cc_final: 0.3461 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0776
  time to fit residues: 19.2550
Evaluate side-chains
  138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.0000
   chunk 6 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0770
   overall best weight:    0.5142

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

Flipped N/Q/H residues before XYZ refinement:
A 489 HIS
C  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.078004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.058315 restraints weight = 25477.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.060050 restraints weight = 16115.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.061249 restraints weight = 11800.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.062096 restraints weight = 9511.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.062629 restraints weight = 8193.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6894  Z= 0.104
  Angle     :  0.559   6.413   9304  Z= 0.294
  Chirality :  0.040   0.127   1029
  Planarity :  0.004   0.049   1206
  Dihedral  :  4.486  20.905    938
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.29), residues: 836
  helix:  0.46 (0.26), residues: 421
  sheet: -1.63 (0.54), residues: 91
  loop : -1.75 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  20 
 TYR   0.020   0.002   TYR A 630 
 PHE   0.023   0.002   PHE A 454 
 TRP   0.034   0.002   TRP C  37 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6893)
  covalent geometry    : angle       0.55836 ( 9302)
  SS BOND              : bond        0.00570 (    1)
  SS BOND              : angle       2.20845 (    2)
  hydrogen bonds       : bond        0.03206 (  353)
  hydrogen bonds       : angle       4.57029 (  999)

*********************** 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
  195 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.7840 (tmm) cc_final: 0.7632 (tmm)
REVERT: A  293 LEU cc_start: 0.8919 (tp) cc_final: 0.8716 (mt)
REVERT: A  394 ILE cc_start: 0.9445 (pt) cc_final: 0.9009 (pt)
REVERT: A  484 GLU cc_start: 0.8322 (pp20) cc_final: 0.7787 (tm-30)
REVERT: A  570 CYS cc_start: 0.7635 (m) cc_final: 0.6890 (m)
REVERT: A  602 PHE cc_start: 0.8268 (p90) cc_final: 0.7273 (p90)
REVERT: A  618 GLU cc_start: 0.8402 (pt0) cc_final: 0.8051 (pp20)
REVERT: A  641 GLU cc_start: 0.8572 (pt0) cc_final: 0.8092 (pt0)
REVERT: A  667 MET cc_start: 0.8378 (tpt) cc_final: 0.7946 (tpp)
REVERT: A  697 ILE cc_start: 0.8922 (mt) cc_final: 0.8684 (mt)
REVERT: A  742 ILE cc_start: 0.7890 (mm) cc_final: 0.7625 (mm)
REVERT: A  754 MET cc_start: 0.8917 (tpt) cc_final: 0.8405 (tpt)
REVERT: A  755 ASN cc_start: 0.9040 (m110) cc_final: 0.8714 (m110)
REVERT: A  803 ARG cc_start: 0.8391 (mmt180) cc_final: 0.7661 (tpt170)
REVERT: A  814 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: B   38 TRP cc_start: 0.7570 (m100) cc_final: 0.6970 (m100)
REVERT: B   98 CYS cc_start: 0.7893 (t) cc_final: 0.6000 (t)
REVERT: B  124 THR cc_start: 0.8691 (m) cc_final: 0.8459 (p)
REVERT: C   30 PHE cc_start: 0.8918 (t80) cc_final: 0.8510 (t80)
REVERT: C   35 MET cc_start: 0.8687 (mmm) cc_final: 0.8132 (mmm)
REVERT: C   53 ASN cc_start: 0.7781 (m110) cc_final: 0.7233 (m-40)
REVERT: C   67 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7171 (mtp-110)
REVERT: C   79 LEU cc_start: 0.8167 (tp) cc_final: 0.7791 (tp)
REVERT: C   96 CYS cc_start: 0.5127 (t) cc_final: 0.3989 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0850
  time to fit residues: 21.6863
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  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0570
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.7504

-------------------------------------------------------------------------------
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 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 = 0.3301 r_free = 0.3301 target = 0.076394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.056674 restraints weight = 25057.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.058414 restraints weight = 15621.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.059619 restraints weight = 11339.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.060405 restraints weight = 9066.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.061009 restraints weight = 7792.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6894  Z= 0.171
  Angle     :  0.618   6.816   9304  Z= 0.329
  Chirality :  0.042   0.225   1029
  Planarity :  0.005   0.086   1206
  Dihedral  :  4.699  20.850    938
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.29), residues: 836
  helix:  0.42 (0.26), residues: 427
  sheet: -1.57 (0.55), residues: 91
  loop : -1.88 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 661 
 TYR   0.020   0.002   TYR A 703 
 PHE   0.021   0.002   PHE A 353 
 TRP   0.037   0.003   TRP C  37 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6893)
  covalent geometry    : angle       0.61816 ( 9302)
  SS BOND              : bond        0.00610 (    1)
  SS BOND              : angle       1.41652 (    2)
  hydrogen bonds       : bond        0.03492 (  353)
  hydrogen bonds       : angle       4.69671 (  999)

*********************** 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
  172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.246 
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: 0.8969 (tp) cc_final: 0.8735 (mt)
REVERT: A  484 GLU cc_start: 0.8361 (pp20) cc_final: 0.7862 (tm-30)
REVERT: A  570 CYS cc_start: 0.7913 (m) cc_final: 0.7379 (m)
REVERT: A  602 PHE cc_start: 0.8191 (p90) cc_final: 0.7272 (p90)
REVERT: A  618 GLU cc_start: 0.8597 (pt0) cc_final: 0.8136 (pp20)
REVERT: A  641 GLU cc_start: 0.8588 (pt0) cc_final: 0.8121 (pt0)
REVERT: A  667 MET cc_start: 0.8502 (tpt) cc_final: 0.8065 (tpp)
REVERT: A  697 ILE cc_start: 0.8968 (mt) cc_final: 0.8718 (mt)
REVERT: A  707 HIS cc_start: 0.6897 (m90) cc_final: 0.6467 (m-70)
REVERT: A  742 ILE cc_start: 0.7985 (mm) cc_final: 0.7629 (mm)
REVERT: A  755 ASN cc_start: 0.9097 (m110) cc_final: 0.8773 (m110)
REVERT: A  814 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8692 (tm-30)
REVERT: B   38 TRP cc_start: 0.7454 (m100) cc_final: 0.6834 (m100)
REVERT: B   98 CYS cc_start: 0.7783 (t) cc_final: 0.5717 (t)
REVERT: B  124 THR cc_start: 0.8766 (m) cc_final: 0.8530 (p)
REVERT: C    5 LEU cc_start: 0.7911 (mm) cc_final: 0.7453 (mt)
REVERT: C   79 LEU cc_start: 0.8222 (tp) cc_final: 0.7741 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0796
  time to fit residues: 18.2667
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  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 52 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0370
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8662

-------------------------------------------------------------------------------
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 = 0.3336 r_free = 0.3336 target = 0.077999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.059669 restraints weight = 25182.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.060405 restraints weight = 17107.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.060935 restraints weight = 12858.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.061392 restraints weight = 11955.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.061482 restraints weight = 11303.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6894  Z= 0.120
  Angle     :  0.594   7.381   9304  Z= 0.313
  Chirality :  0.041   0.170   1029
  Planarity :  0.004   0.057   1206
  Dihedral  :  4.542  23.034    938
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.29), residues: 836
  helix:  0.49 (0.26), residues: 426
  sheet: -1.57 (0.52), residues: 101
  loop : -1.82 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 661 
 TYR   0.016   0.002   TYR C  80 
 PHE   0.023   0.001   PHE A 712 
 TRP   0.039   0.002   TRP C  37 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6893)
  covalent geometry    : angle       0.59292 ( 9302)
  SS BOND              : bond        0.00522 (    1)
  SS BOND              : angle       2.31770 (    2)
  hydrogen bonds       : bond        0.03310 (  353)
  hydrogen bonds       : angle       4.57515 (  999)

*********************** 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
  175 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 MET cc_start: 0.8778 (mmm) cc_final: 0.8536 (mmm)
REVERT: A  293 LEU cc_start: 0.8915 (tp) cc_final: 0.8704 (mt)
REVERT: A  570 CYS cc_start: 0.7618 (m) cc_final: 0.6992 (m)
REVERT: A  602 PHE cc_start: 0.8079 (p90) cc_final: 0.7149 (p90)
REVERT: A  641 GLU cc_start: 0.8485 (pt0) cc_final: 0.8039 (pt0)
REVERT: A  667 MET cc_start: 0.8251 (tpt) cc_final: 0.7892 (tpp)
REVERT: A  697 ILE cc_start: 0.8890 (mt) cc_final: 0.8659 (mt)
REVERT: A  703 TYR cc_start: 0.8528 (t80) cc_final: 0.7826 (t80)
REVERT: A  707 HIS cc_start: 0.6922 (m90) cc_final: 0.6508 (m-70)
REVERT: A  755 ASN cc_start: 0.9035 (m110) cc_final: 0.8751 (m110)
REVERT: A  814 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8761 (tm-30)
REVERT: B   38 TRP cc_start: 0.7515 (m100) cc_final: 0.6977 (m100)
REVERT: B   85 MET cc_start: 0.8676 (mtt) cc_final: 0.8475 (mtm)
REVERT: B   98 CYS cc_start: 0.7904 (t) cc_final: 0.6004 (t)
REVERT: B  107 LEU cc_start: 0.8619 (mp) cc_final: 0.8397 (mp)
REVERT: B  124 THR cc_start: 0.8783 (m) cc_final: 0.8560 (p)
REVERT: C    5 LEU cc_start: 0.7880 (mm) cc_final: 0.7576 (mt)
REVERT: C   30 PHE cc_start: 0.8926 (t80) cc_final: 0.8497 (t80)
REVERT: C   35 MET cc_start: 0.8679 (mmm) cc_final: 0.8115 (mmm)
REVERT: C   46 LEU cc_start: 0.7213 (mp) cc_final: 0.6817 (mp)
REVERT: C   79 LEU cc_start: 0.8090 (tp) cc_final: 0.7671 (tp)
REVERT: C   85 ARG cc_start: 0.7420 (tmm160) cc_final: 0.7143 (ptm-80)
REVERT: C   96 CYS cc_start: 0.5269 (t) cc_final: 0.4956 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0748
  time to fit residues: 17.6933
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  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 37 optimal weight:    0.3980
   chunk 10 optimal weight:    6.9990
   chunk 80 optimal weight:   20.0000
   chunk 78 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3336 r_free = 0.3336 target = 0.078010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.058676 restraints weight = 25342.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.060473 restraints weight = 16027.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.061665 restraints weight = 11567.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.062486 restraints weight = 9253.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.063031 restraints weight = 7915.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6894  Z= 0.123
  Angle     :  0.611   9.497   9304  Z= 0.319
  Chirality :  0.041   0.132   1029
  Planarity :  0.004   0.050   1206
  Dihedral  :  4.503  22.529    938
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.29), residues: 836
  helix:  0.51 (0.26), residues: 425
  sheet: -1.44 (0.54), residues: 94
  loop : -1.69 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 661 
 TYR   0.020   0.002   TYR A 761 
 PHE   0.021   0.002   PHE A 349 
 TRP   0.038   0.002   TRP C  37 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6893)
  covalent geometry    : angle       0.61038 ( 9302)
  SS BOND              : bond        0.00551 (    1)
  SS BOND              : angle       2.21108 (    2)
  hydrogen bonds       : bond        0.03304 (  353)
  hydrogen bonds       : angle       4.56811 (  999)

*********************** 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
  176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 LEU cc_start: 0.6757 (tt) cc_final: 0.6512 (tt)
REVERT: A  231 MET cc_start: 0.8792 (mmm) cc_final: 0.8556 (mmm)
REVERT: A  320 TRP cc_start: 0.8209 (m100) cc_final: 0.7334 (m100)
REVERT: A  570 CYS cc_start: 0.7693 (m) cc_final: 0.6883 (m)
REVERT: A  602 PHE cc_start: 0.8159 (p90) cc_final: 0.7184 (p90)
REVERT: A  641 GLU cc_start: 0.8393 (pt0) cc_final: 0.7964 (pt0)
REVERT: A  667 MET cc_start: 0.8342 (tpt) cc_final: 0.7964 (tpp)
REVERT: A  697 ILE cc_start: 0.8897 (mt) cc_final: 0.8672 (mt)
REVERT: A  707 HIS cc_start: 0.6959 (m90) cc_final: 0.6616 (m-70)
REVERT: A  755 ASN cc_start: 0.9079 (m110) cc_final: 0.8815 (m110)
REVERT: A  803 ARG cc_start: 0.8137 (mmt180) cc_final: 0.7638 (tpt170)
REVERT: B   38 TRP cc_start: 0.7533 (m100) cc_final: 0.7011 (m100)
REVERT: B   98 CYS cc_start: 0.7850 (t) cc_final: 0.5912 (t)
REVERT: C    5 LEU cc_start: 0.7796 (mm) cc_final: 0.7381 (mt)
REVERT: C   30 PHE cc_start: 0.8923 (t80) cc_final: 0.8477 (t80)
REVERT: C   37 TRP cc_start: 0.4667 (m100) cc_final: 0.4365 (m100)
REVERT: C   79 LEU cc_start: 0.8073 (tp) cc_final: 0.7426 (tp)
REVERT: C   96 CYS cc_start: 0.5126 (t) cc_final: 0.4577 (t)
REVERT: C  100 MET cc_start: 0.8680 (pmm) cc_final: 0.7898 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0747
  time to fit residues: 17.6731
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  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.077900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.058430 restraints weight = 25316.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.060078 restraints weight = 16600.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.061237 restraints weight = 12318.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.062043 restraints weight = 9989.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.062648 restraints weight = 8614.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6894  Z= 0.133
  Angle     :  0.606   7.183   9304  Z= 0.321
  Chirality :  0.042   0.211   1029
  Planarity :  0.004   0.039   1206
  Dihedral  :  4.589  22.166    938
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.87
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.29), residues: 836
  helix:  0.52 (0.26), residues: 424
  sheet: -1.42 (0.54), residues: 95
  loop : -1.62 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  85 
 TYR   0.046   0.002   TYR A 630 
 PHE   0.025   0.002   PHE A 712 
 TRP   0.035   0.002   TRP C  37 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6893)
  covalent geometry    : angle       0.60529 ( 9302)
  SS BOND              : bond        0.00512 (    1)
  SS BOND              : angle       2.06743 (    2)
  hydrogen bonds       : bond        0.03334 (  353)
  hydrogen bonds       : angle       4.63951 (  999)

*********************** 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
  173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.276 
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  231 MET cc_start: 0.8803 (mmm) cc_final: 0.8566 (mmm)
REVERT: A  320 TRP cc_start: 0.8199 (m100) cc_final: 0.7311 (m100)
REVERT: A  570 CYS cc_start: 0.7663 (m) cc_final: 0.6964 (m)
REVERT: A  602 PHE cc_start: 0.8015 (p90) cc_final: 0.7049 (p90)
REVERT: A  641 GLU cc_start: 0.8412 (pt0) cc_final: 0.7963 (pt0)
REVERT: A  667 MET cc_start: 0.8332 (tpt) cc_final: 0.7961 (tpp)
REVERT: A  697 ILE cc_start: 0.8914 (mt) cc_final: 0.8684 (mt)
REVERT: A  701 ASP cc_start: 0.9253 (m-30) cc_final: 0.9039 (m-30)
REVERT: A  707 HIS cc_start: 0.7054 (m90) cc_final: 0.6683 (m-70)
REVERT: A  755 ASN cc_start: 0.9120 (m110) cc_final: 0.8874 (m110)
REVERT: A  819 MET cc_start: 0.7963 (ptp) cc_final: 0.7651 (ptm)
REVERT: B   38 TRP cc_start: 0.7467 (m100) cc_final: 0.6951 (m100)
REVERT: B   98 CYS cc_start: 0.7813 (t) cc_final: 0.5804 (t)
REVERT: C    5 LEU cc_start: 0.7777 (mm) cc_final: 0.7392 (mt)
REVERT: C   30 PHE cc_start: 0.8932 (t80) cc_final: 0.8430 (t80)
REVERT: C   79 LEU cc_start: 0.8017 (tp) cc_final: 0.7606 (tp)
REVERT: C   85 ARG cc_start: 0.7365 (ptm-80) cc_final: 0.7156 (ptm-80)
REVERT: C   96 CYS cc_start: 0.5109 (t) cc_final: 0.4741 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0799
  time to fit residues: 18.2891
Evaluate side-chains
  138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 73 optimal weight:    0.4980
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0060
   overall best weight:    1.2400

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.077444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.058145 restraints weight = 25246.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.059864 restraints weight = 16026.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.061073 restraints weight = 11702.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.061927 restraints weight = 9356.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.062436 restraints weight = 7980.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6894  Z= 0.141
  Angle     :  0.624   7.726   9304  Z= 0.330
  Chirality :  0.042   0.184   1029
  Planarity :  0.004   0.039   1206
  Dihedral  :  4.631  21.996    938
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.29), residues: 836
  helix:  0.50 (0.26), residues: 421
  sheet: -1.23 (0.55), residues: 93
  loop : -1.62 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  85 
 TYR   0.043   0.002   TYR A 630 
 PHE   0.024   0.002   PHE A 552 
 TRP   0.042   0.002   TRP C  37 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6893)
  covalent geometry    : angle       0.62376 ( 9302)
  SS BOND              : bond        0.00737 (    1)
  SS BOND              : angle       2.04888 (    2)
  hydrogen bonds       : bond        0.03398 (  353)
  hydrogen bonds       : angle       4.66125 (  999)

********************** 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
  164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.299 
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  231 MET cc_start: 0.8789 (mmm) cc_final: 0.8527 (mmm)
REVERT: A  320 TRP cc_start: 0.8207 (m100) cc_final: 0.7329 (m100)
REVERT: A  570 CYS cc_start: 0.7737 (m) cc_final: 0.6966 (m)
REVERT: A  602 PHE cc_start: 0.8097 (p90) cc_final: 0.7046 (p90)
REVERT: A  618 GLU cc_start: 0.8499 (pp20) cc_final: 0.8004 (pp20)
REVERT: A  641 GLU cc_start: 0.8448 (pt0) cc_final: 0.7953 (pt0)
REVERT: A  667 MET cc_start: 0.8274 (tpt) cc_final: 0.7917 (tpp)
REVERT: A  697 ILE cc_start: 0.8841 (mt) cc_final: 0.8605 (mt)
REVERT: A  701 ASP cc_start: 0.9172 (m-30) cc_final: 0.8880 (m-30)
REVERT: A  707 HIS cc_start: 0.7041 (m90) cc_final: 0.6352 (m170)
REVERT: A  755 ASN cc_start: 0.9058 (m110) cc_final: 0.8834 (m110)
REVERT: A  815 MET cc_start: 0.8391 (ttm) cc_final: 0.8040 (ttp)
REVERT: A  819 MET cc_start: 0.7769 (ptp) cc_final: 0.7547 (ptm)
REVERT: B   38 TRP cc_start: 0.7480 (m100) cc_final: 0.7030 (m100)
REVERT: B   98 CYS cc_start: 0.7783 (t) cc_final: 0.5697 (t)
REVERT: C    5 LEU cc_start: 0.7464 (mm) cc_final: 0.7107 (mt)
REVERT: C   37 TRP cc_start: 0.4629 (m100) cc_final: 0.4297 (m100)
REVERT: C   79 LEU cc_start: 0.8034 (tp) cc_final: 0.7418 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0732
  time to fit residues: 16.2074
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  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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**
B  79 ASN
C  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.078306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.060162 restraints weight = 25582.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.060476 restraints weight = 19437.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.061191 restraints weight = 14188.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.062278 restraints weight = 12520.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.062302 restraints weight = 11269.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6894  Z= 0.124
  Angle     :  0.603   8.118   9304  Z= 0.318
  Chirality :  0.041   0.181   1029
  Planarity :  0.004   0.037   1206
  Dihedral  :  4.511  21.893    938
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.29), residues: 836
  helix:  0.58 (0.25), residues: 421
  sheet: -1.18 (0.55), residues: 93
  loop : -1.60 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 661 
 TYR   0.035   0.002   TYR A 630 
 PHE   0.027   0.002   PHE A 712 
 TRP   0.041   0.003   TRP C  37 
 HIS   0.012   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6893)
  covalent geometry    : angle       0.60213 ( 9302)
  SS BOND              : bond        0.00477 (    1)
  SS BOND              : angle       1.79399 (    2)
  hydrogen bonds       : bond        0.03281 (  353)
  hydrogen bonds       : angle       4.60974 (  999)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1279.10 seconds
wall clock time: 22 minutes 42.46 seconds (1362.46 seconds total)