Starting phenix.real_space_refine
on Wed Mar  5 15:12:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ta6_41130/03_2025/8ta6_41130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ta6_41130/03_2025/8ta6_41130.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ta6_41130/03_2025/8ta6_41130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ta6_41130/03_2025/8ta6_41130.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ta6_41130/03_2025/8ta6_41130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ta6_41130/03_2025/8ta6_41130.cif"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.051
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      10      5.16       5
     C    1368      2.51       5
     N     400      2.21       5
     O     380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2158
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1079
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 5, 'TRANS': 131}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1079
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 5, 'TRANS': 131}
          Chain breaks: 1
  Time building chain proxies: 2.19, per 1000 atoms: 1.01
  Number of scatterers: 2158
  At special positions: 0
  Unit cell: (75.68, 70.004, 80.41, 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      10     16.00
     O     380      8.00
     N     400      7.00
     C    1368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 272.3 milliseconds
  

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  512

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 4 sheets defined
      36.9% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 573 through 578
    Processing helix  chain 'A' and resid 579 through 583
    Processing helix  chain 'A' and resid 596 through 607
      removed outlier: 3.648A  pdb=" N   LEU A 600 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 641
    Processing helix  chain 'A' and resid 784 through 788
    Processing helix  chain 'A' and resid 802 through 811
      removed outlier: 4.575A  pdb=" N   THR A 808 " --> pdb=" O   HIS A 804 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A 810 " --> pdb=" O   THR A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 841
    Processing helix  chain 'B' and resid 599 through 604
      removed outlier: 3.795A  pdb=" N   ALA B 603 " --> pdb=" O   ASP B 599 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 604 " --> pdb=" O   LEU B 600 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 599 through 604'
    Processing helix  chain 'B' and resid 628 through 640
      removed outlier: 3.570A  pdb=" N   VAL B 632 " --> pdb=" O   GLU B 628 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA B 634 " --> pdb=" O   SER B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 802 through 814
      removed outlier: 3.513A  pdb=" N   THR B 806 " --> pdb=" O   SER B 802 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 813 " --> pdb=" O   ILE B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 832 through 839
    Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 592
      removed outlier: 6.330A  pdb=" N   VAL A 591 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LEU A 612 " --> pdb=" O   SER A 626 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LEU A 614 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 796 through 798
      removed outlier: 5.908A  pdb=" N   LEU A 797 " --> pdb=" O   THR A 821 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY A 828 " --> pdb=" O   VAL A 820 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   SER A 822 " --> pdb=" O   LEU A 826 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   LEU A 826 " --> pdb=" O   SER A 822 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 590 through 592
      removed outlier: 6.736A  pdb=" N   VAL B 591 " --> pdb=" O   VAL B 615 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY B 625 " --> pdb=" O   LEU B 614 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 796 through 797
      removed outlier: 3.840A  pdb=" N   GLY B 828 " --> pdb=" O   VAL B 820 " (cutoff:3.500A)

    60 hydrogen bonds defined for protein.
    159 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: 0.46

  Time building geometry restraints manager: 0.65 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: 640
        1.34 -     1.46: 283
        1.46 -     1.58: 1253
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 2192
  Sorted by residual:
  bond pdb=" CA  ASP A 791 "
       pdb=" C   ASP A 791 "
    ideal  model  delta    sigma   weight residual
    1.524  1.556 -0.032 1.26e-02 6.30e+03 6.44e+00
  bond pdb=" CZ  ARG B 629 "
       pdb=" NH2 ARG B 629 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.29e+00
  bond pdb=" CZ  ARG A 629 "
       pdb=" NH2 ARG A 629 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.25e+00
  bond pdb=" CD2 HIS A 804 "
       pdb=" NE2 HIS A 804 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.20e+00
  bond pdb=" CZ  ARG B 577 "
       pdb=" NH2 ARG B 577 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.17e+00
  ... (remaining 2187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 1943
        1.75 -     3.50: 777
        3.50 -     5.24: 196
        5.24 -     6.99: 37
        6.99 -     8.74: 5
  Bond angle restraints: 2958
  Sorted by residual:
  angle pdb=" CA  ASP A 787 "
        pdb=" CB  ASP A 787 "
        pdb=" CG  ASP A 787 "
      ideal   model   delta    sigma   weight residual
     112.60  117.96   -5.36 1.00e+00 1.00e+00 2.87e+01
  angle pdb=" C   MET A 584 "
        pdb=" N   VAL A 585 "
        pdb=" CA  VAL A 585 "
      ideal   model   delta    sigma   weight residual
     120.98  128.03   -7.05 1.36e+00 5.41e-01 2.69e+01
  angle pdb=" N   MET A 611 "
        pdb=" CA  MET A 611 "
        pdb=" C   MET A 611 "
      ideal   model   delta    sigma   weight residual
     108.99  116.66   -7.67 1.57e+00 4.06e-01 2.39e+01
  angle pdb=" OE1 GLN B 639 "
        pdb=" CD  GLN B 639 "
        pdb=" NE2 GLN B 639 "
      ideal   model   delta    sigma   weight residual
     122.60  117.77    4.83 1.00e+00 1.00e+00 2.34e+01
  angle pdb=" N   GLY B 571 "
        pdb=" CA  GLY B 571 "
        pdb=" C   GLY B 571 "
      ideal   model   delta    sigma   weight residual
     111.21  116.18   -4.97 1.04e+00 9.25e-01 2.28e+01
  ... (remaining 2953 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 1196
       17.58 -    35.16: 116
       35.16 -    52.74: 17
       52.74 -    70.31: 5
       70.31 -    87.89: 4
  Dihedral angle restraints: 1338
    sinusoidal: 552
      harmonic: 786
  Sorted by residual:
  dihedral pdb=" CA  ARG A 572 "
           pdb=" C   ARG A 572 "
           pdb=" N   HIS A 573 "
           pdb=" CA  HIS A 573 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.45  -29.55     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  VAL B 585 "
           pdb=" C   VAL B 585 "
           pdb=" N   ARG B 586 "
           pdb=" CA  ARG B 586 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.13  -28.87     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  ARG A 610 "
           pdb=" C   ARG A 610 "
           pdb=" N   MET A 611 "
           pdb=" CA  MET A 611 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.24  -26.76     0      5.00e+00 4.00e-02 2.86e+01
  ... (remaining 1335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 174
       0.072 -    0.143: 120
       0.143 -    0.214: 46
       0.214 -    0.285: 11
       0.285 -    0.357: 1
  Chirality restraints: 352
  Sorted by residual:
  chirality pdb=" CA  MET B 621 "
            pdb=" N   MET B 621 "
            pdb=" C   MET B 621 "
            pdb=" CB  MET B 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CA  GLN A 575 "
            pdb=" N   GLN A 575 "
            pdb=" C   GLN A 575 "
            pdb=" CB  GLN A 575 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  MET A 621 "
            pdb=" N   MET A 621 "
            pdb=" C   MET A 621 "
            pdb=" CB  MET A 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 349 not shown)

  Planarity restraints: 372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 785 "    0.125 2.00e-02 2.50e+03   7.65e-02 1.02e+02
        pdb=" CG  PHE A 785 "   -0.094 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 785 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 785 "   -0.068 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 785 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 785 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 785 "    0.076 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 570 "    0.096 2.00e-02 2.50e+03   4.79e-02 5.72e+01
        pdb=" CG  TRP A 570 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 570 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 570 "   -0.044 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 570 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 570 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 570 "   -0.072 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 570 "    0.043 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 570 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 570 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 570 "    0.080 2.00e-02 2.50e+03   3.96e-02 3.91e+01
        pdb=" CG  TRP B 570 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 570 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 570 "   -0.034 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 570 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 570 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 570 "   -0.057 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 570 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 570 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 570 "    0.047 2.00e-02 2.50e+03
  ... (remaining 369 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 992
        3.00 -     3.47: 2273
        3.47 -     3.95: 3209
        3.95 -     4.42: 3182
        4.42 -     4.90: 5389
  Nonbonded interactions: 15045
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 628 "
            pdb=" OG  SER A 630 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" OE1 GLU B 616 "
            pdb=" OG  SER B 620 "
     model   vdw
     2.543 3.040
  nonbonded pdb=" OG  SER A 617 "
            pdb=" OE2 GLU A 619 "
     model   vdw
     2.547 3.040
  nonbonded pdb=" OG1 THR B 831 "
            pdb=" OE1 GLU B 834 "
     model   vdw
     2.560 3.040
  nonbonded pdb=" N   SER A 822 "
            pdb=" O   SER A 822 "
     model   vdw
     2.579 2.496
  ... (remaining 15040 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.230
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
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      :  0.013   0.039   2192  Z= 0.837
  Angle     :  1.987   8.737   2958  Z= 1.304
  Chirality :  0.103   0.357    352
  Planarity :  0.014   0.087    372
  Dihedral  : 15.103  87.892    826
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 0.91
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  9.40 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.13 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.39 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.49), residues: 266
  helix: -2.32 (0.45), residues: 76
  sheet: -2.24 (0.97), residues: 22
  loop : -0.90 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.096   0.036   TRP A 570 
 HIS   0.006   0.002   HIS B 590 
 PHE   0.125   0.019   PHE A 785 
 TYR   0.052   0.021   TYR A 819 
 ARG   0.002   0.001   ARG A 836 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.9622 (p-80) cc_final: 0.9188 (p-80)
REVERT: A  611 MET cc_start: 0.8216 (tpp) cc_final: 0.7962 (tpp)
REVERT: A  836 ARG cc_start: 0.6537 (mmt180) cc_final: 0.5747 (mpt180)
REVERT: B  577 ARG cc_start: 0.8577 (ttp80) cc_final: 0.7928 (mmt180)
REVERT: B  581 GLU cc_start: 0.8586 (tt0) cc_final: 0.8386 (tt0)
REVERT: B  582 ASP cc_start: 0.8170 (m-30) cc_final: 0.7785 (m-30)
REVERT: B  607 THR cc_start: 0.9365 (p) cc_final: 0.8966 (p)
REVERT: B  629 ARG cc_start: 0.7950 (mtt180) cc_final: 0.5543 (ptm160)
REVERT: B  785 PHE cc_start: 0.8708 (p90) cc_final: 0.8475 (p90)
REVERT: B  834 GLU cc_start: 0.9537 (mp0) cc_final: 0.9121 (mp0)
  outliers start: 5
  outliers final: 1
  residues processed: 72
  average time/residue: 0.2301
  time to fit residues: 18.2326
Evaluate side-chains
  49 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.153979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.135913 restraints weight = 5577.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.139031 restraints weight = 3347.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.141116 restraints weight = 2262.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2192  Z= 0.195
  Angle     :  0.701   5.032   2958  Z= 0.374
  Chirality :  0.046   0.135    352
  Planarity :  0.005   0.041    372
  Dihedral  :  6.887  23.252    300
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.51), residues: 266
  helix: -0.99 (0.54), residues: 79
  sheet: -1.37 (0.82), residues: 40
  loop : -1.07 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 570 
 HIS   0.004   0.001   HIS A 804 
 PHE   0.013   0.002   PHE A 810 
 TYR   0.007   0.001   TYR B 819 
 ARG   0.003   0.000   ARG A 579 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8358 (p-80) cc_final: 0.7973 (p-80)
REVERT: A  784 ASN cc_start: 0.8542 (t0) cc_final: 0.8237 (t0)
REVERT: B  607 THR cc_start: 0.8908 (p) cc_final: 0.8477 (p)
REVERT: B  629 ARG cc_start: 0.6535 (mtt180) cc_final: 0.6010 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2432
  time to fit residues: 18.5612
Evaluate side-chains
  44 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 23 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.153638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.135062 restraints weight = 5402.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.138212 restraints weight = 3208.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.140300 restraints weight = 2168.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2192  Z= 0.178
  Angle     :  0.618   5.911   2958  Z= 0.328
  Chirality :  0.043   0.131    352
  Planarity :  0.004   0.044    372
  Dihedral  :  6.048  20.218    300
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.51), residues: 266
  helix: -0.35 (0.59), residues: 80
  sheet: -0.98 (1.00), residues: 25
  loop : -1.24 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 570 
 HIS   0.003   0.001   HIS B 817 
 PHE   0.009   0.002   PHE A 810 
 TYR   0.004   0.001   TYR B 819 
 ARG   0.004   0.000   ARG A 598 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8401 (p-80) cc_final: 0.7953 (p-80)
REVERT: A  622 ILE cc_start: 0.8575 (mt) cc_final: 0.8326 (mt)
REVERT: A  784 ASN cc_start: 0.8620 (t0) cc_final: 0.8258 (t0)
REVERT: A  836 ARG cc_start: 0.6085 (mmt-90) cc_final: 0.5802 (tmt170)
REVERT: B  607 THR cc_start: 0.8950 (p) cc_final: 0.8472 (p)
REVERT: B  629 ARG cc_start: 0.6577 (mtt180) cc_final: 0.5264 (ttm-80)
REVERT: B  825 ARG cc_start: 0.6445 (tmt170) cc_final: 0.6222 (tmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2465
  time to fit residues: 17.3362
Evaluate side-chains
  43 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0040
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.7994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.158087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.140101 restraints weight = 5794.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.143071 restraints weight = 3725.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.145069 restraints weight = 2657.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2192  Z= 0.174
  Angle     :  0.591   4.727   2958  Z= 0.312
  Chirality :  0.042   0.133    352
  Planarity :  0.004   0.041    372
  Dihedral  :  5.629  18.321    300
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.49), residues: 266
  helix: -0.66 (0.57), residues: 80
  sheet: -1.30 (0.95), residues: 25
  loop : -1.30 (0.47), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 570 
 HIS   0.003   0.001   HIS B 817 
 PHE   0.008   0.001   PHE A 810 
 TYR   0.004   0.001   TYR B 819 
 ARG   0.003   0.000   ARG A 579 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  578 VAL cc_start: 0.9104 (p) cc_final: 0.8802 (p)
REVERT: A  590 HIS cc_start: 0.8246 (p-80) cc_final: 0.7893 (p-80)
REVERT: A  784 ASN cc_start: 0.8684 (t0) cc_final: 0.8305 (t0)
REVERT: B  607 THR cc_start: 0.8956 (p) cc_final: 0.8601 (p)
REVERT: B  629 ARG cc_start: 0.6464 (mtt180) cc_final: 0.5826 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2069
  time to fit residues: 14.6702
Evaluate side-chains
  43 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0270
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0020
   chunk 16 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3046

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.158517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.139782 restraints weight = 5893.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.142937 restraints weight = 3658.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.145024 restraints weight = 2540.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2192  Z= 0.146
  Angle     :  0.566   4.533   2958  Z= 0.294
  Chirality :  0.043   0.169    352
  Planarity :  0.004   0.043    372
  Dihedral  :  5.037  17.655    300
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.49), residues: 266
  helix: -0.35 (0.56), residues: 81
  sheet: -1.14 (0.95), residues: 25
  loop : -1.17 (0.47), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 570 
 HIS   0.004   0.001   HIS A 807 
 PHE   0.005   0.001   PHE A 810 
 TYR   0.009   0.001   TYR B 819 
 ARG   0.004   0.000   ARG A 606 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8244 (p-80) cc_final: 0.7877 (p-80)
REVERT: A  622 ILE cc_start: 0.8440 (mt) cc_final: 0.8023 (mt)
REVERT: A  784 ASN cc_start: 0.8677 (t0) cc_final: 0.8335 (t0)
REVERT: B  607 THR cc_start: 0.8996 (p) cc_final: 0.8709 (p)
REVERT: B  629 ARG cc_start: 0.6364 (mtt180) cc_final: 0.6151 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1807
  time to fit residues: 13.0657
Evaluate side-chains
  45 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 11 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.158251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.139837 restraints weight = 5937.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.142967 restraints weight = 3691.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.144947 restraints weight = 2587.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2192  Z= 0.161
  Angle     :  0.583   6.041   2958  Z= 0.301
  Chirality :  0.043   0.164    352
  Planarity :  0.004   0.043    372
  Dihedral  :  5.057  19.580    300
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.50), residues: 266
  helix: -0.18 (0.58), residues: 81
  sheet: -1.37 (0.91), residues: 25
  loop : -1.20 (0.48), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 570 
 HIS   0.003   0.001   HIS A 807 
 PHE   0.005   0.001   PHE A 810 
 TYR   0.011   0.002   TYR A 576 
 ARG   0.004   0.000   ARG A 606 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8211 (p-80) cc_final: 0.7830 (p-80)
REVERT: A  784 ASN cc_start: 0.8722 (t0) cc_final: 0.8403 (t0)
REVERT: B  607 THR cc_start: 0.8997 (p) cc_final: 0.8716 (p)
REVERT: B  629 ARG cc_start: 0.6367 (mtt180) cc_final: 0.6138 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1875
  time to fit residues: 13.0689
Evaluate side-chains
  43 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    1.4784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.156397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.137331 restraints weight = 6007.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.140367 restraints weight = 3812.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.142457 restraints weight = 2725.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.5015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2192  Z= 0.238
  Angle     :  0.667   5.614   2958  Z= 0.348
  Chirality :  0.044   0.141    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.400  20.225    300
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.50), residues: 266
  helix: -0.22 (0.58), residues: 80
  sheet: -1.60 (0.89), residues: 25
  loop : -1.24 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP A 570 
 HIS   0.005   0.001   HIS A 817 
 PHE   0.007   0.002   PHE A 810 
 TYR   0.009   0.002   TYR B 819 
 ARG   0.005   0.000   ARG A 572 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8232 (p-80) cc_final: 0.7840 (p-80)
REVERT: A  622 ILE cc_start: 0.8304 (mt) cc_final: 0.8059 (mt)
REVERT: A  784 ASN cc_start: 0.8650 (t0) cc_final: 0.8349 (t0)
REVERT: B  629 ARG cc_start: 0.6423 (mtt180) cc_final: 0.5983 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1745
  time to fit residues: 11.3695
Evaluate side-chains
  40 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0170
   chunk 8 optimal weight:    0.0770
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4176

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.160957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.141704 restraints weight = 5907.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.144974 restraints weight = 3678.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.147157 restraints weight = 2572.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.5349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2192  Z= 0.155
  Angle     :  0.609   5.736   2958  Z= 0.316
  Chirality :  0.043   0.137    352
  Planarity :  0.004   0.036    372
  Dihedral  :  5.101  18.883    300
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.50), residues: 266
  helix: -0.05 (0.60), residues: 79
  sheet: -1.39 (0.87), residues: 30
  loop : -1.29 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 570 
 HIS   0.008   0.001   HIS A 817 
 PHE   0.005   0.001   PHE A 810 
 TYR   0.007   0.001   TYR B 819 
 ARG   0.005   0.000   ARG B 800 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8240 (p-80) cc_final: 0.7872 (p-80)
REVERT: A  784 ASN cc_start: 0.8662 (t0) cc_final: 0.8377 (t0)
REVERT: B  629 ARG cc_start: 0.6350 (mtt180) cc_final: 0.6023 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1614
  time to fit residues: 10.7428
Evaluate side-chains
  42 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0070
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0970
   chunk 7 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.160813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.141529 restraints weight = 5817.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.144636 restraints weight = 3639.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.146893 restraints weight = 2590.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.5491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2192  Z= 0.163
  Angle     :  0.613   5.673   2958  Z= 0.315
  Chirality :  0.043   0.144    352
  Planarity :  0.004   0.035    372
  Dihedral  :  4.922  18.900    300
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.50), residues: 266
  helix:  0.01 (0.60), residues: 80
  sheet: -1.70 (0.91), residues: 25
  loop : -1.20 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 570 
 HIS   0.003   0.001   HIS A 807 
 PHE   0.005   0.001   PHE A 810 
 TYR   0.007   0.001   TYR B 819 
 ARG   0.004   0.000   ARG A 825 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8221 (p-80) cc_final: 0.7846 (p-80)
REVERT: A  621 MET cc_start: 0.7433 (ptp) cc_final: 0.6815 (ptp)
REVERT: A  784 ASN cc_start: 0.8624 (t0) cc_final: 0.8362 (t0)
REVERT: B  607 THR cc_start: 0.8870 (p) cc_final: 0.8652 (p)
REVERT: B  629 ARG cc_start: 0.6328 (mtt180) cc_final: 0.6061 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1931
  time to fit residues: 13.2934
Evaluate side-chains
  42 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0970
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0770
   chunk 22 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.2140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.157834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.138742 restraints weight = 5984.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.141774 restraints weight = 3854.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.143548 restraints weight = 2758.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.5445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2192  Z= 0.214
  Angle     :  0.646   5.271   2958  Z= 0.336
  Chirality :  0.044   0.137    352
  Planarity :  0.004   0.035    372
  Dihedral  :  5.195  18.810    300
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.51), residues: 266
  helix: -0.12 (0.59), residues: 80
  sheet: -2.43 (0.73), residues: 35
  loop : -1.08 (0.51), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.005   TRP A 570 
 HIS   0.004   0.001   HIS B 817 
 PHE   0.006   0.001   PHE A 810 
 TYR   0.009   0.002   TYR B 819 
 ARG   0.003   0.000   ARG A 579 

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8221 (p-80) cc_final: 0.7893 (p-80)
REVERT: A  784 ASN cc_start: 0.8659 (t0) cc_final: 0.8407 (t0)
REVERT: B  607 THR cc_start: 0.8924 (p) cc_final: 0.8691 (p)
REVERT: B  629 ARG cc_start: 0.6453 (mtt180) cc_final: 0.5990 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1887
  time to fit residues: 12.2457
Evaluate side-chains
  38 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.9984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.157712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.138829 restraints weight = 5932.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.141796 restraints weight = 3802.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.143799 restraints weight = 2727.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.5552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2192  Z= 0.201
  Angle     :  0.658   5.797   2958  Z= 0.341
  Chirality :  0.044   0.142    352
  Planarity :  0.004   0.034    372
  Dihedral  :  5.162  18.432    300
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.50), residues: 266
  helix:  0.03 (0.59), residues: 80
  sheet: -2.18 (0.73), residues: 36
  loop : -1.27 (0.51), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.005   TRP A 570 
 HIS   0.003   0.001   HIS A 817 
 PHE   0.006   0.001   PHE B 810 
 TYR   0.010   0.001   TYR B 819 
 ARG   0.003   0.000   ARG A 825 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1304.42 seconds
wall clock time: 23 minutes 22.34 seconds (1402.34 seconds total)