Starting phenix.real_space_refine
on Mon Feb 10 20:18:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ta6_41130/02_2025/8ta6_41130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ta6_41130/02_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_41130/02_2025/8ta6_41130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ta6_41130/02_2025/8ta6_41130.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ta6_41130/02_2025/8ta6_41130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ta6_41130/02_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-5592/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: 2.27, per 1000 atoms: 1.05
  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: 0.44
  Conformation dependent library (CDL) restraints added in 293.9 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: 0.26
  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: 0.53 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:             0.860
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.780
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.010
-------------------------------------------------------------------------------
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  : 0.279 
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: 0.2345
  time to fit residues: 18.6171
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  : 0.264 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.154444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.136357 restraints weight = 5574.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.139490 restraints weight = 3352.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.141613 restraints weight = 2257.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2192  Z= 0.192
  Angle     :  0.697   5.014   2958  Z= 0.372
  Chirality :  0.046   0.139    352
  Planarity :  0.005   0.042    372
  Dihedral  :  6.882  23.171    300
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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: -1.44 (0.51), residues: 266
  helix: -0.83 (0.57), residues: 73
  sheet: -1.38 (0.82), residues: 40
  loop : -0.83 (0.53), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 570 
 HIS   0.004   0.001   HIS A 807 
 PHE   0.013   0.002   PHE A 810 
 TYR   0.006   0.001   TYR A 819 
 ARG   0.003   0.001   ARG A 825 

*********************** 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
  71 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8348 (p-80) cc_final: 0.7947 (p-80)
REVERT: A  784 ASN cc_start: 0.8550 (t0) cc_final: 0.8239 (t0)
REVERT: B  607 THR cc_start: 0.8895 (p) cc_final: 0.8477 (p)
REVERT: B  629 ARG cc_start: 0.6526 (mtt180) cc_final: 0.6012 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2192
  time to fit residues: 17.2216
Evaluate side-chains
  46 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0000
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0970
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.153316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.134853 restraints weight = 5459.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.138009 restraints weight = 3257.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.140096 restraints weight = 2210.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2192  Z= 0.177
  Angle     :  0.619   5.815   2958  Z= 0.329
  Chirality :  0.043   0.129    352
  Planarity :  0.005   0.044    372
  Dihedral  :  6.049  20.214    300
  Min Nonbonded Distance : 2.573

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: -1.40 (0.51), residues: 266
  helix: -0.29 (0.59), residues: 80
  sheet: -1.03 (0.99), residues: 25
  loop : -1.25 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 570 
 HIS   0.004   0.001   HIS B 817 
 PHE   0.010   0.002   PHE A 810 
 TYR   0.008   0.001   TYR B 819 
 ARG   0.005   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
  65 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8370 (p-80) cc_final: 0.7923 (p-80)
REVERT: A  622 ILE cc_start: 0.8588 (mt) cc_final: 0.8350 (mt)
REVERT: A  784 ASN cc_start: 0.8633 (t0) cc_final: 0.8267 (t0)
REVERT: B  607 THR cc_start: 0.8951 (p) cc_final: 0.8471 (p)
REVERT: B  629 ARG cc_start: 0.6567 (mtt180) cc_final: 0.5250 (ttm-80)
REVERT: B  825 ARG cc_start: 0.6423 (tmt170) cc_final: 0.6186 (tmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.2168
  time to fit residues: 15.6380
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  : 0.254 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 17 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.4782

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.153303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.134818 restraints weight = 5997.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.137757 restraints weight = 3775.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.139705 restraints weight = 2652.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.4413

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= 0.234
  Angle     :  0.628   5.950   2958  Z= 0.334
  Chirality :  0.044   0.142    352
  Planarity :  0.004   0.041    372
  Dihedral  :  5.956  18.882    300
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  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: -0.58 (0.57), residues: 78
  sheet: -1.99 (1.19), residues: 15
  loop : -1.04 (0.48), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 570 
 HIS   0.003   0.001   HIS A 804 
 PHE   0.009   0.002   PHE A 810 
 TYR   0.009   0.002   TYR B 819 
 ARG   0.004   0.000   ARG A 825 

*********************** 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
  65 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8268 (p-80) cc_final: 0.7892 (p-80)
REVERT: A  784 ASN cc_start: 0.8657 (t0) cc_final: 0.8294 (t0)
REVERT: B  629 ARG cc_start: 0.6466 (mtt180) cc_final: 0.5067 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.2051
  time to fit residues: 14.8303
Evaluate side-chains
  46 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.151241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.132729 restraints weight = 5999.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.135648 restraints weight = 3818.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.137606 restraints weight = 2662.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2192  Z= 0.250
  Angle     :  0.656   5.813   2958  Z= 0.343
  Chirality :  0.044   0.182    352
  Planarity :  0.004   0.038    372
  Dihedral  :  5.918  18.995    300
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  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: -1.56 (0.50), residues: 266
  helix: -0.58 (0.57), residues: 80
  sheet: -1.95 (1.23), residues: 15
  loop : -1.19 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 570 
 HIS   0.004   0.001   HIS A 807 
 PHE   0.009   0.002   PHE A 810 
 TYR   0.010   0.002   TYR B 819 
 ARG   0.005   0.001   ARG B 610 

*********************** 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
  56 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  590 HIS cc_start: 0.8272 (p-80) cc_final: 0.7899 (p-80)
REVERT: A  622 ILE cc_start: 0.8473 (mt) cc_final: 0.8064 (mt)
REVERT: A  784 ASN cc_start: 0.8714 (t0) cc_final: 0.8386 (t0)
REVERT: B  629 ARG cc_start: 0.6435 (mtt180) cc_final: 0.5075 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1766
  time to fit residues: 11.2591
Evaluate side-chains
  41 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    0.1980
   chunk 2 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.157095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.138638 restraints weight = 5903.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.141555 restraints weight = 3812.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.143588 restraints weight = 2733.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.5097

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= 0.167
  Angle     :  0.607   4.938   2958  Z= 0.318
  Chirality :  0.044   0.144    352
  Planarity :  0.004   0.039    372
  Dihedral  :  5.454  17.870    300
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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: -1.46 (0.50), residues: 266
  helix: -0.36 (0.59), residues: 81
  sheet: -1.47 (0.89), residues: 25
  loop : -1.20 (0.49), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 570 
 HIS   0.003   0.001   HIS A 807 
 PHE   0.006   0.001   PHE A 810 
 TYR   0.009   0.001   TYR B 819 
 ARG   0.004   0.000   ARG B 610 

*********************** 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
  60 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8219 (p-80) cc_final: 0.7823 (p-80)
REVERT: A  621 MET cc_start: 0.7513 (ptp) cc_final: 0.7296 (ptp)
REVERT: A  784 ASN cc_start: 0.8711 (t0) cc_final: 0.8390 (t0)
REVERT: B  607 THR cc_start: 0.8842 (p) cc_final: 0.8483 (p)
REVERT: B  629 ARG cc_start: 0.6268 (mtt180) cc_final: 0.4994 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1839
  time to fit residues: 12.5434
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  : 0.268 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0980
   chunk 4 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.155103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.135943 restraints weight = 6001.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.138842 restraints weight = 3815.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.140813 restraints weight = 2738.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.5171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2192  Z= 0.213
  Angle     :  0.632   5.267   2958  Z= 0.332
  Chirality :  0.044   0.143    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.567  20.364    300
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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: -1.50 (0.51), residues: 266
  helix: -0.32 (0.60), residues: 81
  sheet: -1.61 (0.88), residues: 25
  loop : -1.26 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.004   TRP A 570 
 HIS   0.003   0.001   HIS A 807 
 PHE   0.007   0.001   PHE A 810 
 TYR   0.004   0.001   TYR A 819 
 ARG   0.004   0.000   ARG B 610 

*********************** 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
  56 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8205 (p-80) cc_final: 0.7853 (p-80)
REVERT: A  784 ASN cc_start: 0.8659 (t0) cc_final: 0.8371 (t0)
REVERT: B  607 THR cc_start: 0.8900 (p) cc_final: 0.8582 (p)
REVERT: B  629 ARG cc_start: 0.6348 (mtt180) cc_final: 0.5472 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1780
  time to fit residues: 11.3877
Evaluate side-chains
  41 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0970
   chunk 16 optimal weight:    0.0270
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4238

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.158398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.139588 restraints weight = 5995.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.142699 restraints weight = 3768.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.144822 restraints weight = 2657.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.5560

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= 0.154
  Angle     :  0.594   4.759   2958  Z= 0.311
  Chirality :  0.044   0.142    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.096  19.601    300
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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: -1.39 (0.51), residues: 266
  helix: -0.26 (0.61), residues: 80
  sheet: -1.69 (0.89), residues: 25
  loop : -1.14 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 570 
 HIS   0.003   0.001   HIS A 807 
 PHE   0.005   0.001   PHE B 810 
 TYR   0.007   0.001   TYR B 819 
 ARG   0.004   0.000   ARG B 610 

*********************** 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
  61 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8181 (p-80) cc_final: 0.7866 (p-80)
REVERT: A  784 ASN cc_start: 0.8664 (t0) cc_final: 0.8391 (t0)
REVERT: B  607 THR cc_start: 0.8870 (p) cc_final: 0.8613 (p)
REVERT: B  629 ARG cc_start: 0.6199 (mtt180) cc_final: 0.5421 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1611
  time to fit residues: 11.3341
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  : 0.259 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0570
   chunk 10 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.159698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.140853 restraints weight = 5849.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.143974 restraints weight = 3788.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.146090 restraints weight = 2636.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.5656

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= 0.175
  Angle     :  0.616   5.586   2958  Z= 0.321
  Chirality :  0.044   0.235    352
  Planarity :  0.004   0.037    372
  Dihedral  :  4.974  20.382    300
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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 (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: -1.54 (0.51), residues: 266
  helix: -0.27 (0.60), residues: 80
  sheet: -2.55 (0.70), residues: 35
  loop : -1.00 (0.51), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 570 
 HIS   0.003   0.001   HIS A 807 
 PHE   0.004   0.001   PHE A 785 
 TYR   0.003   0.001   TYR A 819 
 ARG   0.004   0.000   ARG B 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  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8149 (p-80) cc_final: 0.7841 (p-80)
REVERT: A  784 ASN cc_start: 0.8638 (t0) cc_final: 0.8384 (t0)
REVERT: B  607 THR cc_start: 0.8890 (p) cc_final: 0.8657 (p)
REVERT: B  629 ARG cc_start: 0.6219 (mtt180) cc_final: 0.5428 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1759
  time to fit residues: 12.2477
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  : 0.244 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 4 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.158118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.139534 restraints weight = 5877.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.142593 restraints weight = 3716.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.144368 restraints weight = 2588.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.5715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2192  Z= 0.184
  Angle     :  0.616   6.334   2958  Z= 0.322
  Chirality :  0.045   0.238    352
  Planarity :  0.004   0.037    372
  Dihedral  :  4.898  20.532    300
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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: -1.50 (0.51), residues: 266
  helix: -0.24 (0.60), residues: 80
  sheet: -2.38 (0.72), residues: 35
  loop : -1.01 (0.52), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 570 
 HIS   0.004   0.001   HIS A 817 
 PHE   0.004   0.001   PHE A 785 
 TYR   0.008   0.001   TYR B 819 
 ARG   0.004   0.000   ARG B 825 

********************** 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
  59 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8157 (p-80) cc_final: 0.7886 (p-80)
REVERT: A  784 ASN cc_start: 0.8659 (t0) cc_final: 0.8413 (t0)
REVERT: B  607 THR cc_start: 0.8928 (p) cc_final: 0.8692 (p)
REVERT: B  629 ARG cc_start: 0.6239 (mtt180) cc_final: 0.5136 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1761
  time to fit residues: 11.8419
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  : 0.234 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0370
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.3864

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.155422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.136646 restraints weight = 5869.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.139585 restraints weight = 3704.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.141496 restraints weight = 2610.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.5607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2192  Z= 0.242
  Angle     :  0.672   5.611   2958  Z= 0.353
  Chirality :  0.045   0.238    352
  Planarity :  0.004   0.036    372
  Dihedral  :  5.260  21.182    300
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  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 (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: -1.64 (0.51), residues: 266
  helix: -0.25 (0.60), residues: 80
  sheet: -2.71 (0.69), residues: 35
  loop : -1.09 (0.52), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.006   TRP A 570 
 HIS   0.003   0.001   HIS B 817 
 PHE   0.006   0.001   PHE A 785 
 TYR   0.013   0.002   TYR B 819 
 ARG   0.004   0.000   ARG B 825 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1231.46 seconds
wall clock time: 22 minutes 34.25 seconds (1354.25 seconds total)