Starting phenix.real_space_refine
on Wed Sep 17 05:59:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dis_46917/09_2025/9dis_46917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dis_46917/09_2025/9dis_46917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dis_46917/09_2025/9dis_46917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dis_46917/09_2025/9dis_46917.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dis_46917/09_2025/9dis_46917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dis_46917/09_2025/9dis_46917.map"
  }
  resolution = 2.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.128
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      15      5.16       5
     C    3570      2.51       5
     N     990      2.21       5
     O    1146      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5721
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 848
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 6, 'TRANS': 107}
    Chain: "B"
      Number of atoms: 4873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4873
          Classifications: {'peptide': 627}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 602}
          Chain breaks: 1
  Time building chain proxies: 1.55, per 1000 atoms: 0.27
  Number of scatterers: 5721
  At special positions: 0
  Unit cell: (105.04, 72.72, 73.73, 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      15     16.00
     O    1146      8.00
     N     990      7.00
     C    3570      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: 0.47
  Conformation dependent library (CDL) restraints added in 238.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 5 sheets defined
      19.2% alpha, 47.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 27
      removed outlier: 3.587A  pdb=" N   GLU A   5 " --> pdb=" O   ALA A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 48
    Processing helix  chain 'A' and resid 48 through 67
    Processing helix  chain 'A' and resid 69 through 90
      removed outlier: 4.698A  pdb=" N   ALA A  74 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   THR A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE A  76 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 113
    Processing helix  chain 'B' and resid 46 through 51
    Processing helix  chain 'B' and resid 101 through 103
      No H-bonds generated for 'chain 'B' and resid 101 through 103'
    Processing helix  chain 'B' and resid 115 through 120
    Processing helix  chain 'B' and resid 134 through 139
    Processing helix  chain 'B' and resid 418 through 424
    Processing helix  chain 'B' and resid 599 through 603
    Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 34
      removed outlier: 4.226A  pdb=" N   MET B  29 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU B  80 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   TYR B 130 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU B  82 " --> pdb=" O   TYR B 130 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   THR B 132 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 58
    Processing sheet with id=AA4, first strand: chain 'B' and resid 427 through 431
      removed outlier: 6.066A  pdb=" N   LYS B 427 " --> pdb=" O   TRP B 439 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   TRP B 439 " --> pdb=" O   LYS B 427 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   THR B 497 " --> pdb=" O   THR B 436 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   TYR B 438 " --> pdb=" O   THR B 497 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   SER B 499 " --> pdb=" O   TYR B 438 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   THR B 530 " --> pdb=" O   PRO B 546 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   ILE B 364 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   SER B 379 " --> pdb=" O   LYS B 383 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   LYS B 383 " --> pdb=" O   SER B 379 " (cutoff:3.500A)
      removed outlier: 10.201A  pdb=" N   TRP B 390 " --> pdb=" O   PHE B 414 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   PHE B 414 " --> pdb=" O   TRP B 390 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   SER B 392 " --> pdb=" O   GLN B 412 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU B 471 " --> pdb=" O   TYR B 516 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   TYR B 516 " --> pdb=" O   LEU B 471 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   PHE B 473 " --> pdb=" O   THR B 514 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   THR B 514 " --> pdb=" O   PHE B 473 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ALA B 475 " --> pdb=" O   VAL B 512 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL B 512 " --> pdb=" O   ALA B 475 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   TYR B 477 " --> pdb=" O   TRP B 510 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP B 510 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASP B 479 " --> pdb=" O   TRP B 508 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   TRP B 508 " --> pdb=" O   ASP B 479 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   LYS B 481 " --> pdb=" O   LYS B 506 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   LYS B 506 " --> pdb=" O   LYS B 481 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LYS B 483 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ASN B 504 " --> pdb=" O   LYS B 483 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188

    376 hydrogen bonds defined for protein.
    1071 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: 1.10

  Time building geometry restraints manager: 0.67 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 1937
        1.34 -     1.46: 1152
        1.46 -     1.57: 2726
        1.57 -     1.69: 0
        1.69 -     1.80: 30
  Bond restraints: 5845
  Sorted by residual:
  bond pdb=" CA  ALA A  68 "
       pdb=" C   ALA A  68 "
    ideal  model  delta    sigma   weight residual
    1.527  1.516  0.011 1.31e-02 5.83e+03 6.76e-01
  bond pdb=" CB  TRP B 510 "
       pdb=" CG  TRP B 510 "
    ideal  model  delta    sigma   weight residual
    1.498  1.473  0.025 3.10e-02 1.04e+03 6.61e-01
  bond pdb=" C   LEU B 366 "
       pdb=" N   LEU B 367 "
    ideal  model  delta    sigma   weight residual
    1.333  1.324  0.009 1.30e-02 5.92e+03 4.94e-01
  bond pdb=" CA  SER B 350 "
       pdb=" CB  SER B 350 "
    ideal  model  delta    sigma   weight residual
    1.536  1.519  0.017 2.53e-02 1.56e+03 4.52e-01
  bond pdb=" CB  ASP B 274 "
       pdb=" CG  ASP B 274 "
    ideal  model  delta    sigma   weight residual
    1.516  1.499  0.017 2.50e-02 1.60e+03 4.42e-01
  ... (remaining 5840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 7621
        1.27 -     2.55: 264
        2.55 -     3.82: 44
        3.82 -     5.09: 7
        5.09 -     6.36: 1
  Bond angle restraints: 7937
  Sorted by residual:
  angle pdb=" CB  ASP B 242 "
        pdb=" CG  ASP B 242 "
        pdb=" OD2 ASP B 242 "
      ideal   model   delta    sigma   weight residual
     118.40  122.97   -4.57 2.30e+00 1.89e-01 3.95e+00
  angle pdb=" CA  GLY B  97 "
        pdb=" C   GLY B  97 "
        pdb=" N   THR B  98 "
      ideal   model   delta    sigma   weight residual
     114.86  116.85   -1.99 1.01e+00 9.80e-01 3.90e+00
  angle pdb=" N   ASP B 157 "
        pdb=" CA  ASP B 157 "
        pdb=" C   ASP B 157 "
      ideal   model   delta    sigma   weight residual
     114.12  111.54    2.58 1.39e+00 5.18e-01 3.44e+00
  angle pdb=" OD1 ASP B 242 "
        pdb=" CG  ASP B 242 "
        pdb=" OD2 ASP B 242 "
      ideal   model   delta    sigma   weight residual
     122.90  118.51    4.39 2.40e+00 1.74e-01 3.35e+00
  angle pdb=" CA  LEU A 105 "
        pdb=" CB  LEU A 105 "
        pdb=" CG  LEU A 105 "
      ideal   model   delta    sigma   weight residual
     116.30  122.66   -6.36 3.50e+00 8.16e-02 3.30e+00
  ... (remaining 7932 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 3190
       17.04 -    34.07: 216
       34.07 -    51.11: 39
       51.11 -    68.14: 9
       68.14 -    85.18: 8
  Dihedral angle restraints: 3462
    sinusoidal: 1333
      harmonic: 2129
  Sorted by residual:
  dihedral pdb=" CA  ASN B 528 "
           pdb=" C   ASN B 528 "
           pdb=" N   ARG B 529 "
           pdb=" CA  ARG B 529 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.82   19.18     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ALA B 229 "
           pdb=" C   ALA B 229 "
           pdb=" N   ARG B 230 "
           pdb=" CA  ARG B 230 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.93   19.07     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  MET B 422 "
           pdb=" C   MET B 422 "
           pdb=" N   TYR B 423 "
           pdb=" CA  TYR B 423 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.16  -17.84     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 3459 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 509
       0.032 -    0.064: 235
       0.064 -    0.095: 69
       0.095 -    0.127: 40
       0.127 -    0.159: 3
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CB  THR B 322 "
            pdb=" CA  THR B 322 "
            pdb=" OG1 THR B 322 "
            pdb=" CG2 THR B 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" CG  LEU B 445 "
            pdb=" CB  LEU B 445 "
            pdb=" CD1 LEU B 445 "
            pdb=" CD2 LEU B 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  ILE B 507 "
            pdb=" N   ILE B 507 "
            pdb=" C   ILE B 507 "
            pdb=" CB  ILE B 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 853 not shown)

  Planarity restraints: 1051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  80 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.39e+00
        pdb=" C   ALA A  80 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ALA A  80 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A  81 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  79 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   TYR A  79 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   TYR A  79 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A  80 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 279 "   -0.012 2.00e-02 2.50e+03   1.09e-02 2.99e+00
        pdb=" CG  TRP B 279 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 279 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 279 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 279 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 279 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 279 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 279 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 279 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 279 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1048 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 347
        2.73 -     3.27: 5656
        3.27 -     3.82: 10037
        3.82 -     4.36: 12416
        4.36 -     4.90: 21246
  Nonbonded interactions: 49702
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 511 "
            pdb=" ND2 ASN B 528 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OG  SER B 241 "
            pdb=" OG  SER B 244 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OD2 ASP B 213 "
            pdb=" NE2 GLN B 216 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OG1 THR B  47 "
            pdb=" OE1 GLN B  67 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" NH1 ARG B 230 "
            pdb=" OD1 ASP B 249 "
     model   vdw
     2.233 3.120
  ... (remaining 49697 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.140
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.200
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
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      :  0.003   0.025   5845  Z= 0.173
  Angle     :  0.558   6.362   7937  Z= 0.312
  Chirality :  0.043   0.159    856
  Planarity :  0.004   0.039   1051
  Dihedral  : 12.977  85.177   2106
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.30), residues: 735
  helix:  1.51 (0.45), residues: 117
  sheet: -0.10 (0.27), residues: 342
  loop :  0.19 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 529 
 TYR   0.017   0.001   TYR B 527 
 PHE   0.011   0.002   PHE B 434 
 TRP   0.029   0.002   TRP B 279 
 HIS   0.002   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5845)
  covalent geometry    : angle       0.55837 ( 7937)
  hydrogen bonds       : bond        0.09921 (  376)
  hydrogen bonds       : angle       6.46291 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   34 MET cc_start: 0.6485 (mmp) cc_final: 0.6081 (mmp)
REVERT: B   35 THR cc_start: 0.7405 (m) cc_final: 0.7047 (p)
REVERT: B   59 ASP cc_start: 0.7795 (m-30) cc_final: 0.7541 (m-30)
REVERT: B  204 MET cc_start: 0.8264 (mpp) cc_final: 0.8041 (mpt)
REVERT: B  285 ASN cc_start: 0.7141 (t0) cc_final: 0.6877 (t0)
REVERT: B  322 THR cc_start: 0.8481 (t) cc_final: 0.8259 (p)
REVERT: B  483 LYS cc_start: 0.7579 (tttp) cc_final: 0.7009 (mmtt)
  outliers start: 0
  outliers final: 1
  residues processed: 145
  average time/residue: 0.7161
  time to fit residues: 107.4491
Evaluate side-chains
  86 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  67 GLN
B 203 ASN
B 216 GLN
B 272 ASN
B 298 GLN
B 354 GLN
B 627 GLN
B 631 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.150119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.124103 restraints weight = 5634.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.50
r_work: 0.3328 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5845  Z= 0.175
  Angle     :  0.552   5.230   7937  Z= 0.300
  Chirality :  0.043   0.147    856
  Planarity :  0.004   0.030   1051
  Dihedral  :  4.964  28.883    817
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 11.28 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.31), residues: 735
  helix:  2.11 (0.44), residues: 117
  sheet:  0.02 (0.27), residues: 343
  loop :  0.22 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 529 
 TYR   0.015   0.002   TYR A  81 
 PHE   0.013   0.002   PHE B 429 
 TRP   0.011   0.001   TRP B 279 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5845)
  covalent geometry    : angle       0.55187 ( 7937)
  hydrogen bonds       : bond        0.03833 (  376)
  hydrogen bonds       : angle       5.95740 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7133 (tptp) cc_final: 0.6691 (ttpp)
REVERT: A   34 MET cc_start: 0.5692 (mmp) cc_final: 0.5161 (mmp)
REVERT: B   35 THR cc_start: 0.7699 (m) cc_final: 0.7289 (p)
REVERT: B  138 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8323 (mt)
REVERT: B  188 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6845 (mtt90)
REVERT: B  274 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7950 (m-30)
REVERT: B  281 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7398 (tt0)
REVERT: B  285 ASN cc_start: 0.7521 (t0) cc_final: 0.7315 (t0)
REVERT: B  333 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6628 (m-70)
REVERT: B  481 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8021 (mtmm)
REVERT: B  483 LYS cc_start: 0.8121 (tttp) cc_final: 0.7642 (mmtt)
REVERT: B  515 LYS cc_start: 0.7936 (tptp) cc_final: 0.6426 (ttpp)
REVERT: B  517 THR cc_start: 0.8629 (t) cc_final: 0.8425 (m)
  outliers start: 20
  outliers final: 4
  residues processed: 88
  average time/residue: 0.8615
  time to fit residues: 78.4751
Evaluate side-chains
  79 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  274 ASP
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  333 HIS
Chi-restraints excluded: chain B residue  551 SER
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  597 GLN
Chi-restraints excluded: chain B residue  605 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** B  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 GLN
B 216 GLN
B 631 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.142695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.115550 restraints weight = 5684.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.49
r_work: 0.3237 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5845  Z= 0.285
  Angle     :  0.605   5.755   7937  Z= 0.327
  Chirality :  0.043   0.141    856
  Planarity :  0.004   0.028   1051
  Dihedral  :  5.468  33.275    817
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 13.47 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.30), residues: 735
  helix:  1.78 (0.45), residues: 117
  sheet:  0.02 (0.26), residues: 351
  loop :  0.20 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 371 
 TYR   0.016   0.002   TYR B 328 
 PHE   0.014   0.003   PHE B 407 
 TRP   0.007   0.002   TRP B 210 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 5845)
  covalent geometry    : angle       0.60525 ( 7937)
  hydrogen bonds       : bond        0.04493 (  376)
  hydrogen bonds       : angle       6.08388 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7331 (tptp) cc_final: 0.6915 (ttpp)
REVERT: A   34 MET cc_start: 0.5546 (mmp) cc_final: 0.5061 (mmp)
REVERT: B   35 THR cc_start: 0.7968 (m) cc_final: 0.7575 (p)
REVERT: B   51 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7161 (mmp80)
REVERT: B  143 GLN cc_start: 0.7910 (tt0) cc_final: 0.7376 (tt0)
REVERT: B  171 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6768 (pp20)
REVERT: B  188 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6775 (mtt90)
REVERT: B  274 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7932 (m-30)
REVERT: B  281 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7561 (tt0)
REVERT: B  285 ASN cc_start: 0.7763 (t0) cc_final: 0.7553 (t0)
REVERT: B  329 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7868 (ttm110)
REVERT: B  481 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8129 (mtmm)
REVERT: B  483 LYS cc_start: 0.8333 (tttp) cc_final: 0.7714 (mmtt)
REVERT: B  517 THR cc_start: 0.8715 (t) cc_final: 0.8411 (m)
REVERT: B  573 ARG cc_start: 0.7316 (mmt180) cc_final: 0.5566 (ptm160)
REVERT: B  577 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8056 (pp)
  outliers start: 24
  outliers final: 10
  residues processed: 88
  average time/residue: 0.7744
  time to fit residues: 70.6188
Evaluate side-chains
  78 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  274 ASP
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  329 ARG
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  361 ASP
Chi-restraints excluded: chain B residue  485 TYR
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  551 SER
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  597 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0770
   chunk 11 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN
B 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.146467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.119740 restraints weight = 5684.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.49
r_work: 0.3298 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5845  Z= 0.157
  Angle     :  0.517   5.255   7937  Z= 0.280
  Chirality :  0.041   0.129    856
  Planarity :  0.004   0.029   1051
  Dihedral  :  4.985  30.657    817
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.49 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.30), residues: 735
  helix:  1.91 (0.45), residues: 117
  sheet: -0.08 (0.27), residues: 342
  loop :  0.19 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 371 
 TYR   0.012   0.001   TYR B 328 
 PHE   0.013   0.002   PHE B 407 
 TRP   0.006   0.001   TRP B 279 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5845)
  covalent geometry    : angle       0.51684 ( 7937)
  hydrogen bonds       : bond        0.03593 (  376)
  hydrogen bonds       : angle       5.90497 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7333 (tptp) cc_final: 0.6899 (ttpp)
REVERT: A   34 MET cc_start: 0.5536 (mmp) cc_final: 0.5161 (mmp)
REVERT: A   94 GLU cc_start: 0.6477 (mp0) cc_final: 0.6187 (mp0)
REVERT: B   51 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7385 (mmp80)
REVERT: B  138 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8375 (mt)
REVERT: B  188 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6805 (mtt90)
REVERT: B  207 LYS cc_start: 0.8668 (tttt) cc_final: 0.8447 (tttm)
REVERT: B  274 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7939 (m-30)
REVERT: B  481 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8065 (mtmm)
REVERT: B  483 LYS cc_start: 0.8334 (tttp) cc_final: 0.7670 (mmtt)
REVERT: B  517 THR cc_start: 0.8612 (t) cc_final: 0.8410 (m)
REVERT: B  573 ARG cc_start: 0.7281 (mmt180) cc_final: 0.5527 (ptm160)
  outliers start: 19
  outliers final: 6
  residues processed: 82
  average time/residue: 0.7093
  time to fit residues: 60.4490
Evaluate side-chains
  78 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  274 ASP
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  551 SER
Chi-restraints excluded: chain B residue  597 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 53 optimal weight:    0.0000
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.9966

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

Flipped N/Q/H residues before XYZ refinement:
B 203 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.142845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.116939 restraints weight = 5995.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.43
r_work: 0.3264 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5845  Z= 0.204
  Angle     :  0.543   5.768   7937  Z= 0.292
  Chirality :  0.042   0.129    856
  Planarity :  0.004   0.031   1051
  Dihedral  :  4.981  19.408    815
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.66 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.30), residues: 735
  helix:  1.97 (0.45), residues: 116
  sheet: -0.07 (0.27), residues: 342
  loop :  0.19 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 304 
 TYR   0.014   0.002   TYR B 328 
 PHE   0.015   0.002   PHE A  41 
 TRP   0.006   0.001   TRP B 566 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 5845)
  covalent geometry    : angle       0.54283 ( 7937)
  hydrogen bonds       : bond        0.03872 (  376)
  hydrogen bonds       : angle       5.87150 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7508 (tptp) cc_final: 0.7062 (ttpp)
REVERT: A   23 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5696 (tp30)
REVERT: A   34 MET cc_start: 0.5521 (mmp) cc_final: 0.5173 (mmp)
REVERT: A   94 GLU cc_start: 0.6457 (mp0) cc_final: 0.6208 (mp0)
REVERT: B  188 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6836 (mtt90)
REVERT: B  274 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7990 (m-30)
REVERT: B  281 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7508 (tt0)
REVERT: B  329 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7924 (ttm110)
REVERT: B  333 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6930 (m-70)
REVERT: B  481 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8078 (mtmm)
REVERT: B  483 LYS cc_start: 0.8400 (tttp) cc_final: 0.7786 (mmtt)
REVERT: B  517 THR cc_start: 0.8665 (t) cc_final: 0.8424 (m)
REVERT: B  573 ARG cc_start: 0.7350 (mmt180) cc_final: 0.5653 (ptm160)
  outliers start: 23
  outliers final: 10
  residues processed: 81
  average time/residue: 0.7405
  time to fit residues: 62.3418
Evaluate side-chains
  83 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  274 ASP
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  329 ARG
Chi-restraints excluded: chain B residue  333 HIS
Chi-restraints excluded: chain B residue  485 TYR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  551 SER
Chi-restraints excluded: chain B residue  597 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN
B 203 ASN
B 399 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.145028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.118164 restraints weight = 5734.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.50
r_work: 0.3267 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5845  Z= 0.185
  Angle     :  0.531   5.478   7937  Z= 0.285
  Chirality :  0.041   0.129    856
  Planarity :  0.004   0.036   1051
  Dihedral  :  4.888  18.809    815
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.16 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.31), residues: 735
  helix:  2.08 (0.45), residues: 116
  sheet: -0.12 (0.27), residues: 341
  loop :  0.18 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 304 
 TYR   0.012   0.002   TYR B 328 
 PHE   0.014   0.002   PHE A  41 
 TRP   0.006   0.001   TRP B 566 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5845)
  covalent geometry    : angle       0.53101 ( 7937)
  hydrogen bonds       : bond        0.03711 (  376)
  hydrogen bonds       : angle       5.83516 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7448 (tptp) cc_final: 0.6997 (ttpp)
REVERT: A   23 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5492 (tp30)
REVERT: A   34 MET cc_start: 0.5521 (mmp) cc_final: 0.5297 (mmp)
REVERT: A   94 GLU cc_start: 0.6515 (mp0) cc_final: 0.6237 (mp0)
REVERT: B  138 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8394 (mt)
REVERT: B  188 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6786 (mtt90)
REVERT: B  274 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8035 (m-30)
REVERT: B  333 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6796 (m-70)
REVERT: B  339 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7468 (p)
REVERT: B  454 GLU cc_start: 0.8497 (tp30) cc_final: 0.8216 (tp30)
REVERT: B  483 LYS cc_start: 0.8357 (tttp) cc_final: 0.7688 (mmtt)
REVERT: B  517 THR cc_start: 0.8644 (t) cc_final: 0.8387 (m)
REVERT: B  573 ARG cc_start: 0.7297 (mmt180) cc_final: 0.5541 (ptm160)
  outliers start: 22
  outliers final: 8
  residues processed: 84
  average time/residue: 0.7131
  time to fit residues: 62.2347
Evaluate side-chains
  79 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  274 ASP
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  333 HIS
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  485 TYR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  597 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0020
   chunk 1 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.1980
   chunk 19 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
B 203 ASN
B 343 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.144433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117406 restraints weight = 5736.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.50
r_work: 0.3251 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5845  Z= 0.196
  Angle     :  0.537   5.757   7937  Z= 0.289
  Chirality :  0.041   0.128    856
  Planarity :  0.004   0.037   1051
  Dihedral  :  4.952  19.862    815
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 16.16 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.31), residues: 735
  helix:  2.08 (0.45), residues: 116
  sheet: -0.12 (0.27), residues: 336
  loop :  0.12 (0.38), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 304 
 TYR   0.013   0.002   TYR B 328 
 PHE   0.014   0.002   PHE A  41 
 TRP   0.006   0.001   TRP B 566 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 5845)
  covalent geometry    : angle       0.53699 ( 7937)
  hydrogen bonds       : bond        0.03759 (  376)
  hydrogen bonds       : angle       5.84872 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7471 (tptp) cc_final: 0.7015 (ttpp)
REVERT: A   23 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5447 (tp30)
REVERT: A   34 MET cc_start: 0.5621 (mmp) cc_final: 0.5401 (mmp)
REVERT: B  138 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8468 (mt)
REVERT: B  188 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6786 (mtt90)
REVERT: B  247 MET cc_start: 0.8772 (tpt) cc_final: 0.8422 (tpt)
REVERT: B  274 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8039 (m-30)
REVERT: B  329 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7906 (ttm110)
REVERT: B  339 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7487 (p)
REVERT: B  454 GLU cc_start: 0.8511 (tp30) cc_final: 0.8268 (tp30)
REVERT: B  481 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8007 (mtmm)
REVERT: B  483 LYS cc_start: 0.8375 (tttp) cc_final: 0.7689 (mmtt)
REVERT: B  517 THR cc_start: 0.8633 (t) cc_final: 0.8375 (m)
REVERT: B  573 ARG cc_start: 0.7304 (mmt180) cc_final: 0.5531 (ptm160)
  outliers start: 21
  outliers final: 9
  residues processed: 81
  average time/residue: 0.7280
  time to fit residues: 61.2160
Evaluate side-chains
  79 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  274 ASP
Chi-restraints excluded: chain B residue  329 ARG
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  485 TYR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  551 SER
Chi-restraints excluded: chain B residue  597 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0060
   chunk 22 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0970
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
B 203 ASN
B 287 GLN
B 298 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.148170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.121648 restraints weight = 5761.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.50
r_work: 0.3308 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5845  Z= 0.123
  Angle     :  0.501   7.463   7937  Z= 0.267
  Chirality :  0.041   0.126    856
  Planarity :  0.003   0.035   1051
  Dihedral  :  4.614  18.639    815
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.17 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.31), residues: 735
  helix:  2.21 (0.45), residues: 116
  sheet: -0.19 (0.27), residues: 341
  loop :  0.20 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 107 
 TYR   0.010   0.001   TYR B 328 
 PHE   0.015   0.002   PHE A  41 
 TRP   0.007   0.001   TRP B 270 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 5845)
  covalent geometry    : angle       0.50099 ( 7937)
  hydrogen bonds       : bond        0.03208 (  376)
  hydrogen bonds       : angle       5.70837 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7459 (tptp) cc_final: 0.7011 (ttpp)
REVERT: A   23 GLU cc_start: 0.5937 (mm-30) cc_final: 0.5441 (tp30)
REVERT: B  138 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8421 (mt)
REVERT: B  329 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7870 (ttm110)
REVERT: B  339 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7206 (p)
REVERT: B  454 GLU cc_start: 0.8416 (tp30) cc_final: 0.8176 (tp30)
REVERT: B  481 LYS cc_start: 0.8852 (mtpt) cc_final: 0.7985 (mtmm)
REVERT: B  483 LYS cc_start: 0.8246 (tttp) cc_final: 0.7630 (mmtt)
REVERT: B  517 THR cc_start: 0.8647 (t) cc_final: 0.8394 (m)
REVERT: B  573 ARG cc_start: 0.7264 (mmt180) cc_final: 0.5489 (ptm160)
  outliers start: 15
  outliers final: 5
  residues processed: 82
  average time/residue: 0.7116
  time to fit residues: 60.7176
Evaluate side-chains
  74 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  329 ARG
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 62 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0870
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 29 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.3558

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

Flipped N/Q/H residues before XYZ refinement:
B 203 ASN
B 287 GLN
B 298 GLN
B 597 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.123364 restraints weight = 5725.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.50
r_work: 0.3328 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5845  Z= 0.117
  Angle     :  0.493   7.211   7937  Z= 0.263
  Chirality :  0.041   0.125    856
  Planarity :  0.003   0.034   1051
  Dihedral  :  4.481  18.284    815
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.18 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.31), residues: 735
  helix:  2.28 (0.45), residues: 117
  sheet: -0.17 (0.27), residues: 341
  loop :  0.27 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 376 
 TYR   0.010   0.001   TYR B 328 
 PHE   0.015   0.002   PHE A  41 
 TRP   0.005   0.001   TRP B 270 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 5845)
  covalent geometry    : angle       0.49309 ( 7937)
  hydrogen bonds       : bond        0.03132 (  376)
  hydrogen bonds       : angle       5.55590 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7434 (tptp) cc_final: 0.6968 (ttpp)
REVERT: A   23 GLU cc_start: 0.5882 (mm-30) cc_final: 0.5410 (tp30)
REVERT: B  138 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8312 (mt)
REVERT: B  280 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8595 (p)
REVERT: B  329 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7928 (ttm110)
REVERT: B  339 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7069 (p)
REVERT: B  481 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8049 (mtmm)
REVERT: B  483 LYS cc_start: 0.8172 (tttp) cc_final: 0.7592 (mmtt)
REVERT: B  517 THR cc_start: 0.8635 (t) cc_final: 0.8393 (m)
REVERT: B  573 ARG cc_start: 0.7218 (mmt180) cc_final: 0.5440 (ptm160)
  outliers start: 14
  outliers final: 5
  residues processed: 79
  average time/residue: 0.7537
  time to fit residues: 61.8166
Evaluate side-chains
  76 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  329 ARG
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  597 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 67 optimal weight:    0.0470
   chunk 64 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0970
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
B 203 ASN
B 298 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.149315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.122928 restraints weight = 5811.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.50
r_work: 0.3328 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5845  Z= 0.125
  Angle     :  0.494   7.153   7937  Z= 0.264
  Chirality :  0.041   0.128    856
  Planarity :  0.003   0.029   1051
  Dihedral  :  4.489  18.468    815
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.52 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.31), residues: 735
  helix:  2.27 (0.45), residues: 117
  sheet: -0.15 (0.27), residues: 341
  loop :  0.26 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 371 
 TYR   0.009   0.001   TYR B 328 
 PHE   0.014   0.002   PHE A  41 
 TRP   0.005   0.001   TRP B 270 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 5845)
  covalent geometry    : angle       0.49409 ( 7937)
  hydrogen bonds       : bond        0.03160 (  376)
  hydrogen bonds       : angle       5.53387 ( 1071)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.7446 (tptp) cc_final: 0.6976 (ttpp)
REVERT: A   23 GLU cc_start: 0.5900 (mm-30) cc_final: 0.5408 (tp30)
REVERT: B  138 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8299 (mt)
REVERT: B  280 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8599 (p)
REVERT: B  329 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7881 (ttm110)
REVERT: B  339 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7085 (p)
REVERT: B  481 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8056 (mtmm)
REVERT: B  483 LYS cc_start: 0.8188 (tttp) cc_final: 0.7608 (mmtt)
REVERT: B  517 THR cc_start: 0.8637 (t) cc_final: 0.8396 (m)
REVERT: B  573 ARG cc_start: 0.7231 (mmt180) cc_final: 0.5449 (ptm160)
REVERT: B  597 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7647 (mm-40)
  outliers start: 12
  outliers final: 4
  residues processed: 78
  average time/residue: 0.7387
  time to fit residues: 59.9237
Evaluate side-chains
  76 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  329 ARG
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  597 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 203 ASN
B 287 GLN
B 597 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.120033 restraints weight = 5712.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.49
r_work: 0.3292 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5845  Z= 0.162
  Angle     :  0.520   6.883   7937  Z= 0.277
  Chirality :  0.041   0.130    856
  Planarity :  0.004   0.043   1051
  Dihedral  :  4.684  18.343    815
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.52 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.31), residues: 735
  helix:  2.20 (0.45), residues: 117
  sheet: -0.11 (0.27), residues: 341
  loop :  0.28 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 107 
 TYR   0.012   0.001   TYR B 328 
 PHE   0.015   0.002   PHE A  41 
 TRP   0.006   0.001   TRP B 270 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5845)
  covalent geometry    : angle       0.52029 ( 7937)
  hydrogen bonds       : bond        0.03442 (  376)
  hydrogen bonds       : angle       5.62021 ( 1071)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2505.88 seconds
wall clock time: 43 minutes 34.58 seconds (2614.58 seconds total)