Starting phenix.real_space_refine
on Fri Aug 22 15:17:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bw7_16280/08_2025/8bw7_16280.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bw7_16280/08_2025/8bw7_16280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bw7_16280/08_2025/8bw7_16280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bw7_16280/08_2025/8bw7_16280.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bw7_16280/08_2025/8bw7_16280.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bw7_16280/08_2025/8bw7_16280.cif"
  }
  resolution = 3.53
  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=  -0.001 sd=   0.060
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: 5
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     Cl      1      4.86       5
     C    3069      2.51       5
     N     804      2.21       5
     O     839      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4748
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3842
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 25, 'TRANS': 471}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 895
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 11
          Unusual residues: {' CL': 1, 'AKG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.34, per 1000 atoms: 0.28
  Number of scatterers: 4748
  At special positions: 0
  Unit cell: (118.144, 69.888, 80.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      35     16.00
     O     839      8.00
     N     804      7.00
     C    3069      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03

  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: 0.43
  Conformation dependent library (CDL) restraints added in 176.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1124

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      67.2% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.726A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 25
    Processing helix  chain 'A' and resid 27 through 37
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 127 through 131
    Processing helix  chain 'A' and resid 132 through 160
      removed outlier: 3.868A  pdb=" N   PHE A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   TYR A 154 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 181
    Processing helix  chain 'A' and resid 184 through 214
      removed outlier: 3.547A  pdb=" N   TYR A 188 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   MET A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   THR A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 244
      removed outlier: 3.867A  pdb=" N   ALA A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA A 238 " --> pdb=" O   GLN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 265
      removed outlier: 3.849A  pdb=" N   LEU A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      Proline residue:  A 257  - end of helix
      removed outlier: 3.675A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 268
      No H-bonds generated for 'chain 'A' and resid 266 through 268'
    Processing helix  chain 'A' and resid 271 through 278
      removed outlier: 3.564A  pdb=" N   TYR A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 296
    Processing helix  chain 'A' and resid 297 through 302
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 326 through 332
      removed outlier: 3.501A  pdb=" N   LEU A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 358
    Processing helix  chain 'A' and resid 366 through 392
      removed outlier: 3.563A  pdb=" N   ASP A 378 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   LEU A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 394 through 415
      removed outlier: 4.098A  pdb=" N   LEU A 404 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 449
      removed outlier: 3.882A  pdb=" N   GLU A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   TYR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 477
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 484 through 501
      Proline residue:  A 494  - end of helix
    Processing helix  chain 'A' and resid 502 through 504
      No H-bonds generated for 'chain 'A' and resid 502 through 504'
    Processing helix  chain 'A' and resid 515 through 525
      removed outlier: 3.509A  pdb=" N   ARG A 524 " --> pdb=" O   LYS A 520 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLY A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 56
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 4.257A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.539A  pdb=" N   SER B  21 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11
      removed outlier: 3.631A  pdb=" N   THR B 109 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL B  93 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN B  39 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    861 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: 0.71

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1309
        1.34 -     1.46: 928
        1.46 -     1.58: 2568
        1.58 -     1.70: 0
        1.70 -     1.82: 55
  Bond restraints: 4860
  Sorted by residual:
  bond pdb=" C1  AKG A 601 "
       pdb=" O2  AKG A 601 "
    ideal  model  delta    sigma   weight residual
    1.239  1.308 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" C5  AKG A 601 "
       pdb=" O3  AKG A 601 "
    ideal  model  delta    sigma   weight residual
    1.247  1.309 -0.062 2.00e-02 2.50e+03 9.48e+00
  bond pdb=" C4  AKG A 601 "
       pdb=" C5  AKG A 601 "
    ideal  model  delta    sigma   weight residual
    1.540  1.500  0.040 2.00e-02 2.50e+03 3.97e+00
  bond pdb=" C   VAL A 493 "
       pdb=" N   PRO A 494 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 1.36e-02 5.41e+03 3.35e+00
  bond pdb=" C5  AKG A 601 "
       pdb=" O4  AKG A 601 "
    ideal  model  delta    sigma   weight residual
    1.249  1.214  0.035 2.00e-02 2.50e+03 3.02e+00
  ... (remaining 4855 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 6475
        1.86 -     3.71: 102
        3.71 -     5.57: 20
        5.57 -     7.43: 8
        7.43 -     9.28: 2
  Bond angle restraints: 6607
  Sorted by residual:
  angle pdb=" C   CYS A 128 "
        pdb=" CA  CYS A 128 "
        pdb=" CB  CYS A 128 "
      ideal   model   delta    sigma   weight residual
     117.23  110.12    7.11 1.36e+00 5.41e-01 2.74e+01
  angle pdb=" O   SER B 114 "
        pdb=" C   SER B 114 "
        pdb=" N   ALA B 115 "
      ideal   model   delta    sigma   weight residual
     121.20  114.21    6.99 1.61e+00 3.86e-01 1.88e+01
  angle pdb=" CA  CYS A 128 "
        pdb=" C   CYS A 128 "
        pdb=" N   SER A 129 "
      ideal   model   delta    sigma   weight residual
     119.98  116.68    3.30 8.50e-01 1.38e+00 1.51e+01
  angle pdb=" N   VAL B  64 "
        pdb=" CA  VAL B  64 "
        pdb=" C   VAL B  64 "
      ideal   model   delta    sigma   weight residual
     113.53  109.77    3.76 9.80e-01 1.04e+00 1.47e+01
  angle pdb=" CA  GLN A 314 "
        pdb=" CB  GLN A 314 "
        pdb=" CG  GLN A 314 "
      ideal   model   delta    sigma   weight residual
     114.10  120.89   -6.79 2.00e+00 2.50e-01 1.15e+01
  ... (remaining 6602 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 2429
       17.94 -    35.88: 319
       35.88 -    53.83: 93
       53.83 -    71.77: 10
       71.77 -    89.71: 8
  Dihedral angle restraints: 2859
    sinusoidal: 1101
      harmonic: 1758
  Sorted by residual:
  dihedral pdb=" CB  CYS A  78 "
           pdb=" SG  CYS A  78 "
           pdb=" SG  CYS A 128 "
           pdb=" CB  CYS A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.65   76.65     1      1.00e+01 1.00e-02 7.38e+01
  dihedral pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 105 "
           pdb=" CB  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.89   49.89     1      1.00e+01 1.00e-02 3.41e+01
  dihedral pdb=" CA  PRO A 215 "
           pdb=" C   PRO A 215 "
           pdb=" N   ILE A 216 "
           pdb=" CA  ILE A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 2856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 512
       0.034 -    0.067: 173
       0.067 -    0.101: 53
       0.101 -    0.135: 15
       0.135 -    0.169: 2
  Chirality restraints: 755
  Sorted by residual:
  chirality pdb=" CG  LEU A 199 "
            pdb=" CB  LEU A 199 "
            pdb=" CD1 LEU A 199 "
            pdb=" CD2 LEU A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.10e-01
  chirality pdb=" CA  ASN A 125 "
            pdb=" N   ASN A 125 "
            pdb=" C   ASN A 125 "
            pdb=" CB  ASN A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  ILE A  44 "
            pdb=" N   ILE A  44 "
            pdb=" C   ILE A  44 "
            pdb=" CB  ILE A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  ... (remaining 752 not shown)

  Planarity restraints: 827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 114 "    0.039 2.00e-02 2.50e+03   7.29e-02 5.32e+01
        pdb=" C   SER B 114 "   -0.126 2.00e-02 2.50e+03
        pdb=" O   SER B 114 "    0.046 2.00e-02 2.50e+03
        pdb=" N   ALA B 115 "    0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 493 "   -0.044 5.00e-02 4.00e+02   6.77e-02 7.32e+00
        pdb=" N   PRO A 494 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 494 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 494 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 214 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO A 215 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 215 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 215 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 824 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 150
        2.71 -     3.26: 4849
        3.26 -     3.81: 8060
        3.81 -     4.35: 9223
        4.35 -     4.90: 16054
  Nonbonded interactions: 38336
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 133 "
            pdb=" OH  TYR A 185 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OG  SER A 175 "
            pdb=" O   PHE A 191 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   ASP A  70 "
            pdb=" NH2 ARG B  59 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" N   GLN A 455 "
            pdb=" OE1 GLN A 455 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE1 GLU A 212 "
            pdb=" OG  SER A 271 "
     model   vdw
     2.297 3.040
  ... (remaining 38331 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 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:             1.620
  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:         0.030
  Set scattering table:                    0.010
  Process input model:                     6.310
  Find NCS groups from input model:        0.020
  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:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
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   0.069   4863  Z= 0.155
  Angle     :  0.623   9.283   6613  Z= 0.324
  Chirality :  0.039   0.169    755
  Planarity :  0.005   0.073    827
  Dihedral  : 17.605  89.709   1726
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 34.58 %
    Favored  : 65.42 %
  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:  0.80 (0.36), residues: 604
  helix:  1.55 (0.29), residues: 357
  sheet: -1.79 (0.69), residues: 44
  loop : -0.69 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  59 
 TYR   0.008   0.001   TYR A 169 
 PHE   0.008   0.001   PHE A 191 
 TRP   0.011   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4860)
  covalent geometry    : angle       0.62220 ( 6607)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       0.98330 (    6)
  hydrogen bonds       : bond        0.14251 (  297)
  hydrogen bonds       : angle       5.44880 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   31 MET cc_start: 0.7041 (tpt) cc_final: 0.6324 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0526
  time to fit residues: 6.1152
Evaluate side-chains
  77 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.4772 r_free = 0.4772 target = 0.253492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.206779 restraints weight = 6265.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.212118 restraints weight = 3439.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.215266 restraints weight = 2383.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.217613 restraints weight = 1919.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.218622 restraints weight = 1682.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.4478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4863  Z= 0.135
  Angle     :  0.573   7.210   6613  Z= 0.291
  Chirality :  0.039   0.158    755
  Planarity :  0.004   0.056    827
  Dihedral  :  4.317  47.084    671
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 33.01 %
    Favored  : 63.65 %
  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:  0.71 (0.36), residues: 604
  helix:  1.50 (0.28), residues: 364
  sheet: -1.85 (0.69), residues: 44
  loop : -0.85 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  59 
 TYR   0.010   0.001   TYR B  80 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4860)
  covalent geometry    : angle       0.57217 ( 6607)
  SS BOND              : bond        0.00657 (    3)
  SS BOND              : angle       1.28526 (    6)
  hydrogen bonds       : bond        0.04569 (  297)
  hydrogen bonds       : angle       4.62781 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   31 MET cc_start: 0.7064 (tpt) cc_final: 0.6296 (tpt)
  outliers start: 17
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0486
  time to fit residues: 6.2379
Evaluate side-chains
  90 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0370
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.8860

-------------------------------------------------------------------------------
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 = 0.4766 r_free = 0.4766 target = 0.251789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.205957 restraints weight = 6179.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.211129 restraints weight = 3393.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.214383 restraints weight = 2347.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.216518 restraints weight = 1882.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.217524 restraints weight = 1649.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4863  Z= 0.144
  Angle     :  0.560   6.456   6613  Z= 0.285
  Chirality :  0.040   0.160    755
  Planarity :  0.004   0.052    827
  Dihedral  :  4.307  45.784    671
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 33.20 %
    Favored  : 62.08 %
  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:  0.64 (0.36), residues: 604
  helix:  1.44 (0.28), residues: 364
  sheet: -1.80 (0.64), residues: 50
  loop : -0.86 (0.48), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  59 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4860)
  covalent geometry    : angle       0.55878 ( 6607)
  SS BOND              : bond        0.00693 (    3)
  SS BOND              : angle       1.17047 (    6)
  hydrogen bonds       : bond        0.04559 (  297)
  hydrogen bonds       : angle       4.54829 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   31 MET cc_start: 0.7071 (tpt) cc_final: 0.6269 (tpt)
REVERT: B   84 ASN cc_start: 0.4801 (p0) cc_final: 0.3665 (m-40)
  outliers start: 24
  outliers final: 15
  residues processed: 96
  average time/residue: 0.0498
  time to fit residues: 6.7902
Evaluate side-chains
  95 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0570
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.4713 r_free = 0.4713 target = 0.235073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.197599 restraints weight = 6043.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.201771 restraints weight = 3732.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.204558 restraints weight = 2748.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.206243 restraints weight = 2276.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.207088 restraints weight = 2031.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.4497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4863  Z= 0.122
  Angle     :  0.555   6.707   6613  Z= 0.279
  Chirality :  0.039   0.164    755
  Planarity :  0.004   0.055    827
  Dihedral  :  4.221  43.023    671
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 35.36 %
    Favored  : 61.49 %
  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:  0.67 (0.36), residues: 604
  helix:  1.47 (0.28), residues: 370
  sheet: -1.69 (0.65), residues: 50
  loop : -0.97 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 4860)
  covalent geometry    : angle       0.55251 ( 6607)
  SS BOND              : bond        0.00522 (    3)
  SS BOND              : angle       1.71189 (    6)
  hydrogen bonds       : bond        0.04252 (  297)
  hydrogen bonds       : angle       4.43091 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   31 MET cc_start: 0.7117 (tpt) cc_final: 0.6448 (tpt)
REVERT: A  212 GLU cc_start: 0.7416 (tt0) cc_final: 0.7176 (mt-10)
REVERT: B   84 ASN cc_start: 0.4576 (p0) cc_final: 0.3666 (m-40)
  outliers start: 16
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0505
  time to fit residues: 7.0028
Evaluate side-chains
  92 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4709 r_free = 0.4709 target = 0.234630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.197061 restraints weight = 6032.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.201259 restraints weight = 3740.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.203974 restraints weight = 2753.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.205323 restraints weight = 2285.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.206675 restraints weight = 2053.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4863  Z= 0.128
  Angle     :  0.565   7.618   6613  Z= 0.284
  Chirality :  0.039   0.164    755
  Planarity :  0.004   0.056    827
  Dihedral  :  4.197  41.647    671
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 33.60 %
    Favored  : 62.28 %
  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:  0.76 (0.36), residues: 604
  helix:  1.54 (0.28), residues: 364
  sheet: -1.67 (0.65), residues: 50
  loop : -0.84 (0.48), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.010   0.001   PHE A 351 
 TRP   0.007   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4860)
  covalent geometry    : angle       0.56386 ( 6607)
  SS BOND              : bond        0.00516 (    3)
  SS BOND              : angle       1.39225 (    6)
  hydrogen bonds       : bond        0.04249 (  297)
  hydrogen bonds       : angle       4.38226 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   31 MET cc_start: 0.7102 (tpt) cc_final: 0.6457 (tpt)
REVERT: A  212 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7183 (mt-10)
REVERT: B   84 ASN cc_start: 0.4595 (p0) cc_final: 0.3659 (m-40)
  outliers start: 21
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0496
  time to fit residues: 6.9059
Evaluate side-chains
  97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 6 optimal weight:    0.0970
   chunk 4 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.4655 r_free = 0.4655 target = 0.229632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.190334 restraints weight = 6236.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.194578 restraints weight = 3917.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.196896 restraints weight = 2907.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.198919 restraints weight = 2431.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.199667 restraints weight = 2181.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4863  Z= 0.130
  Angle     :  0.557   6.790   6613  Z= 0.282
  Chirality :  0.039   0.164    755
  Planarity :  0.004   0.056    827
  Dihedral  :  4.149  40.342    671
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 34.18 %
    Favored  : 61.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.36), residues: 604
  helix:  1.48 (0.28), residues: 370
  sheet: -1.58 (0.65), residues: 50
  loop : -0.89 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 247 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4860)
  covalent geometry    : angle       0.55502 ( 6607)
  SS BOND              : bond        0.00519 (    3)
  SS BOND              : angle       1.54761 (    6)
  hydrogen bonds       : bond        0.04273 (  297)
  hydrogen bonds       : angle       4.34153 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.206 
Fit side-chains
REVERT: B   84 ASN cc_start: 0.4748 (p0) cc_final: 0.3818 (m-40)
  outliers start: 21
  outliers final: 17
  residues processed: 99
  average time/residue: 0.0545
  time to fit residues: 7.6689
Evaluate side-chains
  98 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 51 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0050
   chunk 27 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0870
   overall best weight:    0.4372

-------------------------------------------------------------------------------
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 = 0.4741 r_free = 0.4741 target = 0.247157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.204829 restraints weight = 6424.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.209716 restraints weight = 3747.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.212818 restraints weight = 2657.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.214394 restraints weight = 2158.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.215742 restraints weight = 1917.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4863  Z= 0.119
  Angle     :  0.561   6.909   6613  Z= 0.280
  Chirality :  0.039   0.165    755
  Planarity :  0.004   0.057    827
  Dihedral  :  4.142  38.542    671
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 33.20 %
    Favored  : 62.08 %
  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:  0.80 (0.36), residues: 604
  helix:  1.55 (0.28), residues: 369
  sheet: -1.71 (0.69), residues: 44
  loop : -0.87 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4860)
  covalent geometry    : angle       0.55968 ( 6607)
  SS BOND              : bond        0.00504 (    3)
  SS BOND              : angle       1.53367 (    6)
  hydrogen bonds       : bond        0.04091 (  297)
  hydrogen bonds       : angle       4.27852 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6878 (tpt) cc_final: 0.6271 (tpt)
REVERT: A   64 GLU cc_start: 0.6289 (tm-30) cc_final: 0.5811 (mp0)
REVERT: A  206 CYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7762 (t)
REVERT: B   84 ASN cc_start: 0.4800 (p0) cc_final: 0.3841 (m-40)
  outliers start: 24
  outliers final: 17
  residues processed: 102
  average time/residue: 0.0532
  time to fit residues: 7.6193
Evaluate side-chains
  97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0000
   chunk 9 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.231416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.192583 restraints weight = 6197.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.196773 restraints weight = 3893.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.199206 restraints weight = 2891.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.201212 restraints weight = 2407.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.201457 restraints weight = 2153.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4863  Z= 0.120
  Angle     :  0.563   6.823   6613  Z= 0.280
  Chirality :  0.039   0.165    755
  Planarity :  0.004   0.057    827
  Dihedral  :  4.086  37.232    671
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 34.18 %
    Favored  : 61.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.36), residues: 604
  helix:  1.56 (0.28), residues: 369
  sheet: -1.73 (0.69), residues: 44
  loop : -0.81 (0.48), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 351 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4860)
  covalent geometry    : angle       0.56131 ( 6607)
  SS BOND              : bond        0.00456 (    3)
  SS BOND              : angle       1.35688 (    6)
  hydrogen bonds       : bond        0.04073 (  297)
  hydrogen bonds       : angle       4.25241 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6998 (tpt) cc_final: 0.6388 (tpt)
REVERT: A   64 GLU cc_start: 0.6238 (tm-30) cc_final: 0.5835 (mp0)
REVERT: A  206 CYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7773 (t)
REVERT: A  512 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5749 (mt)
REVERT: B   84 ASN cc_start: 0.4669 (p0) cc_final: 0.3770 (m-40)
  outliers start: 21
  outliers final: 17
  residues processed: 101
  average time/residue: 0.0512
  time to fit residues: 7.4331
Evaluate side-chains
  101 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0270
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.6040

-------------------------------------------------------------------------------
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 = 0.4669 r_free = 0.4669 target = 0.231051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.192394 restraints weight = 6086.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.196529 restraints weight = 3846.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.199260 restraints weight = 2868.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.200624 restraints weight = 2394.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.201839 restraints weight = 2156.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4863  Z= 0.126
  Angle     :  0.583   7.253   6613  Z= 0.288
  Chirality :  0.040   0.164    755
  Planarity :  0.004   0.057    827
  Dihedral  :  4.098  36.730    671
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 34.58 %
    Favored  : 61.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.36), residues: 604
  helix:  1.57 (0.28), residues: 369
  sheet: -1.73 (0.71), residues: 44
  loop : -0.79 (0.48), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.010   0.001   PHE A 351 
 TRP   0.007   0.001   TRP A 247 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4860)
  covalent geometry    : angle       0.58156 ( 6607)
  SS BOND              : bond        0.00488 (    3)
  SS BOND              : angle       1.29850 (    6)
  hydrogen bonds       : bond        0.04076 (  297)
  hydrogen bonds       : angle       4.25135 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   31 MET cc_start: 0.7074 (tpt) cc_final: 0.6479 (tpt)
REVERT: A   64 GLU cc_start: 0.6248 (tm-30) cc_final: 0.5818 (mp0)
REVERT: A  206 CYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7767 (t)
REVERT: B   84 ASN cc_start: 0.4532 (p0) cc_final: 0.3666 (m-40)
  outliers start: 19
  outliers final: 17
  residues processed: 102
  average time/residue: 0.0475
  time to fit residues: 7.0363
Evaluate side-chains
  101 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0670
   chunk 50 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6920

-------------------------------------------------------------------------------
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 = 0.4654 r_free = 0.4654 target = 0.229353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.190274 restraints weight = 6108.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.194327 restraints weight = 3878.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.196862 restraints weight = 2907.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.198693 restraints weight = 2432.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.199374 restraints weight = 2179.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4863  Z= 0.134
  Angle     :  0.595   7.953   6613  Z= 0.295
  Chirality :  0.040   0.165    755
  Planarity :  0.004   0.057    827
  Dihedral  :  4.104  36.263    671
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 34.77 %
    Favored  : 61.30 %
  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:  0.81 (0.36), residues: 604
  helix:  1.55 (0.28), residues: 368
  sheet: -1.71 (0.73), residues: 44
  loop : -0.82 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.009   0.001   TRP B  52 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4860)
  covalent geometry    : angle       0.59369 ( 6607)
  SS BOND              : bond        0.00542 (    3)
  SS BOND              : angle       1.38622 (    6)
  hydrogen bonds       : bond        0.04196 (  297)
  hydrogen bonds       : angle       4.27983 (  861)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   31 MET cc_start: 0.7094 (tpt) cc_final: 0.6525 (tpt)
REVERT: A   64 GLU cc_start: 0.6381 (tm-30) cc_final: 0.5904 (mp0)
REVERT: A  206 CYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7800 (t)
REVERT: A  512 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5720 (mt)
REVERT: B   84 ASN cc_start: 0.4590 (p0) cc_final: 0.3731 (m-40)
  outliers start: 20
  outliers final: 18
  residues processed: 103
  average time/residue: 0.0450
  time to fit residues: 6.6834
Evaluate side-chains
  103 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 58 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4647 r_free = 0.4647 target = 0.228759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.189526 restraints weight = 6203.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.193748 restraints weight = 3899.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.196132 restraints weight = 2898.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.198152 restraints weight = 2425.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.198891 restraints weight = 2176.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4863  Z= 0.137
  Angle     :  0.595   9.023   6613  Z= 0.296
  Chirality :  0.040   0.165    755
  Planarity :  0.004   0.058    827
  Dihedral  :  4.132  36.243    671
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 34.58 %
    Favored  : 61.30 %
  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:  0.81 (0.36), residues: 604
  helix:  1.55 (0.28), residues: 368
  sheet: -1.71 (0.75), residues: 44
  loop : -0.83 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.022   0.001   TRP B  52 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4860)
  covalent geometry    : angle       0.59413 ( 6607)
  SS BOND              : bond        0.00538 (    3)
  SS BOND              : angle       1.39714 (    6)
  hydrogen bonds       : bond        0.04213 (  297)
  hydrogen bonds       : angle       4.26213 (  861)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1130.08 seconds
wall clock time: 20 minutes 8.97 seconds (1208.97 seconds total)