Starting phenix.real_space_refine
on Wed Sep 17 04:51:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j7m_61207/09_2025/9j7m_61207.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j7m_61207/09_2025/9j7m_61207.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j7m_61207/09_2025/9j7m_61207.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j7m_61207/09_2025/9j7m_61207.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j7m_61207/09_2025/9j7m_61207.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j7m_61207/09_2025/9j7m_61207.map"
  }
  resolution = 2.82
  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=   0.070
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: 6
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    3093      2.51       5
     N     664      2.21       5
     O     760      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  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: 4552
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4329
          Classifications: {'peptide': 543}
          Link IDs: {'PTRANS': 28, 'TRANS': 514}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 223
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 223
          Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 3, 'R16': 5, 'TAU': 1, 'Y01': 1}
          Classifications: {'undetermined': 12, 'water': 15}
          Link IDs: {None: 26}
  Time building chain proxies: 1.61, per 1000 atoms: 0.35
  Number of scatterers: 4552
  At special positions: 0
  Unit cell: (73.1, 64.6, 95.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      33     16.00
     Na      1     11.00
     O     760      8.00
     N     664      7.00
     C    3093      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 172.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  990

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 1 sheets defined
      75.7% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 59
      removed outlier: 3.599A  pdb=" N   PHE A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 65
      removed outlier: 3.620A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.980A  pdb=" N   TYR A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 90 through 106
    Processing helix  chain 'A' and resid 111 through 115
    Processing helix  chain 'A' and resid 121 through 138
      removed outlier: 4.313A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   TYR A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 152
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 217 through 237
    Processing helix  chain 'A' and resid 242 through 250
    Processing helix  chain 'A' and resid 251 through 266
      removed outlier: 3.716A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 3.671A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 4.019A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   PHE A 299 " --> pdb=" O   GLY A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 314
      removed outlier: 3.610A  pdb=" N   SER A 311 " --> pdb=" O   GLY A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 356
      removed outlier: 3.573A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 362
      removed outlier: 4.133A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
      Proline residue:  A 375  - end of helix
    Processing helix  chain 'A' and resid 383 through 416
      removed outlier: 3.565A  pdb=" N   TRP A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 444
      removed outlier: 3.522A  pdb=" N   PHE A 431 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 447
      No H-bonds generated for 'chain 'A' and resid 445 through 447'
    Processing helix  chain 'A' and resid 450 through 462
      removed outlier: 4.266A  pdb=" N   VAL A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 482
    Processing helix  chain 'A' and resid 484 through 497
      removed outlier: 3.568A  pdb=" N   GLY A 491 " --> pdb=" O   ASN A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 510
      removed outlier: 4.729A  pdb=" N   LYS A 505 " --> pdb=" O   GLY A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 526
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 4.406A  pdb=" N   SER A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   MET A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 567
      removed outlier: 3.652A  pdb=" N   LEU A 559 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532

    268 hydrogen bonds defined for protein.
    783 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: 0.66

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 899
        1.33 -     1.45: 1170
        1.45 -     1.57: 2564
        1.57 -     1.69: 3
        1.69 -     1.81: 47
  Bond restraints: 4683
  Sorted by residual:
  bond pdb=" N   ILE A 235 "
       pdb=" CA  ILE A 235 "
    ideal  model  delta    sigma   weight residual
    1.455  1.497 -0.042 1.06e-02 8.90e+03 1.54e+01
  bond pdb=" CAY Y01 A 710 "
       pdb=" OAW Y01 A 710 "
    ideal  model  delta    sigma   weight residual
    1.332  1.394 -0.062 2.00e-02 2.50e+03 9.59e+00
  bond pdb=" CAI Y01 A 710 "
       pdb=" CAZ Y01 A 710 "
    ideal  model  delta    sigma   weight residual
    1.332  1.394 -0.062 2.00e-02 2.50e+03 9.52e+00
  bond pdb=" N   HIS A 161 "
       pdb=" CA  HIS A 161 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.041 1.33e-02 5.65e+03 9.29e+00
  bond pdb=" N   THR A 168 "
       pdb=" CA  THR A 168 "
    ideal  model  delta    sigma   weight residual
    1.452  1.485 -0.033 1.11e-02 8.12e+03 8.97e+00
  ... (remaining 4678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 6258
        2.70 -     5.40: 102
        5.40 -     8.10: 11
        8.10 -    10.80: 1
       10.80 -    13.50: 2
  Bond angle restraints: 6374
  Sorted by residual:
  angle pdb=" CAM Y01 A 710 "
        pdb=" CAY Y01 A 710 "
        pdb=" OAW Y01 A 710 "
      ideal   model   delta    sigma   weight residual
     111.19  124.69  -13.50 3.00e+00 1.11e-01 2.03e+01
  angle pdb=" C   CYS A 162 "
        pdb=" CA  CYS A 162 "
        pdb=" CB  CYS A 162 "
      ideal   model   delta    sigma   weight residual
     111.46  103.92    7.54 1.71e+00 3.42e-01 1.94e+01
  angle pdb=" O2  TAU A 701 "
        pdb=" S   TAU A 701 "
        pdb=" O3  TAU A 701 "
      ideal   model   delta    sigma   weight residual
     113.11  101.14   11.97 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" N   PRO A 585 "
        pdb=" CA  PRO A 585 "
        pdb=" C   PRO A 585 "
      ideal   model   delta    sigma   weight residual
     110.95  104.73    6.22 1.62e+00 3.81e-01 1.47e+01
  angle pdb=" N   ILE A 235 "
        pdb=" CA  ILE A 235 "
        pdb=" C   ILE A 235 "
      ideal   model   delta    sigma   weight residual
     112.12  108.90    3.22 8.40e-01 1.42e+00 1.47e+01
  ... (remaining 6369 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 2472
       17.17 -    34.35: 285
       34.35 -    51.52: 90
       51.52 -    68.69: 18
       68.69 -    85.87: 3
  Dihedral angle restraints: 2868
    sinusoidal: 1304
      harmonic: 1564
  Sorted by residual:
  dihedral pdb=" CG  ARG A 177 "
           pdb=" CD  ARG A 177 "
           pdb=" NE  ARG A 177 "
           pdb=" CZ  ARG A 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.75  -43.75     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CB  LYS A  73 "
           pdb=" CG  LYS A  73 "
           pdb=" CD  LYS A  73 "
           pdb=" CE  LYS A  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.33  -58.33     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CA  LYS A 577 "
           pdb=" CB  LYS A 577 "
           pdb=" CG  LYS A 577 "
           pdb=" CD  LYS A 577 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.38   57.38     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 2865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 589
       0.064 -    0.129: 80
       0.129 -    0.193: 26
       0.193 -    0.257: 4
       0.257 -    0.322: 2
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" CBH Y01 A 710 "
            pdb=" CAT Y01 A 710 "
            pdb=" CAZ Y01 A 710 "
            pdb=" CBF Y01 A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.53   -0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CBF Y01 A 710 "
            pdb=" CAS Y01 A 710 "
            pdb=" CBD Y01 A 710 "
            pdb=" CBH Y01 A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.73    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" C14 CLR A 707 "
            pdb=" C13 CLR A 707 "
            pdb=" C15 CLR A 707 "
            pdb=" C8  CLR A 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.57    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 698 not shown)

  Planarity restraints: 746
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 423 "    0.259 9.50e-02 1.11e+02   1.16e-01 8.26e+00
        pdb=" NE  ARG A 423 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 423 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 423 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 423 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 427 "    0.227 9.50e-02 1.11e+02   1.02e-01 6.38e+00
        pdb=" NE  ARG A 427 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 427 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 427 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 427 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 577 "    0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   LYS A 577 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   LYS A 577 "    0.013 2.00e-02 2.50e+03
        pdb=" N   TYR A 578 "    0.012 2.00e-02 2.50e+03
  ... (remaining 743 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 391
        2.74 -     3.28: 4246
        3.28 -     3.82: 7407
        3.82 -     4.36: 8607
        4.36 -     4.90: 15665
  Nonbonded interactions: 36316
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 489 "
            pdb=" O   GLY A 501 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" ND2 ASN A  63 "
            pdb=" OD1 ASN A 333 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" O   VAL A  59 "
            pdb="NA    NA A 711 "
     model   vdw
     2.337 2.470
  nonbonded pdb=" O   SER A 365 "
            pdb=" OG  SER A 365 "
     model   vdw
     2.348 3.040
  nonbonded pdb="NA    NA A 711 "
            pdb=" O   HOH A 808 "
     model   vdw
     2.368 2.470
  ... (remaining 36311 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.980
  Find NCS groups from input model:        0.030
  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:6.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
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      :  0.006   0.062   4684  Z= 0.341
  Angle     :  0.817  13.502   6376  Z= 0.445
  Chirality :  0.055   0.322    701
  Planarity :  0.008   0.116    746
  Dihedral  : 15.915  85.866   1875
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.38 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.38), residues: 539
  helix:  1.79 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.58 (0.46), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 423 
 TYR   0.012   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A 474 
 TRP   0.020   0.001   TRP A 470 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 4683)
  covalent geometry    : angle       0.81639 ( 6374)
  SS BOND              : bond        0.01038 (    1)
  SS BOND              : angle       2.33479 (    2)
  hydrogen bonds       : bond        0.12678 (  268)
  hydrogen bonds       : angle       4.76216 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  442 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8140 (tt)
  outliers start: 16
  outliers final: 14
  residues processed: 62
  average time/residue: 0.4173
  time to fit residues: 27.3134
Evaluate side-chains
  62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  552 SER
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  573 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0050
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0070
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.4812

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.131549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.101088 restraints weight = 5097.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.70
r_work: 0.2936 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.0769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4684  Z= 0.102
  Angle     :  0.480   6.635   6376  Z= 0.248
  Chirality :  0.037   0.161    701
  Planarity :  0.004   0.040    746
  Dihedral  :  9.187  58.415    944
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.31 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.35 (0.38), residues: 539
  helix:  1.85 (0.28), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.53 (0.47), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 423 
 TYR   0.016   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A  79 
 TRP   0.017   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 4683)
  covalent geometry    : angle       0.47621 ( 6374)
  SS BOND              : bond        0.00326 (    1)
  SS BOND              : angle       3.47344 (    2)
  hydrogen bonds       : bond        0.04317 (  268)
  hydrogen bonds       : angle       3.90085 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7538 (p90)
REVERT: A  114 GLU cc_start: 0.7839 (tp30) cc_final: 0.7548 (mm-30)
REVERT: A  358 ASP cc_start: 0.7331 (m-30) cc_final: 0.7058 (m-30)
REVERT: A  380 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7041 (mtp)
  outliers start: 12
  outliers final: 3
  residues processed: 56
  average time/residue: 0.4549
  time to fit residues: 26.8235
Evaluate side-chains
  48 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  380 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 49 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.127095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.096871 restraints weight = 5063.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.65
r_work: 0.2887 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4684  Z= 0.128
  Angle     :  0.507   5.820   6376  Z= 0.266
  Chirality :  0.038   0.151    701
  Planarity :  0.004   0.044    746
  Dihedral  :  8.234  56.209    927
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.17 %
    Favored  : 79.83 %
  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:  1.44 (0.37), residues: 539
  helix:  1.96 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.33 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  41 
 TYR   0.022   0.001   TYR A  69 
 PHE   0.017   0.002   PHE A  79 
 TRP   0.015   0.001   TRP A 470 
 HIS   0.003   0.002   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4683)
  covalent geometry    : angle       0.50579 ( 6374)
  SS BOND              : bond        0.00293 (    1)
  SS BOND              : angle       1.85443 (    2)
  hydrogen bonds       : bond        0.05402 (  268)
  hydrogen bonds       : angle       3.98665 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7623 (p90)
REVERT: A  358 ASP cc_start: 0.7354 (m-30) cc_final: 0.7137 (m-30)
REVERT: A  380 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7036 (mtp)
  outliers start: 14
  outliers final: 8
  residues processed: 57
  average time/residue: 0.4106
  time to fit residues: 24.6916
Evaluate side-chains
  56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0370
   chunk 51 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0970
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.3656

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.132452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.102167 restraints weight = 5059.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.71
r_work: 0.2988 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4684  Z= 0.091
  Angle     :  0.439   5.510   6376  Z= 0.228
  Chirality :  0.035   0.121    701
  Planarity :  0.004   0.039    746
  Dihedral  :  7.476  59.926    927
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.24 %
    Favored  : 79.61 %
  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:  1.77 (0.37), residues: 539
  helix:  2.22 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.21 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  66 
 TYR   0.013   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A 474 
 TRP   0.019   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 4683)
  covalent geometry    : angle       0.43836 ( 6374)
  SS BOND              : bond        0.00357 (    1)
  SS BOND              : angle       1.42186 (    2)
  hydrogen bonds       : bond        0.03730 (  268)
  hydrogen bonds       : angle       3.77855 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7427 (p90)
REVERT: A  358 ASP cc_start: 0.7426 (m-30) cc_final: 0.7185 (m-30)
REVERT: A  380 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7075 (mtp)
  outliers start: 10
  outliers final: 6
  residues processed: 56
  average time/residue: 0.4905
  time to fit residues: 28.7878
Evaluate side-chains
  53 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.126288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.095506 restraints weight = 5050.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 1.74
r_work: 0.2867 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4684  Z= 0.142
  Angle     :  0.521   5.932   6376  Z= 0.272
  Chirality :  0.039   0.154    701
  Planarity :  0.005   0.044    746
  Dihedral  :  7.824  57.155    925
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.38 %
    Favored  : 80.04 %
  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:  1.48 (0.37), residues: 539
  helix:  1.98 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.29 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  41 
 TYR   0.023   0.001   TYR A  69 
 PHE   0.017   0.002   PHE A  79 
 TRP   0.017   0.001   TRP A 236 
 HIS   0.003   0.002   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4683)
  covalent geometry    : angle       0.51973 ( 6374)
  SS BOND              : bond        0.00424 (    1)
  SS BOND              : angle       1.85265 (    2)
  hydrogen bonds       : bond        0.05673 (  268)
  hydrogen bonds       : angle       3.97122 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8062 (p90)
REVERT: A  358 ASP cc_start: 0.7669 (m-30) cc_final: 0.7448 (m-30)
REVERT: A  380 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7442 (mtp)
REVERT: A  563 ILE cc_start: 0.7026 (mt) cc_final: 0.6758 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 56
  average time/residue: 0.4052
  time to fit residues: 23.9906
Evaluate side-chains
  53 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3455 r_free = 0.3455 target = 0.129396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.098908 restraints weight = 5153.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.71
r_work: 0.2943 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4684  Z= 0.102
  Angle     :  0.463   5.680   6376  Z= 0.242
  Chirality :  0.037   0.136    701
  Planarity :  0.004   0.043    746
  Dihedral  :  7.387  52.402    925
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.38 %
    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:  1.71 (0.37), residues: 539
  helix:  2.12 (0.28), residues: 368
  sheet:  None (None), residues: 0
  loop : -1.13 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  41 
 TYR   0.017   0.001   TYR A  69 
 PHE   0.013   0.001   PHE A 474 
 TRP   0.019   0.001   TRP A 236 
 HIS   0.002   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 4683)
  covalent geometry    : angle       0.46231 ( 6374)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       1.56677 (    2)
  hydrogen bonds       : bond        0.04413 (  268)
  hydrogen bonds       : angle       3.84471 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7477 (p90)
REVERT: A  358 ASP cc_start: 0.7381 (m-30) cc_final: 0.7143 (m-30)
REVERT: A  380 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7044 (mtp)
  outliers start: 10
  outliers final: 6
  residues processed: 54
  average time/residue: 0.4678
  time to fit residues: 26.5907
Evaluate side-chains
  53 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 51 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0370
   chunk 52 optimal weight:    0.0770
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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 = 0.3467 r_free = 0.3467 target = 0.130478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.100030 restraints weight = 5154.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 1.71
r_work: 0.2991 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4684  Z= 0.091
  Angle     :  0.439   5.573   6376  Z= 0.228
  Chirality :  0.035   0.121    701
  Planarity :  0.004   0.040    746
  Dihedral  :  7.000  58.757    925
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.60 %
    Favored  : 79.83 %
  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:  1.93 (0.37), residues: 539
  helix:  2.30 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.05 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 583 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.011   0.001   PHE A 474 
 TRP   0.024   0.001   TRP A 236 
 HIS   0.001   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 4683)
  covalent geometry    : angle       0.43841 ( 6374)
  SS BOND              : bond        0.00286 (    1)
  SS BOND              : angle       1.33945 (    2)
  hydrogen bonds       : bond        0.03777 (  268)
  hydrogen bonds       : angle       3.72167 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7497 (p90)
REVERT: A  358 ASP cc_start: 0.7435 (m-30) cc_final: 0.6814 (t0)
REVERT: A  359 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7247 (mt)
REVERT: A  380 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7090 (mtp)
REVERT: A  498 TYR cc_start: 0.8079 (p90) cc_final: 0.7793 (p90)
  outliers start: 12
  outliers final: 6
  residues processed: 57
  average time/residue: 0.4447
  time to fit residues: 26.7474
Evaluate side-chains
  57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0170
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 = 0.3467 r_free = 0.3467 target = 0.130458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.100037 restraints weight = 5152.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.70
r_work: 0.2986 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4684  Z= 0.093
  Angle     :  0.445   5.571   6376  Z= 0.231
  Chirality :  0.036   0.126    701
  Planarity :  0.004   0.040    746
  Dihedral  :  6.787  53.499    925
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.60 %
    Favored  : 80.04 %
  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:  1.86 (0.37), residues: 539
  helix:  2.22 (0.28), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.14 (0.47), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 583 
 TYR   0.016   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A  79 
 TRP   0.029   0.001   TRP A 236 
 HIS   0.001   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 4683)
  covalent geometry    : angle       0.44444 ( 6374)
  SS BOND              : bond        0.00277 (    1)
  SS BOND              : angle       1.30381 (    2)
  hydrogen bonds       : bond        0.03919 (  268)
  hydrogen bonds       : angle       3.71686 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7368 (p90)
REVERT: A  358 ASP cc_start: 0.7293 (m-30) cc_final: 0.6665 (t0)
REVERT: A  359 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7155 (mt)
REVERT: A  380 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6991 (mtp)
  outliers start: 11
  outliers final: 8
  residues processed: 56
  average time/residue: 0.4409
  time to fit residues: 26.0362
Evaluate side-chains
  58 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0670
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7318

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.128133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.097592 restraints weight = 5122.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.69
r_work: 0.2928 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4684  Z= 0.106
  Angle     :  0.468   5.712   6376  Z= 0.244
  Chirality :  0.037   0.137    701
  Planarity :  0.004   0.041    746
  Dihedral  :  6.806  55.950    925
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.17 %
    Favored  : 80.26 %
  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:  1.86 (0.37), residues: 539
  helix:  2.25 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -1.09 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 583 
 TYR   0.019   0.001   TYR A  69 
 PHE   0.013   0.001   PHE A  79 
 TRP   0.033   0.001   TRP A 236 
 HIS   0.002   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 4683)
  covalent geometry    : angle       0.46782 ( 6374)
  SS BOND              : bond        0.00316 (    1)
  SS BOND              : angle       1.48979 (    2)
  hydrogen bonds       : bond        0.04524 (  268)
  hydrogen bonds       : angle       3.78377 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7649 (p90)
REVERT: A  358 ASP cc_start: 0.7352 (m-30) cc_final: 0.6743 (t0)
REVERT: A  359 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7238 (mt)
REVERT: A  380 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7094 (mtp)
  outliers start: 12
  outliers final: 8
  residues processed: 57
  average time/residue: 0.4480
  time to fit residues: 26.9603
Evaluate side-chains
  57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0020
   chunk 9 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0570
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5106

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.129684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.099334 restraints weight = 5158.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.70
r_work: 0.2981 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4684  Z= 0.095
  Angle     :  0.452   5.592   6376  Z= 0.235
  Chirality :  0.036   0.128    701
  Planarity :  0.004   0.040    746
  Dihedral  :  6.602  55.151    925
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.81 %
    Favored  : 79.83 %
  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:  1.99 (0.37), residues: 539
  helix:  2.34 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.99 (0.45), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 583 
 TYR   0.016   0.001   TYR A  69 
 PHE   0.011   0.001   PHE A  79 
 TRP   0.038   0.001   TRP A 236 
 HIS   0.001   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 4683)
  covalent geometry    : angle       0.45154 ( 6374)
  SS BOND              : bond        0.00302 (    1)
  SS BOND              : angle       1.36456 (    2)
  hydrogen bonds       : bond        0.04015 (  268)
  hydrogen bonds       : angle       3.72277 (  783)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7368 (p90)
REVERT: A  358 ASP cc_start: 0.7329 (m-30) cc_final: 0.6711 (t0)
REVERT: A  359 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7164 (mt)
REVERT: A  380 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7025 (mtp)
  outliers start: 11
  outliers final: 7
  residues processed: 54
  average time/residue: 0.4772
  time to fit residues: 27.2019
Evaluate side-chains
  56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.128815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.098400 restraints weight = 5196.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.70
r_work: 0.2970 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4684  Z= 0.100
  Angle     :  0.461   5.656   6376  Z= 0.240
  Chirality :  0.036   0.132    701
  Planarity :  0.004   0.040    746
  Dihedral  :  6.647  57.369    925
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.60 %
    Favored  : 80.04 %
  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:  1.85 (0.37), residues: 539
  helix:  2.21 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.13 (0.46), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 583 
 TYR   0.018   0.001   TYR A  69 
 PHE   0.013   0.001   PHE A  79 
 TRP   0.039   0.001   TRP A 236 
 HIS   0.001   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 4683)
  covalent geometry    : angle       0.46005 ( 6374)
  SS BOND              : bond        0.00306 (    1)
  SS BOND              : angle       1.40963 (    2)
  hydrogen bonds       : bond        0.04239 (  268)
  hydrogen bonds       : angle       3.73736 (  783)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1616.79 seconds
wall clock time: 28 minutes 22.78 seconds (1702.78 seconds total)