Starting phenix.real_space_refine
on Wed Jun  4 11:29:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c8p_16490/06_2025/8c8p_16490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c8p_16490/06_2025/8c8p_16490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c8p_16490/06_2025/8c8p_16490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c8p_16490/06_2025/8c8p_16490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c8p_16490/06_2025/8c8p_16490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c8p_16490/06_2025/8c8p_16490.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    1564      2.51       5
     N     409      2.21       5
     O     464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 2449
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "H"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 913
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
  Time building chain proxies: 4.02, per 1000 atoms: 1.64
  Number of scatterers: 2449
  At special positions: 0
  Unit cell: (60.1938, 67.9967, 85.8319, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     464      8.00
     N     409      7.00
     C    1564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " 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: 0.66
  Conformation dependent library (CDL) restraints added in 345.2 milliseconds
  

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  566

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 6 sheets defined
      13.4% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.775A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.901A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.677A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 4.008A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.733A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.682A  pdb=" N   ALA H  23 " --> pdb=" O   VAL H   5 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   THR H   7 " --> pdb=" O   SER H  21 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER H  21 " --> pdb=" O   THR H   7 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR H  77 " --> pdb=" O   ASP H  72 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN H  81 " --> pdb=" O   THR H  68 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR H  68 " --> pdb=" O   GLN H  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.420A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA H  96 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR H 114 " --> pdb=" O   TYR H  93 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.232A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474

    57 hydrogen bonds defined for protein.
    141 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: 0.93

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 785
        1.34 -     1.46: 673
        1.46 -     1.58: 1041
        1.58 -     1.70: 0
        1.70 -     1.82: 14
  Bond restraints: 2513
  Sorted by residual:
  bond pdb=" CA  ILE A 410 "
       pdb=" CB  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.527  1.543 -0.016 1.31e-02 5.83e+03 1.56e+00
  bond pdb=" CA  ASN H  76 "
       pdb=" CB  ASN H  76 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.54e-02 4.22e+03 1.40e+00
  bond pdb=" CA  VAL H 118 "
       pdb=" CB  VAL H 118 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.05e-02 9.07e+03 7.01e-01
  bond pdb=" CA  VAL H  48 "
       pdb=" CB  VAL H  48 "
    ideal  model  delta    sigma   weight residual
    1.545  1.538  0.007 9.10e-03 1.21e+04 6.61e-01
  bond pdb=" N   GLY A 476 "
       pdb=" CA  GLY A 476 "
    ideal  model  delta    sigma   weight residual
    1.458  1.451  0.007 9.20e-03 1.18e+04 6.27e-01
  ... (remaining 2508 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 3330
        1.82 -     3.64: 71
        3.64 -     5.46: 9
        5.46 -     7.29: 4
        7.29 -     9.11: 1
  Bond angle restraints: 3415
  Sorted by residual:
  angle pdb=" C   LYS H  75 "
        pdb=" N   ASN H  76 "
        pdb=" CA  ASN H  76 "
      ideal   model   delta    sigma   weight residual
     122.08  128.13   -6.05 1.47e+00 4.63e-01 1.69e+01
  angle pdb=" CA  LEU H  31 "
        pdb=" CB  LEU H  31 "
        pdb=" CG  LEU H  31 "
      ideal   model   delta    sigma   weight residual
     116.30  125.41   -9.11 3.50e+00 8.16e-02 6.77e+00
  angle pdb=" C   PHE A 486 "
        pdb=" N   ASN A 487 "
        pdb=" CA  ASN A 487 "
      ideal   model   delta    sigma   weight residual
     121.54  126.10   -4.56 1.91e+00 2.74e-01 5.71e+00
  angle pdb=" C   PHE A 497 "
        pdb=" N   GLN A 498 "
        pdb=" CA  GLN A 498 "
      ideal   model   delta    sigma   weight residual
     120.97  126.69   -5.72 2.84e+00 1.24e-01 4.06e+00
  angle pdb=" C   SER A 371 "
        pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
      ideal   model   delta    sigma   weight residual
     122.40  125.31   -2.91 1.45e+00 4.76e-01 4.04e+00
  ... (remaining 3410 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 1317
       17.44 -    34.87: 124
       34.87 -    52.31: 19
       52.31 -    69.75: 2
       69.75 -    87.19: 2
  Dihedral angle restraints: 1464
    sinusoidal: 565
      harmonic: 899
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    1.19  -87.19     1      1.00e+01 1.00e-02 9.13e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.86   31.86     1      1.00e+01 1.00e-02 1.45e+01
  dihedral pdb=" CA  GLU H 103 "
           pdb=" C   GLU H 103 "
           pdb=" N   LEU H 104 "
           pdb=" CA  LEU H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.78   18.22     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 1461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 220
       0.034 -    0.068: 92
       0.068 -    0.102: 31
       0.102 -    0.135: 16
       0.135 -    0.169: 4
  Chirality restraints: 363
  Sorted by residual:
  chirality pdb=" CB  ILE A 472 "
            pdb=" CA  ILE A 472 "
            pdb=" CG1 ILE A 472 "
            pdb=" CG2 ILE A 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CA  ASN H  76 "
            pdb=" N   ASN H  76 "
            pdb=" C   ASN H  76 "
            pdb=" CB  ASN H  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CB  VAL H  37 "
            pdb=" CA  VAL H  37 "
            pdb=" CG1 VAL H  37 "
            pdb=" CG2 VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 360 not shown)

  Planarity restraints: 444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO A 463 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 511 "    0.005 2.00e-02 2.50e+03   1.06e-02 1.11e+00
        pdb=" C   VAL A 511 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL A 511 "    0.007 2.00e-02 2.50e+03
        pdb=" N   VAL A 512 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 383 "   -0.017 5.00e-02 4.00e+02   2.58e-02 1.06e+00
        pdb=" N   PRO A 384 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 384 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 384 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 441 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 654
        2.79 -     3.32: 2058
        3.32 -     3.85: 4163
        3.85 -     4.37: 4467
        4.37 -     4.90: 7751
  Nonbonded interactions: 19093
  Sorted by model distance:
  nonbonded pdb=" O   GLU H   1 "
            pdb=" OG  SER H  25 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   GLY H  10 "
            pdb=" OG1 THR H 117 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG  SER H  17 "
            pdb=" O   MET H  82 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" OG  SER H  17 "
            pdb=" OD1 ASN H  83 "
     model   vdw
     2.368 3.040
  ... (remaining 19088 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=0.00 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:             2.640
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     15.610
  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:3.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
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      :  0.002   0.018   2518  Z= 0.133
  Angle     :  0.673   9.107   3425  Z= 0.349
  Chirality :  0.048   0.169    363
  Planarity :  0.004   0.031    444
  Dihedral  : 13.499  77.692    883
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.45), residues: 310
  helix: -4.21 (0.52), residues: 34
  sheet: -0.20 (0.60), residues: 74
  loop : -1.37 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.008   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 453 
 ARG   0.005   0.000   ARG H  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27763 (   57)
  hydrogen bonds       : angle      12.54723 (  141)
  SS BOND              : bond        0.00334 (    5)
  SS BOND              : angle       1.37889 (   10)
  covalent geometry    : bond        0.00242 ( 2513)
  covalent geometry    : angle       0.66970 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   20 LEU cc_start: 0.8907 (tp) cc_final: 0.8552 (tp)
REVERT: H   34 MET cc_start: 0.7425 (tmm) cc_final: 0.6735 (tmm)
REVERT: H   36 TRP cc_start: 0.7575 (m100) cc_final: 0.6672 (t-100)
REVERT: H   78 LEU cc_start: 0.7812 (tt) cc_final: 0.7470 (tt)
REVERT: A  340 GLU cc_start: 0.9163 (pt0) cc_final: 0.8881 (pm20)
REVERT: A  452 LEU cc_start: 0.9286 (mm) cc_final: 0.8854 (mm)
REVERT: A  454 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8809 (mtt-85)
REVERT: A  465 GLU cc_start: 0.9101 (tt0) cc_final: 0.8689 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2522
  time to fit residues: 23.7019
Evaluate side-chains
  42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 498 GLN
A 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.077342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.059937 restraints weight = 15967.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.061653 restraints weight = 11286.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.062861 restraints weight = 8727.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.4654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083   2518  Z= 0.231
  Angle     :  0.743   9.736   3425  Z= 0.391
  Chirality :  0.046   0.143    363
  Planarity :  0.004   0.035    444
  Dihedral  :  5.439  21.273    348
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 20.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  7.55 %
    Favored  : 92.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.45), residues: 310
  helix: -4.20 (0.43), residues: 39
  sheet: -1.18 (0.49), residues: 98
  loop : -1.09 (0.47), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 110 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.019   0.002   PHE A 338 
 TYR   0.015   0.002   TYR H  93 
 ARG   0.006   0.001   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05006 (   57)
  hydrogen bonds       : angle       9.32867 (  141)
  SS BOND              : bond        0.00776 (    5)
  SS BOND              : angle       3.84401 (   10)
  covalent geometry    : bond        0.00499 ( 2513)
  covalent geometry    : angle       0.71419 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7905 (tmm) cc_final: 0.7098 (tmm)
REVERT: H   36 TRP cc_start: 0.7893 (m100) cc_final: 0.7321 (t-100)
REVERT: H   76 ASN cc_start: 0.8830 (p0) cc_final: 0.8457 (t0)
REVERT: H   78 LEU cc_start: 0.8005 (tt) cc_final: 0.7410 (tt)
REVERT: H  107 PHE cc_start: 0.8075 (m-10) cc_final: 0.7357 (m-80)
REVERT: A  392 PHE cc_start: 0.8836 (m-80) cc_final: 0.8536 (m-80)
REVERT: A  405 ASP cc_start: 0.7752 (p0) cc_final: 0.7118 (p0)
REVERT: A  454 ARG cc_start: 0.9373 (ttm-80) cc_final: 0.8785 (mmt180)
REVERT: A  461 LEU cc_start: 0.8548 (pt) cc_final: 0.8124 (pp)
REVERT: A  465 GLU cc_start: 0.8881 (tt0) cc_final: 0.8196 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 46
  average time/residue: 0.2032
  time to fit residues: 10.7249
Evaluate side-chains
  32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    0.1980
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 437 ASN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.080650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.065629 restraints weight = 16314.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.067617 restraints weight = 11717.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.068958 restraints weight = 8571.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.4836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2518  Z= 0.107
  Angle     :  0.594   5.561   3425  Z= 0.298
  Chirality :  0.043   0.128    363
  Planarity :  0.004   0.041    444
  Dihedral  :  4.549  22.638    348
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.46), residues: 310
  helix: -3.90 (0.59), residues: 33
  sheet: -0.65 (0.52), residues: 95
  loop : -1.01 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 110 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.007   0.001   PHE A 486 
 TYR   0.009   0.001   TYR H  94 
 ARG   0.003   0.000   ARG H  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03208 (   57)
  hydrogen bonds       : angle       8.17920 (  141)
  SS BOND              : bond        0.00171 (    5)
  SS BOND              : angle       1.91760 (   10)
  covalent geometry    : bond        0.00233 ( 2513)
  covalent geometry    : angle       0.58532 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8050 (tmm) cc_final: 0.7467 (tmm)
REVERT: H   36 TRP cc_start: 0.8094 (m100) cc_final: 0.6962 (t-100)
REVERT: H   71 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7285 (ttp-170)
REVERT: H   78 LEU cc_start: 0.8141 (tt) cc_final: 0.7667 (tt)
REVERT: H  110 TRP cc_start: 0.8226 (m-90) cc_final: 0.7796 (m-90)
REVERT: A  392 PHE cc_start: 0.8875 (m-80) cc_final: 0.8638 (m-80)
REVERT: A  402 ILE cc_start: 0.9330 (tp) cc_final: 0.8957 (tp)
REVERT: A  454 ARG cc_start: 0.9386 (ttm-80) cc_final: 0.9013 (mmt90)
REVERT: A  461 LEU cc_start: 0.8570 (pt) cc_final: 0.7932 (pp)
REVERT: A  465 GLU cc_start: 0.9029 (tt0) cc_final: 0.8226 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.2145
  time to fit residues: 11.9201
Evaluate side-chains
  34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 9 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 14 optimal weight:    0.2980
   chunk 8 optimal weight:    5.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN
A 394 ASN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.072693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.058919 restraints weight = 17302.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.061520 restraints weight = 16454.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.062464 restraints weight = 9274.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.6614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   2518  Z= 0.262
  Angle     :  0.770   7.405   3425  Z= 0.405
  Chirality :  0.047   0.123    363
  Planarity :  0.005   0.036    444
  Dihedral  :  6.095  24.316    348
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 23.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.44), residues: 310
  helix: -3.69 (0.56), residues: 33
  sheet: -0.67 (0.49), residues: 94
  loop : -1.38 (0.44), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 436 
 HIS   0.004   0.003   HIS A 519 
 PHE   0.032   0.002   PHE A 338 
 TYR   0.018   0.003   TYR H  33 
 ARG   0.004   0.001   ARG H  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (   57)
  hydrogen bonds       : angle       8.43240 (  141)
  SS BOND              : bond        0.00628 (    5)
  SS BOND              : angle       3.10283 (   10)
  covalent geometry    : bond        0.00552 ( 2513)
  covalent geometry    : angle       0.75255 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7947 (tmm) cc_final: 0.7495 (tmm)
REVERT: H   36 TRP cc_start: 0.8215 (m100) cc_final: 0.7251 (t-100)
REVERT: H   78 LEU cc_start: 0.8347 (tt) cc_final: 0.8045 (tt)
REVERT: H  107 PHE cc_start: 0.7574 (m-80) cc_final: 0.7159 (m-80)
REVERT: A  454 ARG cc_start: 0.9271 (ttm-80) cc_final: 0.8717 (mmt90)
REVERT: A  461 LEU cc_start: 0.8499 (pt) cc_final: 0.8121 (pp)
REVERT: A  465 GLU cc_start: 0.8828 (tt0) cc_final: 0.8105 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1918
  time to fit residues: 7.9262
Evaluate side-chains
  28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.074400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.058245 restraints weight = 17316.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.059639 restraints weight = 12835.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.060307 restraints weight = 10436.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.6555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2518  Z= 0.143
  Angle     :  0.653   7.570   3425  Z= 0.331
  Chirality :  0.044   0.154    363
  Planarity :  0.004   0.037    444
  Dihedral  :  5.252  22.318    348
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.45), residues: 310
  helix: -3.19 (0.72), residues: 33
  sheet: -0.22 (0.52), residues: 83
  loop : -1.53 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 110 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.021   0.001   PHE A 347 
 TYR   0.015   0.001   TYR H  33 
 ARG   0.003   0.001   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03199 (   57)
  hydrogen bonds       : angle       7.89102 (  141)
  SS BOND              : bond        0.00244 (    5)
  SS BOND              : angle       2.75836 (   10)
  covalent geometry    : bond        0.00311 ( 2513)
  covalent geometry    : angle       0.63624 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8032 (tmm) cc_final: 0.7339 (tmm)
REVERT: H   36 TRP cc_start: 0.8258 (m100) cc_final: 0.7250 (t-100)
REVERT: H   72 ASP cc_start: 0.8668 (m-30) cc_final: 0.8349 (m-30)
REVERT: H   78 LEU cc_start: 0.8489 (tt) cc_final: 0.8004 (tt)
REVERT: H  107 PHE cc_start: 0.7915 (m-80) cc_final: 0.7428 (m-80)
REVERT: A  454 ARG cc_start: 0.9392 (ttm-80) cc_final: 0.8908 (mmt90)
REVERT: A  461 LEU cc_start: 0.8550 (pt) cc_final: 0.7827 (pp)
REVERT: A  465 GLU cc_start: 0.8887 (tt0) cc_final: 0.8082 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1771
  time to fit residues: 8.6912
Evaluate side-chains
  32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.074053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.059288 restraints weight = 17320.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.061560 restraints weight = 16615.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.062825 restraints weight = 10217.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.7024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2518  Z= 0.170
  Angle     :  0.715   9.416   3425  Z= 0.360
  Chirality :  0.048   0.335    363
  Planarity :  0.004   0.041    444
  Dihedral  :  5.400  21.383    348
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.45), residues: 310
  helix: -3.32 (0.73), residues: 33
  sheet: -0.09 (0.52), residues: 83
  loop : -1.62 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 110 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.017   0.002   PHE A 338 
 TYR   0.015   0.001   TYR H  33 
 ARG   0.003   0.001   ARG H  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (   57)
  hydrogen bonds       : angle       8.20290 (  141)
  SS BOND              : bond        0.00809 (    5)
  SS BOND              : angle       3.66069 (   10)
  covalent geometry    : bond        0.00379 ( 2513)
  covalent geometry    : angle       0.68789 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8113 (tmm) cc_final: 0.7347 (tmm)
REVERT: H   36 TRP cc_start: 0.8190 (m100) cc_final: 0.7578 (t-100)
REVERT: H   78 LEU cc_start: 0.8476 (tt) cc_final: 0.8132 (tt)
REVERT: H  107 PHE cc_start: 0.7815 (m-80) cc_final: 0.7522 (m-80)
REVERT: A  461 LEU cc_start: 0.8605 (pt) cc_final: 0.7880 (pp)
REVERT: A  465 GLU cc_start: 0.8874 (tt0) cc_final: 0.8123 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.2078
  time to fit residues: 9.2505
Evaluate side-chains
  28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.076329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.059907 restraints weight = 16931.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.061469 restraints weight = 12334.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.062703 restraints weight = 9742.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.7173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2518  Z= 0.129
  Angle     :  0.682   8.050   3425  Z= 0.336
  Chirality :  0.046   0.242    363
  Planarity :  0.003   0.038    444
  Dihedral  :  5.182  27.456    348
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.45), residues: 310
  helix: -3.30 (0.72), residues: 33
  sheet:  0.05 (0.54), residues: 83
  loop : -1.66 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 110 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.008   0.001   PHE A 392 
 TYR   0.016   0.001   TYR H  33 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02978 (   57)
  hydrogen bonds       : angle       7.89659 (  141)
  SS BOND              : bond        0.00691 (    5)
  SS BOND              : angle       3.05192 (   10)
  covalent geometry    : bond        0.00294 ( 2513)
  covalent geometry    : angle       0.66258 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7855 (tmm) cc_final: 0.6823 (tmm)
REVERT: H   36 TRP cc_start: 0.8224 (m100) cc_final: 0.7524 (t-100)
REVERT: H  107 PHE cc_start: 0.7827 (m-80) cc_final: 0.7590 (m-80)
REVERT: A  461 LEU cc_start: 0.8669 (pt) cc_final: 0.7972 (pp)
REVERT: A  465 GLU cc_start: 0.8901 (tt0) cc_final: 0.8132 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1873
  time to fit residues: 7.5787
Evaluate side-chains
  24 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0030
   chunk 5 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.076851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.060671 restraints weight = 16672.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.062245 restraints weight = 12140.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.063441 restraints weight = 9625.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.7200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2518  Z= 0.092
  Angle     :  0.619   6.818   3425  Z= 0.302
  Chirality :  0.044   0.155    363
  Planarity :  0.003   0.034    444
  Dihedral  :  4.491  18.685    348
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.46), residues: 310
  helix: -3.30 (0.69), residues: 33
  sheet:  0.36 (0.55), residues: 83
  loop : -1.61 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H 110 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.009   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 351 
 ARG   0.001   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02715 (   57)
  hydrogen bonds       : angle       7.19574 (  141)
  SS BOND              : bond        0.00668 (    5)
  SS BOND              : angle       2.33720 (   10)
  covalent geometry    : bond        0.00211 ( 2513)
  covalent geometry    : angle       0.60651 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7928 (tmm) cc_final: 0.6895 (tmm)
REVERT: H   36 TRP cc_start: 0.8077 (m100) cc_final: 0.7454 (t-100)
REVERT: H  107 PHE cc_start: 0.8068 (m-80) cc_final: 0.7493 (m-80)
REVERT: A  402 ILE cc_start: 0.9353 (tp) cc_final: 0.9124 (tp)
REVERT: A  409 GLN cc_start: 0.9693 (mt0) cc_final: 0.9391 (tt0)
REVERT: A  461 LEU cc_start: 0.8719 (pt) cc_final: 0.7957 (pp)
REVERT: A  465 GLU cc_start: 0.8971 (tt0) cc_final: 0.8186 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1617
  time to fit residues: 7.8803
Evaluate side-chains
  30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:   20.0000
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.074645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.060649 restraints weight = 17452.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.063189 restraints weight = 16506.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.064669 restraints weight = 9972.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.7522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2518  Z= 0.109
  Angle     :  0.624   7.915   3425  Z= 0.307
  Chirality :  0.043   0.144    363
  Planarity :  0.003   0.032    444
  Dihedral  :  4.651  18.281    348
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.46), residues: 310
  helix: -3.34 (0.68), residues: 33
  sheet:  0.52 (0.54), residues: 83
  loop : -1.46 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H 110 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.015   0.001   PHE H 101 
 TYR   0.011   0.001   TYR H  33 
 ARG   0.003   0.000   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02751 (   57)
  hydrogen bonds       : angle       7.17385 (  141)
  SS BOND              : bond        0.00508 (    5)
  SS BOND              : angle       2.37676 (   10)
  covalent geometry    : bond        0.00245 ( 2513)
  covalent geometry    : angle       0.61150 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7869 (tmm) cc_final: 0.6914 (tmm)
REVERT: H   36 TRP cc_start: 0.7981 (m100) cc_final: 0.7410 (t-100)
REVERT: H  101 PHE cc_start: 0.8565 (t80) cc_final: 0.8351 (t80)
REVERT: H  107 PHE cc_start: 0.7863 (m-80) cc_final: 0.7594 (m-80)
REVERT: A  461 LEU cc_start: 0.8792 (pt) cc_final: 0.8144 (pp)
REVERT: A  465 GLU cc_start: 0.9006 (tt0) cc_final: 0.8166 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1771
  time to fit residues: 7.6193
Evaluate side-chains
  26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0170
   chunk 12 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3745 r_free = 0.3745 target = 0.076728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.061519 restraints weight = 16563.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.063214 restraints weight = 11738.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.064355 restraints weight = 9131.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.7558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2518  Z= 0.093
  Angle     :  0.638   7.485   3425  Z= 0.315
  Chirality :  0.044   0.152    363
  Planarity :  0.003   0.029    444
  Dihedral  :  4.523  18.163    348
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.46), residues: 310
  helix: -3.38 (0.67), residues: 33
  sheet:  0.49 (0.55), residues: 83
  loop : -1.41 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H 110 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.011   0.001   PHE A 429 
 TYR   0.009   0.001   TYR A 351 
 ARG   0.002   0.000   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02823 (   57)
  hydrogen bonds       : angle       7.00352 (  141)
  SS BOND              : bond        0.00684 (    5)
  SS BOND              : angle       2.58047 (   10)
  covalent geometry    : bond        0.00201 ( 2513)
  covalent geometry    : angle       0.62341 ( 3415)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7874 (tmm) cc_final: 0.6842 (tmm)
REVERT: H   36 TRP cc_start: 0.8063 (m100) cc_final: 0.6972 (t-100)
REVERT: H  107 PHE cc_start: 0.7976 (m-80) cc_final: 0.7616 (m-80)
REVERT: A  461 LEU cc_start: 0.8785 (pt) cc_final: 0.8090 (pp)
REVERT: A  465 GLU cc_start: 0.9022 (tt0) cc_final: 0.8220 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1713
  time to fit residues: 7.7545
Evaluate side-chains
  25 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.075968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.061265 restraints weight = 17057.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.063751 restraints weight = 12143.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.064512 restraints weight = 8382.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.7696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2518  Z= 0.099
  Angle     :  0.634   7.611   3425  Z= 0.315
  Chirality :  0.043   0.155    363
  Planarity :  0.003   0.027    444
  Dihedral  :  4.656  20.281    348
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.46), residues: 310
  helix: -3.74 (0.58), residues: 32
  sheet:  0.37 (0.54), residues: 83
  loop : -1.39 (0.44), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H 110 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.008   0.001   TYR A 351 
 ARG   0.003   0.000   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02947 (   57)
  hydrogen bonds       : angle       7.13738 (  141)
  SS BOND              : bond        0.00562 (    5)
  SS BOND              : angle       2.86025 (   10)
  covalent geometry    : bond        0.00217 ( 2513)
  covalent geometry    : angle       0.61623 ( 3415)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1516.67 seconds
wall clock time: 26 minutes 52.17 seconds (1612.17 seconds total)