Starting phenix.real_space_refine
on Tue Feb 11 10:44:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e27_27827/02_2025/8e27_27827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e27_27827/02_2025/8e27_27827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e27_27827/02_2025/8e27_27827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e27_27827/02_2025/8e27_27827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e27_27827/02_2025/8e27_27827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e27_27827/02_2025/8e27_27827.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.018
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      30      5.16       5
     C    3430      2.51       5
     N     927      2.21       5
     O     984      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5371
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5371
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 39, 'TRANS': 636}
          Chain breaks: 3
  Time building chain proxies: 4.20, per 1000 atoms: 0.78
  Number of scatterers: 5371
  At special positions: 0
  Unit cell: (75.24, 83.16, 93.06, 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      30     16.00
     O     984      8.00
     N     927      7.00
     C    3430      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 666.3 milliseconds
  

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1290

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 10 sheets defined
      34.3% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 66
    Processing helix  chain 'A' and resid 99 through 103
    Processing helix  chain 'A' and resid 286 through 292
      removed outlier: 3.814A  pdb=" N   VAL A 290 " --> pdb=" O   PRO A 286 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ALA A 291 " --> pdb=" O   GLN A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
    Processing helix  chain 'A' and resid 329 through 341
    Processing helix  chain 'A' and resid 348 through 353
    Processing helix  chain 'A' and resid 364 through 369
      removed outlier: 3.641A  pdb=" N   PHE A 368 " --> pdb=" O   PRO A 365 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER A 369 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 430
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'A' and resid 495 through 503
      removed outlier: 3.542A  pdb=" N   SER A 499 " --> pdb=" O   GLU A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 513
      removed outlier: 3.726A  pdb=" N   GLU A 512 " --> pdb=" O   PRO A 509 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 513 " --> pdb=" O   ALA A 510 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 509 through 513'
    Processing helix  chain 'A' and resid 521 through 546
      removed outlier: 3.673A  pdb=" N   VAL A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLN A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 601
      removed outlier: 3.752A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU A 583 " --> pdb=" O   ASN A 579 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   PHE A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 601 " --> pdb=" O   ILE A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 626
      removed outlier: 3.772A  pdb=" N   ASP A 620 " --> pdb=" O   ARG A 616 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU A 621 " --> pdb=" O   MET A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 647
      removed outlier: 3.679A  pdb=" N   THR A 647 " --> pdb=" O   SER A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 666
      removed outlier: 4.329A  pdb=" N   ALA A 656 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 719
    Processing helix  chain 'A' and resid 728 through 765
      removed outlier: 3.620A  pdb=" N   GLN A 733 " --> pdb=" O   PRO A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 800
      No H-bonds generated for 'chain 'A' and resid 798 through 800'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 72
      removed outlier: 7.598A  pdb=" N   LEU A 110 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A 239 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75
    Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 252
      removed outlier: 7.316A  pdb=" N   LEU A 316 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ILE A 302 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   SER A 322 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   LEU A 300 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   THR A 299 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   LEU A 251 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373
      removed outlier: 3.862A  pdb=" N   ASP A 478 " --> pdb=" O   THR A 469 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   THR A 469 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382
      removed outlier: 6.325A  pdb=" N   THR A 381 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435
    Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560
    Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 609
    Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 796
      removed outlier: 6.974A  pdb=" N   ALA A 781 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   ILE A 777 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ASP A 783 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   MET A 773 " --> pdb=" O   LEU A 785 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 804 through 810

    231 hydrogen bonds defined for protein.
    642 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.47 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: 1458
        1.33 -     1.45: 925
        1.45 -     1.57: 3059
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 5487
  Sorted by residual:
  bond pdb=" CB  ASN A 391 "
       pdb=" CG  ASN A 391 "
    ideal  model  delta    sigma   weight residual
    1.516  1.469  0.047 2.50e-02 1.60e+03 3.46e+00
  bond pdb=" CB  TRP A 468 "
       pdb=" CG  TRP A 468 "
    ideal  model  delta    sigma   weight residual
    1.498  1.443  0.055 3.10e-02 1.04e+03 3.20e+00
  bond pdb=" CG  PRO A 702 "
       pdb=" CD  PRO A 702 "
    ideal  model  delta    sigma   weight residual
    1.503  1.443  0.060 3.40e-02 8.65e+02 3.16e+00
  bond pdb=" CB  PRO A 702 "
       pdb=" CG  PRO A 702 "
    ideal  model  delta    sigma   weight residual
    1.492  1.404  0.088 5.00e-02 4.00e+02 3.11e+00
  bond pdb=" C   ARG A 743 "
       pdb=" O   ARG A 743 "
    ideal  model  delta    sigma   weight residual
    1.237  1.216  0.020 1.17e-02 7.31e+03 3.06e+00
  ... (remaining 5482 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 6956
        2.02 -     4.05: 393
        4.05 -     6.07: 55
        6.07 -     8.10: 19
        8.10 -    10.12: 4
  Bond angle restraints: 7427
  Sorted by residual:
  angle pdb=" N   PHE A 464 "
        pdb=" CA  PHE A 464 "
        pdb=" C   PHE A 464 "
      ideal   model   delta    sigma   weight residual
     107.69  100.15    7.54 2.01e+00 2.48e-01 1.41e+01
  angle pdb=" N   THR A 700 "
        pdb=" CA  THR A 700 "
        pdb=" C   THR A 700 "
      ideal   model   delta    sigma   weight residual
     112.92  117.25   -4.33 1.23e+00 6.61e-01 1.24e+01
  angle pdb=" CA  GLN A 538 "
        pdb=" CB  GLN A 538 "
        pdb=" CG  GLN A 538 "
      ideal   model   delta    sigma   weight residual
     114.10  107.46    6.64 2.00e+00 2.50e-01 1.10e+01
  angle pdb=" N   ARG A 667 "
        pdb=" CA  ARG A 667 "
        pdb=" C   ARG A 667 "
      ideal   model   delta    sigma   weight residual
     109.81  116.73   -6.92 2.21e+00 2.05e-01 9.80e+00
  angle pdb=" C   VAL A 236 "
        pdb=" N   TYR A 237 "
        pdb=" CA  TYR A 237 "
      ideal   model   delta    sigma   weight residual
     121.85  116.34    5.51 1.77e+00 3.19e-01 9.69e+00
  ... (remaining 7422 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 3023
       17.81 -    35.62: 259
       35.62 -    53.43: 67
       53.43 -    71.24: 8
       71.24 -    89.06: 3
  Dihedral angle restraints: 3360
    sinusoidal: 1379
      harmonic: 1981
  Sorted by residual:
  dihedral pdb=" CA  MET A 617 "
           pdb=" C   MET A 617 "
           pdb=" N   LEU A 618 "
           pdb=" CA  LEU A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.28   22.72     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  ARG A 277 "
           pdb=" C   ARG A 277 "
           pdb=" N   ILE A 278 "
           pdb=" CA  ILE A 278 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.56  -19.44     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  LEU A 673 "
           pdb=" C   LEU A 673 "
           pdb=" N   TYR A 674 "
           pdb=" CA  TYR A 674 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.41   16.59     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 3357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 476
       0.050 -    0.099: 248
       0.099 -    0.148: 85
       0.148 -    0.197: 22
       0.197 -    0.247: 6
  Chirality restraints: 837
  Sorted by residual:
  chirality pdb=" CB  ILE A 508 "
            pdb=" CA  ILE A 508 "
            pdb=" CG1 ILE A 508 "
            pdb=" CG2 ILE A 508 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  ILE A 379 "
            pdb=" N   ILE A 379 "
            pdb=" C   ILE A 379 "
            pdb=" CB  ILE A 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  GLU A 450 "
            pdb=" N   GLU A 450 "
            pdb=" C   GLU A 450 "
            pdb=" CB  GLU A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 834 not shown)

  Planarity restraints: 958
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 464 "   -0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   PHE A 464 "    0.062 2.00e-02 2.50e+03
        pdb=" O   PHE A 464 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   SER A 465 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 699 "    0.015 2.00e-02 2.50e+03   3.01e-02 9.06e+00
        pdb=" C   PHE A 699 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   PHE A 699 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR A 700 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 508 "   -0.014 2.00e-02 2.50e+03   2.74e-02 7.53e+00
        pdb=" C   ILE A 508 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ILE A 508 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PRO A 509 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 955 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1474
        2.82 -     3.34: 4320
        3.34 -     3.86: 7906
        3.86 -     4.38: 8806
        4.38 -     4.90: 15989
  Nonbonded interactions: 38495
  Sorted by model distance:
  nonbonded pdb=" O   SER A 701 "
            pdb=" OD2 ASP A 708 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OE2 GLU A 419 "
            pdb=" NH2 ARG A 722 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" OD1 ASP A 343 "
            pdb=" OG  SER A 345 "
     model   vdw
     2.394 3.040
  nonbonded pdb=" N   ASP A 633 "
            pdb=" OD1 ASP A 633 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" OG  SER A 701 "
            pdb=" OD2 ASP A 708 "
     model   vdw
     2.434 3.040
  ... (remaining 38490 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:             1.350
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.040
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:2.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
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      :  0.010   0.088   5487  Z= 0.660
  Angle     :  1.095  10.119   7427  Z= 0.598
  Chirality :  0.067   0.247    837
  Planarity :  0.008   0.067    958
  Dihedral  : 14.240  89.056   2070
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.05 %
    Favored  : 95.62 %
  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: -0.92 (0.29), residues: 668
  helix: -0.31 (0.32), residues: 213
  sheet:  0.33 (0.50), residues: 103
  loop : -1.05 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 468 
 HIS   0.011   0.003   HIS A 409 
 PHE   0.026   0.003   PHE A  95 
 TYR   0.024   0.003   TYR A 796 
 ARG   0.013   0.002   ARG A 371 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A   79 LYS cc_start: 0.8136 (tttm) cc_final: 0.7791 (tttp)
REVERT: A   95 PHE cc_start: 0.7518 (t80) cc_final: 0.7276 (t80)
REVERT: A  242 LYS cc_start: 0.8429 (mttt) cc_final: 0.8180 (mttp)
REVERT: A  293 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.8013 (Cg_exo)
REVERT: A  309 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8069 (mmtp)
REVERT: A  424 ASP cc_start: 0.8355 (t70) cc_final: 0.8085 (t0)
REVERT: A  659 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7949 (tp30)
REVERT: A  783 ASP cc_start: 0.7875 (m-30) cc_final: 0.7204 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 0.2533
  time to fit residues: 27.9650
Evaluate side-chains
  57 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  309 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 34 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 20 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.145854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.101505 restraints weight = 7430.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.99
r_work: 0.3118 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5487  Z= 0.162
  Angle     :  0.532   5.334   7427  Z= 0.279
  Chirality :  0.042   0.144    837
  Planarity :  0.005   0.047    958
  Dihedral  :  4.580  29.912    738
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.60 %
    Favored  : 89.88 %
  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: -0.22 (0.31), residues: 668
  helix:  0.80 (0.37), residues: 211
  sheet:  0.50 (0.50), residues: 112
  loop : -0.96 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 526 
 PHE   0.017   0.001   PHE A 634 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  253 LEU cc_start: 0.7551 (mm) cc_final: 0.6860 (tt)
REVERT: A  293 PRO cc_start: 0.8273 (Cg_endo) cc_final: 0.7976 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8767 (t70) cc_final: 0.8558 (t0)
REVERT: A  634 PHE cc_start: 0.7939 (m-10) cc_final: 0.7635 (m-10)
REVERT: A  659 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8027 (tp30)
REVERT: A  783 ASP cc_start: 0.8155 (m-30) cc_final: 0.7569 (m-30)
REVERT: A  794 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7898 (ttm170)
  outliers start: 9
  outliers final: 6
  residues processed: 75
  average time/residue: 0.2122
  time to fit residues: 20.2444
Evaluate side-chains
  66 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 GLU
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0870
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.3360

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.143691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.099313 restraints weight = 7437.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.98
r_work: 0.3089 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5487  Z= 0.203
  Angle     :  0.516   6.775   7427  Z= 0.268
  Chirality :  0.042   0.143    837
  Planarity :  0.004   0.044    958
  Dihedral  :  4.118  17.406    732
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.80 %
    Favored  : 86.85 %
  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: -0.03 (0.32), residues: 668
  helix:  0.90 (0.37), residues: 213
  sheet:  0.75 (0.50), residues: 116
  loop : -0.88 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 468 
 HIS   0.005   0.001   HIS A 526 
 PHE   0.013   0.001   PHE A 837 
 TYR   0.010   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6758 (mtm110)
REVERT: A  253 LEU cc_start: 0.7566 (mm) cc_final: 0.7089 (tp)
REVERT: A  293 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7774 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8766 (t70) cc_final: 0.8550 (t0)
REVERT: A  550 ARG cc_start: 0.7011 (ttt-90) cc_final: 0.6518 (ptm160)
REVERT: A  659 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8042 (tp30)
REVERT: A  783 ASP cc_start: 0.8235 (m-30) cc_final: 0.7687 (m-30)
REVERT: A  794 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7879 (ttm170)
REVERT: A  820 TRP cc_start: 0.7098 (m100) cc_final: 0.6498 (m100)
  outliers start: 8
  outliers final: 5
  residues processed: 69
  average time/residue: 0.2507
  time to fit residues: 21.2640
Evaluate side-chains
  64 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 520 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.141952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.097787 restraints weight = 7702.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.06
r_work: 0.3044 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5487  Z= 0.283
  Angle     :  0.538   6.079   7427  Z= 0.280
  Chirality :  0.043   0.144    837
  Planarity :  0.004   0.043    958
  Dihedral  :  4.157  19.639    732
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.80 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.32), residues: 668
  helix:  0.79 (0.37), residues: 214
  sheet:  0.64 (0.48), residues: 130
  loop : -0.84 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 468 
 HIS   0.006   0.001   HIS A 526 
 PHE   0.017   0.002   PHE A  95 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6777 (mtm110)
REVERT: A   95 PHE cc_start: 0.7165 (t80) cc_final: 0.6945 (t80)
REVERT: A  253 LEU cc_start: 0.7544 (mm) cc_final: 0.7058 (tp)
REVERT: A  293 PRO cc_start: 0.8175 (Cg_endo) cc_final: 0.7773 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8768 (t70) cc_final: 0.8542 (t0)
REVERT: A  659 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8035 (tp30)
REVERT: A  783 ASP cc_start: 0.8323 (m-30) cc_final: 0.7825 (m-30)
REVERT: A  794 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7935 (ttm170)
REVERT: A  820 TRP cc_start: 0.7167 (m100) cc_final: 0.6655 (m100)
  outliers start: 13
  outliers final: 11
  residues processed: 70
  average time/residue: 0.2197
  time to fit residues: 19.4570
Evaluate side-chains
  66 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 GLU
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0770
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 39 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A 598 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.144775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.101960 restraints weight = 7393.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.93
r_work: 0.3133 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5487  Z= 0.136
  Angle     :  0.472   5.241   7427  Z= 0.241
  Chirality :  0.040   0.132    837
  Planarity :  0.004   0.048    958
  Dihedral  :  3.867  20.867    732
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.49 %
    Favored  : 85.16 %
  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:  0.30 (0.32), residues: 668
  helix:  1.11 (0.37), residues: 214
  sheet:  0.87 (0.50), residues: 121
  loop : -0.64 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 688 
 PHE   0.014   0.001   PHE A  95 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.008   0.000   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6841 (mtm110)
REVERT: A   95 PHE cc_start: 0.7254 (t80) cc_final: 0.6743 (t80)
REVERT: A  253 LEU cc_start: 0.7499 (mm) cc_final: 0.7047 (tp)
REVERT: A  293 PRO cc_start: 0.8136 (Cg_endo) cc_final: 0.7697 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8722 (t70) cc_final: 0.8501 (t0)
REVERT: A  783 ASP cc_start: 0.8285 (m-30) cc_final: 0.7777 (m-30)
REVERT: A  794 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7910 (ttm170)
REVERT: A  820 TRP cc_start: 0.7274 (m100) cc_final: 0.6810 (m100)
  outliers start: 8
  outliers final: 7
  residues processed: 69
  average time/residue: 0.2251
  time to fit residues: 19.9917
Evaluate side-chains
  66 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 GLU
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0270
   chunk 55 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 59 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    0.5440

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.145053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.102272 restraints weight = 7440.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.93
r_work: 0.3138 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5487  Z= 0.135
  Angle     :  0.469   5.643   7427  Z= 0.237
  Chirality :  0.040   0.131    837
  Planarity :  0.004   0.044    958
  Dihedral  :  3.731  20.592    732
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 14.00 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.47 (0.33), residues: 668
  helix:  1.26 (0.37), residues: 214
  sheet:  0.93 (0.50), residues: 121
  loop : -0.53 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 468 
 HIS   0.009   0.001   HIS A 688 
 PHE   0.013   0.001   PHE A  95 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.009   0.000   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.625 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7060 (ttp80) cc_final: 0.6818 (mtm110)
REVERT: A   95 PHE cc_start: 0.7128 (t80) cc_final: 0.6627 (t80)
REVERT: A  253 LEU cc_start: 0.7477 (mm) cc_final: 0.7035 (tp)
REVERT: A  293 PRO cc_start: 0.8109 (Cg_endo) cc_final: 0.7670 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8717 (t70) cc_final: 0.8501 (t0)
REVERT: A  586 MET cc_start: 0.8465 (mmt) cc_final: 0.8210 (mmt)
REVERT: A  659 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7879 (tp30)
REVERT: A  783 ASP cc_start: 0.8288 (m-30) cc_final: 0.7768 (m-30)
REVERT: A  794 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7826 (ttm170)
REVERT: A  820 TRP cc_start: 0.7244 (m100) cc_final: 0.6767 (m100)
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 0.2246
  time to fit residues: 18.8185
Evaluate side-chains
  63 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A 579 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.145757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.102603 restraints weight = 7387.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.94
r_work: 0.3132 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5487  Z= 0.147
  Angle     :  0.475   8.335   7427  Z= 0.239
  Chirality :  0.040   0.130    837
  Planarity :  0.004   0.044    958
  Dihedral  :  3.718  20.658    732
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.18 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.33), residues: 668
  helix:  1.15 (0.37), residues: 220
  sheet:  0.97 (0.50), residues: 121
  loop : -0.49 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 688 
 PHE   0.013   0.001   PHE A  95 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.009   0.000   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6819 (mtm110)
REVERT: A   95 PHE cc_start: 0.7182 (t80) cc_final: 0.6665 (t80)
REVERT: A  253 LEU cc_start: 0.7478 (mm) cc_final: 0.7047 (tp)
REVERT: A  293 PRO cc_start: 0.8116 (Cg_endo) cc_final: 0.7676 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8721 (t70) cc_final: 0.8504 (t0)
REVERT: A  783 ASP cc_start: 0.8244 (m-30) cc_final: 0.7727 (m-30)
REVERT: A  794 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7823 (ttm170)
REVERT: A  820 TRP cc_start: 0.7237 (m100) cc_final: 0.6759 (m100)
  outliers start: 7
  outliers final: 7
  residues processed: 65
  average time/residue: 0.2054
  time to fit residues: 17.3317
Evaluate side-chains
  66 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 GLU
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.140864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.102801 restraints weight = 7467.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 3.28
r_work: 0.3049 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5487  Z= 0.306
  Angle     :  0.555  10.310   7427  Z= 0.283
  Chirality :  0.043   0.140    837
  Planarity :  0.004   0.045    958
  Dihedral  :  3.987  20.802    732
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.35 %
    Favored  : 82.80 %
  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:  0.29 (0.33), residues: 668
  helix:  0.93 (0.36), residues: 220
  sheet:  0.90 (0.50), residues: 121
  loop : -0.55 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 468 
 HIS   0.006   0.001   HIS A 526 
 PHE   0.013   0.001   PHE A  95 
 TYR   0.012   0.001   TYR A 340 
 ARG   0.010   0.001   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6855 (mtm110)
REVERT: A  293 PRO cc_start: 0.8141 (Cg_endo) cc_final: 0.7698 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8743 (t70) cc_final: 0.8504 (t0)
REVERT: A  586 MET cc_start: 0.8656 (mmt) cc_final: 0.8422 (mmt)
REVERT: A  783 ASP cc_start: 0.8309 (m-30) cc_final: 0.7329 (m-30)
REVERT: A  794 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7615 (ttm170)
REVERT: A  820 TRP cc_start: 0.7264 (m100) cc_final: 0.6705 (m100)
  outliers start: 11
  outliers final: 8
  residues processed: 69
  average time/residue: 0.2315
  time to fit residues: 20.1049
Evaluate side-chains
  66 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 GLU
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 24 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 11 optimal weight:    0.2980
   chunk 52 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.144763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.100815 restraints weight = 7365.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.99
r_work: 0.3102 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5487  Z= 0.146
  Angle     :  0.492   8.532   7427  Z= 0.249
  Chirality :  0.040   0.129    837
  Planarity :  0.004   0.044    958
  Dihedral  :  3.794  21.152    732
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.35 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.45 (0.33), residues: 668
  helix:  1.10 (0.37), residues: 220
  sheet:  0.98 (0.50), residues: 121
  loop : -0.48 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 688 
 PHE   0.007   0.001   PHE A 837 
 TYR   0.008   0.001   TYR A 340 
 ARG   0.010   0.000   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6813 (mtm110)
REVERT: A   95 PHE cc_start: 0.7156 (t80) cc_final: 0.6746 (t80)
REVERT: A  253 LEU cc_start: 0.7665 (mm) cc_final: 0.6900 (tp)
REVERT: A  293 PRO cc_start: 0.8096 (Cg_endo) cc_final: 0.7647 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8689 (t70) cc_final: 0.8464 (t0)
REVERT: A  586 MET cc_start: 0.8414 (mmt) cc_final: 0.8136 (mmt)
REVERT: A  783 ASP cc_start: 0.8216 (m-30) cc_final: 0.7495 (m-30)
REVERT: A  794 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7669 (ttm170)
REVERT: A  820 TRP cc_start: 0.7217 (m100) cc_final: 0.6683 (m100)
  outliers start: 8
  outliers final: 8
  residues processed: 67
  average time/residue: 0.2064
  time to fit residues: 17.7123
Evaluate side-chains
  67 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 GLU
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.140318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.096181 restraints weight = 7478.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 3.00
r_work: 0.3035 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   5487  Z= 0.318
  Angle     :  0.572  10.331   7427  Z= 0.292
  Chirality :  0.044   0.140    837
  Planarity :  0.004   0.043    958
  Dihedral  :  4.025  20.788    732
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.51 %
    Favored  : 82.97 %
  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:  0.23 (0.33), residues: 668
  helix:  0.83 (0.36), residues: 220
  sheet:  0.89 (0.50), residues: 121
  loop : -0.56 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 468 
 HIS   0.006   0.001   HIS A 526 
 PHE   0.014   0.001   PHE A 585 
 TYR   0.012   0.001   TYR A 340 
 ARG   0.009   0.001   ARG A 277 

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7065 (ttp80) cc_final: 0.6802 (mtm110)
REVERT: A   95 PHE cc_start: 0.7159 (t80) cc_final: 0.6739 (t80)
REVERT: A  242 LYS cc_start: 0.8452 (mttt) cc_final: 0.8119 (tttt)
REVERT: A  253 LEU cc_start: 0.7694 (mm) cc_final: 0.6978 (tt)
REVERT: A  293 PRO cc_start: 0.8160 (Cg_endo) cc_final: 0.7703 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8704 (t70) cc_final: 0.8460 (t0)
REVERT: A  783 ASP cc_start: 0.8189 (m-30) cc_final: 0.6971 (m-30)
REVERT: A  794 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7553 (ttm170)
  outliers start: 9
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2090
  time to fit residues: 17.4704
Evaluate side-chains
  63 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  805 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   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 = 0.3744 r_free = 0.3744 target = 0.143121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.106637 restraints weight = 7501.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 3.53
r_work: 0.3056 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5487  Z= 0.183
  Angle     :  0.510   8.502   7427  Z= 0.259
  Chirality :  0.041   0.132    837
  Planarity :  0.004   0.041    958
  Dihedral  :  3.889  21.321    732
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.68 %
    Favored  : 82.97 %
  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:  0.37 (0.33), residues: 668
  helix:  0.95 (0.36), residues: 220
  sheet:  1.02 (0.48), residues: 129
  loop : -0.55 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 688 
 PHE   0.008   0.001   PHE A 837 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.009   0.000   ARG A 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2674.00 seconds
wall clock time: 48 minutes 7.01 seconds (2887.01 seconds total)