Starting phenix.real_space_refine
on Fri Aug 22 15:49:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e27_27827/08_2025/8e27_27827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e27_27827/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e27_27827/08_2025/8e27_27827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e27_27827/08_2025/8e27_27827.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e27_27827/08_2025/8e27_27827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e27_27827/08_2025/8e27_27827.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.29, per 1000 atoms: 0.24
  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: 0.40
  Conformation dependent library (CDL) restraints added in 165.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.15
  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: 0.61

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.820
  Find NCS groups from input model:        0.010
  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:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.450
-------------------------------------------------------------------------------
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= 0.395
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (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
 ARG   0.013   0.002   ARG A 371 
 TYR   0.024   0.003   TYR A 796 
 PHE   0.026   0.003   PHE A  95 
 TRP   0.030   0.002   TRP A 468 
 HIS   0.011   0.003   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00969 ( 5487)
  covalent geometry    : angle       1.09547 ( 7427)
  hydrogen bonds       : bond        0.13786 (  231)
  hydrogen bonds       : angle       5.53588 (  642)

*********************** 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  : 0.140 
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: 0.7205 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 0.0945
  time to fit residues: 10.3336
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  : 0.130 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.143849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.100858 restraints weight = 7297.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.87
r_work: 0.3108 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5487  Z= 0.120
  Angle     :  0.541   5.257   7427  Z= 0.285
  Chirality :  0.042   0.149    837
  Planarity :  0.005   0.048    958
  Dihedral  :  4.602  29.841    738
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.77 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.31), residues: 668
  helix:  0.67 (0.36), residues: 217
  sheet:  0.73 (0.51), residues: 107
  loop : -1.02 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 277 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.015   0.001   PHE A 634 
 TRP   0.016   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5487)
  covalent geometry    : angle       0.54100 ( 7427)
  hydrogen bonds       : bond        0.05591 (  231)
  hydrogen bonds       : angle       4.59746 (  642)

*********************** 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
  75 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  253 LEU cc_start: 0.7545 (mm) cc_final: 0.7036 (tp)
REVERT: A  293 PRO cc_start: 0.8285 (Cg_endo) cc_final: 0.7977 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8769 (t70) cc_final: 0.8550 (t0)
REVERT: A  634 PHE cc_start: 0.7915 (m-10) cc_final: 0.7706 (m-10)
REVERT: A  659 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8067 (tp30)
REVERT: A  783 ASP cc_start: 0.8161 (m-30) cc_final: 0.7553 (m-30)
REVERT: A  794 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7839 (ttm170)
  outliers start: 9
  outliers final: 6
  residues processed: 72
  average time/residue: 0.1018
  time to fit residues: 9.2674
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  : 0.240 
-------------------------------------------------------------------------------
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  791 VAL
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 8 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0970
   chunk 29 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0870
   chunk 13 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.147730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.109959 restraints weight = 7385.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 3.07
r_work: 0.3150 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5487  Z= 0.093
  Angle     :  0.489   6.401   7427  Z= 0.252
  Chirality :  0.041   0.135    837
  Planarity :  0.004   0.043    958
  Dihedral  :  4.042  18.058    732
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.46 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.32), residues: 668
  helix:  1.03 (0.37), residues: 213
  sheet:  0.67 (0.50), residues: 118
  loop : -0.86 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 277 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A 837 
 TRP   0.011   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 5487)
  covalent geometry    : angle       0.48888 ( 7427)
  hydrogen bonds       : bond        0.04387 (  231)
  hydrogen bonds       : angle       4.23057 (  642)

*********************** 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
  74 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  253 LEU cc_start: 0.7558 (mm) cc_final: 0.7103 (tp)
REVERT: A  293 PRO cc_start: 0.8201 (Cg_endo) cc_final: 0.7830 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8809 (t70) cc_final: 0.8584 (t0)
REVERT: A  550 ARG cc_start: 0.7072 (ttt-90) cc_final: 0.6573 (ptm160)
REVERT: A  659 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8102 (tp30)
REVERT: A  783 ASP cc_start: 0.8242 (m-30) cc_final: 0.7747 (m-30)
REVERT: A  794 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7896 (ttm170)
REVERT: A  820 TRP cc_start: 0.7121 (m100) cc_final: 0.6532 (m100)
  outliers start: 8
  outliers final: 6
  residues processed: 73
  average time/residue: 0.1028
  time to fit residues: 9.3862
Evaluate side-chains
  64 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  564 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 64 optimal weight:    0.0270
   chunk 30 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.8640

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.147207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.104766 restraints weight = 7445.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.87
r_work: 0.3178 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2105

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= 0.099
  Angle     :  0.481   5.487   7427  Z= 0.246
  Chirality :  0.041   0.135    837
  Planarity :  0.004   0.040    958
  Dihedral  :  3.890  19.323    732
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.14 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.32), residues: 668
  helix:  1.13 (0.37), residues: 214
  sheet:  0.72 (0.48), residues: 130
  loop : -0.72 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 724 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A 634 
 TRP   0.011   0.001   TRP A 468 
 HIS   0.008   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5487)
  covalent geometry    : angle       0.48068 ( 7427)
  hydrogen bonds       : bond        0.04196 (  231)
  hydrogen bonds       : angle       4.09494 (  642)

*********************** 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
  69 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6749 (mtm110)
REVERT: A  253 LEU cc_start: 0.7541 (mm) cc_final: 0.7099 (tp)
REVERT: A  293 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7773 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8753 (t70) cc_final: 0.8532 (t0)
REVERT: A  659 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8008 (tp30)
REVERT: A  783 ASP cc_start: 0.8231 (m-30) cc_final: 0.7644 (m-30)
REVERT: A  794 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7869 (ttm170)
REVERT: A  820 TRP cc_start: 0.7231 (m100) cc_final: 0.6564 (m100)
  outliers start: 9
  outliers final: 8
  residues processed: 67
  average time/residue: 0.0983
  time to fit residues: 8.2546
Evaluate side-chains
  65 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
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  564 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    1.1588

-------------------------------------------------------------------------------
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 = 0.3807 r_free = 0.3807 target = 0.145867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103418 restraints weight = 7510.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.87
r_work: 0.3155 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5487  Z= 0.110
  Angle     :  0.480   5.694   7427  Z= 0.245
  Chirality :  0.041   0.138    837
  Planarity :  0.004   0.039    958
  Dihedral  :  3.852  19.504    732
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.31 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.33), residues: 668
  helix:  1.18 (0.37), residues: 214
  sheet:  0.91 (0.50), residues: 121
  loop : -0.58 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 724 
 TYR   0.010   0.001   TYR A 340 
 PHE   0.016   0.001   PHE A  95 
 TRP   0.011   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5487)
  covalent geometry    : angle       0.47993 ( 7427)
  hydrogen bonds       : bond        0.04360 (  231)
  hydrogen bonds       : angle       4.07133 (  642)

*********************** 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
  72 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6831 (mtm110)
REVERT: A   95 PHE cc_start: 0.7297 (t80) cc_final: 0.6838 (t80)
REVERT: A  293 PRO cc_start: 0.8158 (Cg_endo) cc_final: 0.7752 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8752 (t70) cc_final: 0.8524 (t0)
REVERT: A  659 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7985 (tp30)
REVERT: A  783 ASP cc_start: 0.8278 (m-30) cc_final: 0.7755 (m-30)
REVERT: A  794 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7895 (ttm170)
REVERT: A  820 TRP cc_start: 0.7276 (m100) cc_final: 0.6815 (m100)
  outliers start: 11
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0809
  time to fit residues: 7.0528
Evaluate side-chains
  69 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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  363 ILE
Chi-restraints excluded: chain A residue  366 GLU
Chi-restraints excluded: chain A residue  564 THR
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  791 VAL
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 59 optimal weight:    9.9990
   chunk 41 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 9 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0670
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6320

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.147418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.108836 restraints weight = 7465.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.92
r_work: 0.3165 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2400

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= 0.085
  Angle     :  0.462   5.555   7427  Z= 0.233
  Chirality :  0.040   0.132    837
  Planarity :  0.003   0.036    958
  Dihedral  :  3.702  19.690    732
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.33), residues: 668
  helix:  1.37 (0.38), residues: 214
  sheet:  0.81 (0.49), residues: 128
  loop : -0.44 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 724 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.015   0.001   PHE A  95 
 TRP   0.010   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 5487)
  covalent geometry    : angle       0.46180 ( 7427)
  hydrogen bonds       : bond        0.03730 (  231)
  hydrogen bonds       : angle       3.87840 (  642)

*********************** 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
  72 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6908 (mtm110)
REVERT: A   95 PHE cc_start: 0.7228 (t80) cc_final: 0.6776 (t80)
REVERT: A  253 LEU cc_start: 0.7699 (mm) cc_final: 0.6918 (tt)
REVERT: A  293 PRO cc_start: 0.8171 (Cg_endo) cc_final: 0.7739 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8748 (t70) cc_final: 0.8517 (t0)
REVERT: A  659 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7955 (tp30)
REVERT: A  783 ASP cc_start: 0.8291 (m-30) cc_final: 0.7982 (m-30)
REVERT: A  820 TRP cc_start: 0.7291 (m100) cc_final: 0.6827 (m100)
  outliers start: 8
  outliers final: 7
  residues processed: 70
  average time/residue: 0.0994
  time to fit residues: 8.6903
Evaluate side-chains
  64 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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  564 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3824 r_free = 0.3824 target = 0.147276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.109634 restraints weight = 7468.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 3.07
r_work: 0.3142 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5487  Z= 0.095
  Angle     :  0.476   6.250   7427  Z= 0.239
  Chirality :  0.040   0.131    837
  Planarity :  0.004   0.036    958
  Dihedral  :  3.684  19.825    732
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.33), residues: 668
  helix:  1.21 (0.37), residues: 220
  sheet:  0.84 (0.48), residues: 128
  loop : -0.42 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 724 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A  95 
 TRP   0.009   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 5487)
  covalent geometry    : angle       0.47588 ( 7427)
  hydrogen bonds       : bond        0.03795 (  231)
  hydrogen bonds       : angle       3.92349 (  642)

*********************** 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
  73 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6920 (mtm110)
REVERT: A   95 PHE cc_start: 0.7221 (t80) cc_final: 0.6760 (t80)
REVERT: A  253 LEU cc_start: 0.7712 (mm) cc_final: 0.6962 (tt)
REVERT: A  293 PRO cc_start: 0.8114 (Cg_endo) cc_final: 0.7672 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8773 (t70) cc_final: 0.8542 (t0)
REVERT: A  659 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7937 (tp30)
REVERT: A  783 ASP cc_start: 0.8259 (m-30) cc_final: 0.7804 (m-30)
REVERT: A  794 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7718 (ttm170)
REVERT: A  820 TRP cc_start: 0.7264 (m100) cc_final: 0.6797 (m100)
  outliers start: 11
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0914
  time to fit residues: 8.3188
Evaluate side-chains
  68 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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  381 THR
Chi-restraints excluded: chain A residue  564 THR
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 33 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 15 optimal weight:    0.3980
   chunk 64 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0870
   overall best weight:    0.8160

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.147509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.109938 restraints weight = 7378.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 3.04
r_work: 0.3149 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5487  Z= 0.094
  Angle     :  0.480   8.592   7427  Z= 0.241
  Chirality :  0.040   0.131    837
  Planarity :  0.003   0.036    958
  Dihedral  :  3.675  19.978    732
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.00 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.33), residues: 668
  helix:  1.25 (0.37), residues: 220
  sheet:  1.34 (0.49), residues: 116
  loop : -0.40 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 724 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A  95 
 TRP   0.009   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 5487)
  covalent geometry    : angle       0.48006 ( 7427)
  hydrogen bonds       : bond        0.03768 (  231)
  hydrogen bonds       : angle       3.90720 (  642)

*********************** 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
  76 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7166 (ttp80) cc_final: 0.6899 (mtm110)
REVERT: A   95 PHE cc_start: 0.7216 (t80) cc_final: 0.6748 (t80)
REVERT: A  293 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7664 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8761 (t70) cc_final: 0.8530 (t0)
REVERT: A  783 ASP cc_start: 0.8231 (m-30) cc_final: 0.7848 (m-30)
REVERT: A  820 TRP cc_start: 0.7298 (m100) cc_final: 0.6809 (m100)
  outliers start: 13
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0883
  time to fit residues: 8.1364
Evaluate side-chains
  69 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
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  381 THR
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  572 ILE
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 7 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 50 optimal weight:    0.0670
   chunk 45 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.148405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.105996 restraints weight = 7477.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.88
r_work: 0.3187 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5487  Z= 0.092
  Angle     :  0.486   7.980   7427  Z= 0.244
  Chirality :  0.040   0.130    837
  Planarity :  0.003   0.036    958
  Dihedral  :  3.661  20.078    732
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.84 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.33), residues: 668
  helix:  1.30 (0.37), residues: 220
  sheet:  1.37 (0.49), residues: 116
  loop : -0.38 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 724 
 TYR   0.008   0.001   TYR A 340 
 PHE   0.013   0.001   PHE A  95 
 TRP   0.009   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 5487)
  covalent geometry    : angle       0.48634 ( 7427)
  hydrogen bonds       : bond        0.03635 (  231)
  hydrogen bonds       : angle       3.91903 (  642)

*********************** 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
  74 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7111 (ttp80) cc_final: 0.6843 (mtm110)
REVERT: A   95 PHE cc_start: 0.7217 (t80) cc_final: 0.6751 (t80)
REVERT: A  293 PRO cc_start: 0.8114 (Cg_endo) cc_final: 0.7668 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8736 (t70) cc_final: 0.8499 (t0)
REVERT: A  783 ASP cc_start: 0.8154 (m-30) cc_final: 0.7891 (m-30)
REVERT: A  820 TRP cc_start: 0.7316 (m100) cc_final: 0.6820 (m100)
  outliers start: 10
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0787
  time to fit residues: 7.3565
Evaluate side-chains
  69 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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  381 THR
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  572 ILE
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 14 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.145185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.108529 restraints weight = 7533.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 3.25
r_work: 0.3104 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5487  Z= 0.136
  Angle     :  0.521   9.533   7427  Z= 0.263
  Chirality :  0.042   0.137    837
  Planarity :  0.004   0.037    958
  Dihedral  :  3.805  20.313    732
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.33), residues: 668
  helix:  1.15 (0.37), residues: 220
  sheet:  0.83 (0.47), residues: 134
  loop : -0.34 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 724 
 TYR   0.011   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A  95 
 TRP   0.009   0.001   TRP A 468 
 HIS   0.005   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 5487)
  covalent geometry    : angle       0.52105 ( 7427)
  hydrogen bonds       : bond        0.04632 (  231)
  hydrogen bonds       : angle       4.08843 (  642)

********************** 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: 10
    poor density    : 57
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7196 (ttp80) cc_final: 0.6929 (mtm110)
REVERT: A   95 PHE cc_start: 0.7213 (t80) cc_final: 0.6747 (t80)
REVERT: A  293 PRO cc_start: 0.8150 (Cg_endo) cc_final: 0.7714 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8755 (t70) cc_final: 0.8517 (t0)
REVERT: A  783 ASP cc_start: 0.8228 (m-30) cc_final: 0.7967 (m-30)
  outliers start: 10
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0798
  time to fit residues: 6.9036
Evaluate side-chains
  65 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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  381 THR
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  572 ILE
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 20 optimal weight:    0.1980
   chunk 66 optimal weight:    0.5980
   chunk 61 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0270
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.148803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.111308 restraints weight = 7380.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 3.16
r_work: 0.3167 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5487  Z= 0.087
  Angle     :  0.484   8.038   7427  Z= 0.243
  Chirality :  0.040   0.128    837
  Planarity :  0.003   0.035    958
  Dihedral  :  3.655  20.071    732
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.85 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.33), residues: 668
  helix:  1.27 (0.37), residues: 220
  sheet:  1.32 (0.48), residues: 121
  loop : -0.39 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 724 
 TYR   0.008   0.001   TYR A 340 
 PHE   0.013   0.001   PHE A  95 
 TRP   0.010   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 5487)
  covalent geometry    : angle       0.48450 ( 7427)
  hydrogen bonds       : bond        0.03580 (  231)
  hydrogen bonds       : angle       3.89056 (  642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1234.10 seconds
wall clock time: 21 minutes 50.47 seconds (1310.47 seconds total)