Starting phenix.real_space_refine
on Thu Mar  6 07:23:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e27_27827/03_2025/8e27_27827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e27_27827/03_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_27827/03_2025/8e27_27827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e27_27827/03_2025/8e27_27827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e27_27827/03_2025/8e27_27827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e27_27827/03_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-5624/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: 3.91, per 1000 atoms: 0.73
  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: 1.24
  Conformation dependent library (CDL) restraints added in 652.3 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: 0.67
  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: 1.69

  Time building geometry restraints manager: 1.49 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:             1.990
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.000
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.010
-------------------------------------------------------------------------------
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  : 0.671 
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: 0.2361
  time to fit residues: 25.9609
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  : 0.591 
-------------------------------------------------------------------------------
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 = 44)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.101508 restraints weight = 7430.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.99
r_work: 0.3120 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
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  : 0.679 
Fit side-chains
REVERT: A  253 LEU cc_start: 0.7548 (mm) cc_final: 0.6860 (tt)
REVERT: A  293 PRO cc_start: 0.8279 (Cg_endo) cc_final: 0.7981 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8769 (t70) cc_final: 0.8560 (t0)
REVERT: A  634 PHE cc_start: 0.7953 (m-10) cc_final: 0.7647 (m-10)
REVERT: A  659 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8027 (tp30)
REVERT: A  783 ASP cc_start: 0.8159 (m-30) cc_final: 0.7577 (m-30)
REVERT: A  794 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7908 (ttm170)
  outliers start: 9
  outliers final: 6
  residues processed: 75
  average time/residue: 0.2224
  time to fit residues: 21.1749
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  : 0.646 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 18 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.147539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.105067 restraints weight = 7401.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.87
r_work: 0.3175 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5487  Z= 0.152
  Angle     :  0.492   6.582   7427  Z= 0.255
  Chirality :  0.041   0.138    837
  Planarity :  0.004   0.042    958
  Dihedral  :  4.043  17.871    732
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.96 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.01 (0.32), residues: 668
  helix:  0.99 (0.37), residues: 213
  sheet:  0.65 (0.50), residues: 118
  loop : -0.87 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 526 
 PHE   0.014   0.001   PHE A 837 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.006   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
  72 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.599 
Fit side-chains
REVERT: A  253 LEU cc_start: 0.7564 (mm) cc_final: 0.7108 (tp)
REVERT: A  293 PRO cc_start: 0.8133 (Cg_endo) cc_final: 0.7760 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8778 (t70) cc_final: 0.8555 (t0)
REVERT: A  783 ASP cc_start: 0.8222 (m-30) cc_final: 0.7698 (m-30)
REVERT: A  794 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7890 (ttm170)
REVERT: A  820 TRP cc_start: 0.7177 (m100) cc_final: 0.6607 (m100)
  outliers start: 8
  outliers final: 5
  residues processed: 70
  average time/residue: 0.2355
  time to fit residues: 20.5704
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  : 0.605 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 44 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.147849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.105240 restraints weight = 7601.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.92
r_work: 0.3182 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2185

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= 0.148
  Angle     :  0.475   5.387   7427  Z= 0.243
  Chirality :  0.040   0.134    837
  Planarity :  0.004   0.039    958
  Dihedral  :  3.868  19.132    732
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.31 %
    Favored  : 86.51 %
  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:  0.25 (0.32), residues: 668
  helix:  1.13 (0.37), residues: 214
  sheet:  0.83 (0.50), residues: 121
  loop : -0.71 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 468 
 HIS   0.006   0.001   HIS A 688 
 PHE   0.009   0.001   PHE A 634 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.004   0.000   ARG A 724 

*********************** 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
  68 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7050 (ttp80) cc_final: 0.6747 (mtm110)
REVERT: A  253 LEU cc_start: 0.7570 (mm) cc_final: 0.7096 (tp)
REVERT: A  293 PRO cc_start: 0.8140 (Cg_endo) cc_final: 0.7746 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8753 (t70) cc_final: 0.8535 (t0)
REVERT: A  783 ASP cc_start: 0.8256 (m-30) cc_final: 0.7696 (m-30)
REVERT: A  794 ARG cc_start: 0.8116 (ttm170) cc_final: 0.7860 (ttm170)
REVERT: A  820 TRP cc_start: 0.7205 (m100) cc_final: 0.6526 (m100)
  outliers start: 7
  outliers final: 7
  residues processed: 66
  average time/residue: 0.2097
  time to fit residues: 17.7507
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  : 0.665 
-------------------------------------------------------------------------------
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  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 41 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0370
   chunk 39 optimal weight:    0.0020
   chunk 33 optimal weight:    0.0020
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.2474

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.150372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.108488 restraints weight = 7339.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.86
r_work: 0.3227 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2468

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= 0.121
  Angle     :  0.461   5.415   7427  Z= 0.232
  Chirality :  0.040   0.131    837
  Planarity :  0.003   0.035    958
  Dihedral  :  3.716  19.361    732
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.82 %
    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:  0.53 (0.33), residues: 668
  helix:  1.31 (0.38), residues: 214
  sheet:  1.24 (0.51), residues: 110
  loop : -0.55 (0.32), residues: 344

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   0.008   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 724 

*********************** 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: 7
    poor density    : 65
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7087 (ttp80) cc_final: 0.6825 (mtm110)
REVERT: A   95 PHE cc_start: 0.7260 (t80) cc_final: 0.6797 (t80)
REVERT: A  253 LEU cc_start: 0.7555 (mm) cc_final: 0.7089 (tp)
REVERT: A  293 PRO cc_start: 0.8147 (Cg_endo) cc_final: 0.7743 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8762 (t70) cc_final: 0.8533 (t0)
REVERT: A  783 ASP cc_start: 0.8245 (m-30) cc_final: 0.7606 (m-30)
REVERT: A  794 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7803 (ttm170)
REVERT: A  820 TRP cc_start: 0.7280 (m100) cc_final: 0.6842 (m100)
  outliers start: 7
  outliers final: 5
  residues processed: 71
  average time/residue: 0.2062
  time to fit residues: 18.8430
Evaluate side-chains
  66 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
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  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:    9.9990
   chunk 29 optimal weight:    0.3980
   chunk 43 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0370
   chunk 55 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
A 526 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.146655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.103845 restraints weight = 7401.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.94
r_work: 0.3164 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2534

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= 0.140
  Angle     :  0.460   5.529   7427  Z= 0.233
  Chirality :  0.041   0.146    837
  Planarity :  0.003   0.035    958
  Dihedral  :  3.628  19.620    732
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 13.66 %
    Favored  : 85.33 %
  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:  0.65 (0.33), residues: 668
  helix:  1.38 (0.38), residues: 214
  sheet:  1.24 (0.50), residues: 110
  loop : -0.42 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 526 
 PHE   0.015   0.001   PHE A  95 
 TYR   0.008   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 724 

*********************** 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
  73 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6801 (mtm110)
REVERT: A   95 PHE cc_start: 0.7258 (t80) cc_final: 0.6789 (t80)
REVERT: A  253 LEU cc_start: 0.7542 (mm) cc_final: 0.7079 (tp)
REVERT: A  293 PRO cc_start: 0.8114 (Cg_endo) cc_final: 0.7696 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8723 (t70) cc_final: 0.8505 (t0)
REVERT: A  783 ASP cc_start: 0.8261 (m-30) cc_final: 0.7609 (m-30)
REVERT: A  794 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7758 (ttm170)
REVERT: A  820 TRP cc_start: 0.7255 (m100) cc_final: 0.6770 (m100)
  outliers start: 6
  outliers final: 6
  residues processed: 71
  average time/residue: 0.2114
  time to fit residues: 19.2182
Evaluate side-chains
  67 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 520 HIS
A 526 HIS
A 579 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.143917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.100803 restraints weight = 7336.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.91
r_work: 0.3118 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5487  Z= 0.197
  Angle     :  0.490   6.542   7427  Z= 0.250
  Chirality :  0.041   0.135    837
  Planarity :  0.004   0.036    958
  Dihedral  :  3.737  19.861    732
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 14.33 %
    Favored  : 84.32 %
  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:  0.50 (0.33), residues: 668
  helix:  1.16 (0.37), residues: 220
  sheet:  0.76 (0.47), residues: 128
  loop : -0.37 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 712 
 PHE   0.014   0.001   PHE A  95 
 TYR   0.010   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 724 

*********************** 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
  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: 0.7039 (ttp80) cc_final: 0.6790 (mtm110)
REVERT: A   95 PHE cc_start: 0.7186 (t80) cc_final: 0.6717 (t80)
REVERT: A  293 PRO cc_start: 0.8087 (Cg_endo) cc_final: 0.7654 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8731 (t70) cc_final: 0.8507 (t0)
REVERT: A  783 ASP cc_start: 0.8300 (m-30) cc_final: 0.7740 (m-30)
REVERT: A  794 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7795 (ttm170)
REVERT: A  820 TRP cc_start: 0.7226 (m100) cc_final: 0.6689 (m100)
  outliers start: 8
  outliers final: 7
  residues processed: 69
  average time/residue: 0.2025
  time to fit residues: 18.0035
Evaluate side-chains
  68 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 7 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0570
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.2500

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.143755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.100672 restraints weight = 7368.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.91
r_work: 0.3115 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5487  Z= 0.193
  Angle     :  0.507   9.214   7427  Z= 0.256
  Chirality :  0.042   0.136    837
  Planarity :  0.004   0.036    958
  Dihedral  :  3.788  19.938    732
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.50 %
    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:  0.57 (0.33), residues: 668
  helix:  1.15 (0.37), residues: 220
  sheet:  0.79 (0.46), residues: 134
  loop : -0.30 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 526 
 PHE   0.014   0.001   PHE A  95 
 TYR   0.010   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 724 

*********************** 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  : 0.578 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6803 (mtm110)
REVERT: A   95 PHE cc_start: 0.7185 (t80) cc_final: 0.6707 (t80)
REVERT: A  253 LEU cc_start: 0.7682 (mp) cc_final: 0.7030 (tp)
REVERT: A  293 PRO cc_start: 0.8082 (Cg_endo) cc_final: 0.7636 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8712 (t70) cc_final: 0.8482 (t0)
REVERT: A  783 ASP cc_start: 0.8247 (m-30) cc_final: 0.7714 (m-30)
REVERT: A  794 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7802 (ttm170)
REVERT: A  820 TRP cc_start: 0.7257 (m100) cc_final: 0.6699 (m100)
  outliers start: 11
  outliers final: 9
  residues processed: 68
  average time/residue: 0.2040
  time to fit residues: 17.9622
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  : 0.628 
-------------------------------------------------------------------------------
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  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  791 VAL
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:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.1990

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.145951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.101970 restraints weight = 7374.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.97
r_work: 0.3107 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5487  Z= 0.189
  Angle     :  0.499   8.446   7427  Z= 0.252
  Chirality :  0.041   0.135    837
  Planarity :  0.004   0.035    958
  Dihedral  :  3.790  20.194    732
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.01 %
    Favored  : 83.14 %
  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:  0.60 (0.33), residues: 668
  helix:  1.22 (0.37), residues: 220
  sheet:  0.81 (0.46), residues: 134
  loop : -0.32 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 526 
 PHE   0.014   0.001   PHE A  95 
 TYR   0.010   0.001   TYR A 340 
 ARG   0.004   0.000   ARG A 724 

*********************** 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
  72 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6826 (mtm110)
REVERT: A   95 PHE cc_start: 0.7181 (t80) cc_final: 0.6697 (t80)
REVERT: A  253 LEU cc_start: 0.7693 (mp) cc_final: 0.7031 (tp)
REVERT: A  293 PRO cc_start: 0.8094 (Cg_endo) cc_final: 0.7653 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8709 (t70) cc_final: 0.8484 (t0)
REVERT: A  783 ASP cc_start: 0.8232 (m-30) cc_final: 0.7636 (m-30)
REVERT: A  794 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7756 (ttm170)
  outliers start: 11
  outliers final: 10
  residues processed: 67
  average time/residue: 0.2016
  time to fit residues: 17.6415
Evaluate side-chains
  70 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
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  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  791 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 13 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 61 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 44 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.5984

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.146336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.103620 restraints weight = 7339.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.90
r_work: 0.3153 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5487  Z= 0.143
  Angle     :  0.480   7.375   7427  Z= 0.241
  Chirality :  0.040   0.130    837
  Planarity :  0.003   0.034    958
  Dihedral  :  3.652  20.227    732
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.35 %
    Favored  : 83.14 %
  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:  0.74 (0.33), residues: 668
  helix:  1.37 (0.37), residues: 220
  sheet:  1.21 (0.47), residues: 121
  loop : -0.35 (0.34), residues: 327

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

********************** 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
  74 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7046 (ttp80) cc_final: 0.6813 (mtm110)
REVERT: A   95 PHE cc_start: 0.7186 (t80) cc_final: 0.6705 (t80)
REVERT: A  253 LEU cc_start: 0.7657 (mp) cc_final: 0.7025 (tp)
REVERT: A  293 PRO cc_start: 0.8096 (Cg_endo) cc_final: 0.7657 (Cg_exo)
REVERT: A  424 ASP cc_start: 0.8721 (t70) cc_final: 0.8490 (t0)
REVERT: A  783 ASP cc_start: 0.8161 (m-30) cc_final: 0.7464 (m-30)
REVERT: A  794 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7695 (ttm170)
  outliers start: 9
  outliers final: 7
  residues processed: 72
  average time/residue: 0.2045
  time to fit residues: 18.8384
Evaluate side-chains
  65 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
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  572 ILE
Chi-restraints excluded: chain A residue  593 VAL
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 25 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0870
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0770
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.3819 r_free = 0.3819 target = 0.148439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.104633 restraints weight = 7529.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 3.00
r_work: 0.3145 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2874

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= 0.140
  Angle     :  0.476   7.949   7427  Z= 0.239
  Chirality :  0.040   0.131    837
  Planarity :  0.003   0.034    958
  Dihedral  :  3.567  19.881    732
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.02 %
    Favored  : 82.29 %
  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:  0.77 (0.33), residues: 668
  helix:  1.39 (0.37), residues: 220
  sheet:  1.24 (0.47), residues: 121
  loop : -0.34 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 688 
 PHE   0.013   0.001   PHE A  95 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.005   0.000   ARG A 724 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2622.29 seconds
wall clock time: 45 minutes 43.17 seconds (2743.17 seconds total)