Starting phenix.real_space_refine
on Tue Feb 11 01:45:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxg_32878/02_2025/7wxg_32878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxg_32878/02_2025/7wxg_32878.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxg_32878/02_2025/7wxg_32878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxg_32878/02_2025/7wxg_32878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxg_32878/02_2025/7wxg_32878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxg_32878/02_2025/7wxg_32878.cif"
  }
  resolution = 4.2
  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=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      15      5.16       5
     C    2048      2.51       5
     N     593      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3295
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3247
          Classifications: {'peptide': 430}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 414}
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'NAP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.99, per 1000 atoms: 0.91
  Number of scatterers: 3295
  At special positions: 0
  Unit cell: (80.56, 93.28, 60.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P       3     15.00
     O     636      8.00
     N     593      7.00
     C    2048      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: 0.82
  Conformation dependent library (CDL) restraints added in 391.6 milliseconds
  

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  798

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 5 sheets defined
      49.5% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 348 through 364
    Processing helix  chain 'A' and resid 366 through 384
      removed outlier: 3.901A  pdb=" N   ARG A 370 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   SER A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 403
      removed outlier: 3.814A  pdb=" N   ILE A 388 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 413
    Processing helix  chain 'A' and resid 415 through 432
    Processing helix  chain 'A' and resid 471 through 484
      removed outlier: 4.333A  pdb=" N   GLN A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 511
    Processing helix  chain 'A' and resid 524 through 534
      removed outlier: 3.672A  pdb=" N   ILE A 528 " --> pdb=" O   THR A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 579 through 592
    Processing helix  chain 'A' and resid 609 through 611
      No H-bonds generated for 'chain 'A' and resid 609 through 611'
    Processing helix  chain 'A' and resid 614 through 626
      removed outlier: 3.610A  pdb=" N   ASP A 618 " --> pdb=" O   ALA A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 640
    Processing helix  chain 'A' and resid 666 through 678
    Processing helix  chain 'A' and resid 689 through 700
    Processing helix  chain 'A' and resid 716 through 720
    Processing helix  chain 'A' and resid 740 through 742
      No H-bonds generated for 'chain 'A' and resid 740 through 742'
    Processing helix  chain 'A' and resid 757 through 761
      removed outlier: 3.557A  pdb=" N   PHE A 760 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444
      removed outlier: 7.232A  pdb=" N   VAL A 440 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   THR A 456 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG A 442 " --> pdb=" O   GLN A 454 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A 751 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 749 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 486 through 488
      removed outlier: 6.258A  pdb=" N   LEU A 462 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   VAL A 461 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   ILE A 542 " --> pdb=" O   VAL A 461 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LEU A 463 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ARG A 544 " --> pdb=" O   LEU A 463 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ILE A 465 " --> pdb=" O   ARG A 544 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 604 through 607
      removed outlier: 6.131A  pdb=" N   LEU A 604 " --> pdb=" O   GLU A 662 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   VAL A 664 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE A 606 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 683 through 685
      removed outlier: 6.862A  pdb=" N   ASP A 683 " --> pdb=" O   PHE A 706 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 728

    149 hydrogen bonds defined for protein.
    435 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: 0.84

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 571
        1.31 -     1.43: 791
        1.43 -     1.56: 1955
        1.56 -     1.68: 8
        1.68 -     1.81: 24
  Bond restraints: 3349
  Sorted by residual:
  bond pdb=" C1D NAP A 801 "
       pdb=" C2D NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.533  1.271  0.262 2.00e-02 2.50e+03 1.72e+02
  bond pdb=" C3D NAP A 801 "
       pdb=" C4D NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.518  1.261  0.257 2.00e-02 2.50e+03 1.65e+02
  bond pdb=" C3B NAP A 801 "
       pdb=" C4B NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.543  1.294  0.249 2.00e-02 2.50e+03 1.56e+02
  bond pdb=" C4B NAP A 801 "
       pdb=" O4B NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.426  1.623 -0.197 2.00e-02 2.50e+03 9.67e+01
  bond pdb=" C1D NAP A 801 "
       pdb=" O4D NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.375  1.550 -0.175 2.00e-02 2.50e+03 7.65e+01
  ... (remaining 3344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.97: 4500
        3.97 -     7.94: 33
        7.94 -    11.90: 5
       11.90 -    15.87: 3
       15.87 -    19.84: 3
  Bond angle restraints: 4544
  Sorted by residual:
  angle pdb=" N1A NAP A 801 "
        pdb=" C6A NAP A 801 "
        pdb=" N6A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     119.30   99.46   19.84 3.00e+00 1.11e-01 4.37e+01
  angle pdb=" C1B NAP A 801 "
        pdb=" N9A NAP A 801 "
        pdb=" C4A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     124.31  107.08   17.23 3.00e+00 1.11e-01 3.30e+01
  angle pdb=" C5A NAP A 801 "
        pdb=" C6A NAP A 801 "
        pdb=" N6A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     122.73  139.91  -17.18 3.00e+00 1.11e-01 3.28e+01
  angle pdb=" C1B NAP A 801 "
        pdb=" N9A NAP A 801 "
        pdb=" C8A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     129.84  145.62  -15.78 3.00e+00 1.11e-01 2.77e+01
  angle pdb=" O1N NAP A 801 "
        pdb=" PN  NAP A 801 "
        pdb=" O2N NAP A 801 "
      ideal   model   delta    sigma   weight residual
     122.51  109.58   12.93 3.00e+00 1.11e-01 1.86e+01
  ... (remaining 4539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.77: 1765
       14.77 -    29.54: 216
       29.54 -    44.30: 84
       44.30 -    59.07: 15
       59.07 -    73.84: 5
  Dihedral angle restraints: 2085
    sinusoidal: 853
      harmonic: 1232
  Sorted by residual:
  dihedral pdb=" CA  PHE A 642 "
           pdb=" C   PHE A 642 "
           pdb=" N   GLY A 643 "
           pdb=" CA  GLY A 643 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.98   21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  CYS A 598 "
           pdb=" C   CYS A 598 "
           pdb=" N   ASN A 599 "
           pdb=" CA  ASN A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.95  -17.05     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  ALA A 714 "
           pdb=" C   ALA A 714 "
           pdb=" N   ASP A 715 "
           pdb=" CA  ASP A 715 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.01   15.99     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2082 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 466
       0.072 -    0.144: 58
       0.144 -    0.215: 5
       0.215 -    0.287: 1
       0.287 -    0.359: 1
  Chirality restraints: 531
  Sorted by residual:
  chirality pdb=" C3D NAP A 801 "
            pdb=" C2D NAP A 801 "
            pdb=" C4D NAP A 801 "
            pdb=" O3D NAP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.38   -0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C2B NAP A 801 "
            pdb=" C1B NAP A 801 "
            pdb=" C3B NAP A 801 "
            pdb=" O2B NAP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.50   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C2D NAP A 801 "
            pdb=" C1D NAP A 801 "
            pdb=" C3D NAP A 801 "
            pdb=" O2D NAP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.37   -0.18 2.00e-01 2.50e+01 8.07e-01
  ... (remaining 528 not shown)

  Planarity restraints: 588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 560 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO A 561 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 561 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 561 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 594 "    0.022 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A 595 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 595 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 595 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 469 "    0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO A 470 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 470 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 470 "    0.018 5.00e-02 4.00e+02
  ... (remaining 585 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 278
        2.73 -     3.27: 3683
        3.27 -     3.81: 5261
        3.81 -     4.36: 5991
        4.36 -     4.90: 10082
  Nonbonded interactions: 25295
  Sorted by model distance:
  nonbonded pdb=" O   SER A 410 "
            pdb=" OG  SER A 413 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   CYS A 570 "
            pdb=" ND1 HIS A 571 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" O   ASP A 530 "
            pdb=" OG  SER A 533 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   ALA A 399 "
            pdb=" OG  SER A 402 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" NH1 ARG A 525 "
            pdb=" O4B NAP A 801 "
     model   vdw
     2.272 3.120
  ... (remaining 25290 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.930
  Find NCS groups from input model:        0.040
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
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      :  0.012   0.262   3349  Z= 0.784
  Angle     :  1.073  19.838   4544  Z= 0.492
  Chirality :  0.050   0.359    531
  Planarity :  0.004   0.033    588
  Dihedral  : 15.420  73.837   1287
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  7.54 %
    Favored  : 92.17 %
  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: -5.16 (0.29), residues: 428
  helix: -2.48 (0.29), residues: 186
  sheet: -4.14 (0.44), residues: 61
  loop : -4.14 (0.33), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 768 
 HIS   0.003   0.001   HIS A 681 
 PHE   0.021   0.002   PHE A 642 
 TYR   0.010   0.002   TYR A 573 
 ARG   0.002   0.000   ARG A 370 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 MET cc_start: 0.8692 (mtp) cc_final: 0.8466 (mtp)
REVERT: A  497 HIS cc_start: 0.8544 (m90) cc_final: 0.8323 (m90)
REVERT: A  521 LEU cc_start: 0.8997 (mt) cc_final: 0.8744 (mp)
REVERT: A  536 ASN cc_start: 0.8874 (t0) cc_final: 0.8492 (t0)
REVERT: A  594 TYR cc_start: 0.8507 (m-10) cc_final: 0.8192 (m-80)
REVERT: A  602 GLU cc_start: 0.8841 (pt0) cc_final: 0.8314 (mt-10)
REVERT: A  651 LYS cc_start: 0.9059 (mttt) cc_final: 0.8254 (tptt)
REVERT: A  652 HIS cc_start: 0.7686 (t-90) cc_final: 0.7388 (t-90)
REVERT: A  668 ASP cc_start: 0.7950 (t0) cc_final: 0.7628 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1970
  time to fit residues: 19.6775
Evaluate side-chains
  63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    0.2980
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0060
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 375 ASN
A 392 ASN
A 434 HIS
A 536 ASN
A 607 HIS
A 672 ASN
A 681 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.122390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.098595 restraints weight = 6404.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.101877 restraints weight = 4057.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.104276 restraints weight = 2926.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3349  Z= 0.162
  Angle     :  0.639   6.304   4544  Z= 0.320
  Chirality :  0.045   0.151    531
  Planarity :  0.005   0.044    588
  Dihedral  :  9.325  46.948    526
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.64 %
    Favored  : 94.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.37), residues: 428
  helix: -0.62 (0.35), residues: 191
  sheet: -3.35 (0.49), residues: 60
  loop : -2.89 (0.42), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 748 
 HIS   0.004   0.001   HIS A 673 
 PHE   0.012   0.001   PHE A 616 
 TYR   0.007   0.001   TYR A 631 
 ARG   0.003   0.000   ARG A 712 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 MET cc_start: 0.8970 (mtp) cc_final: 0.8756 (mtt)
REVERT: A  428 GLN cc_start: 0.8687 (mt0) cc_final: 0.8359 (tm-30)
REVERT: A  489 LEU cc_start: 0.9224 (mm) cc_final: 0.8948 (mm)
REVERT: A  497 HIS cc_start: 0.8375 (m90) cc_final: 0.8075 (t70)
REVERT: A  536 ASN cc_start: 0.8719 (t0) cc_final: 0.8392 (t0)
REVERT: A  556 GLN cc_start: 0.8053 (mt0) cc_final: 0.7776 (tt0)
REVERT: A  651 LYS cc_start: 0.8895 (mttt) cc_final: 0.8065 (tptt)
REVERT: A  668 ASP cc_start: 0.7839 (t0) cc_final: 0.7537 (t0)
REVERT: A  712 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7659 (ttp-170)
  outliers start: 2
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1678
  time to fit residues: 18.5908
Evaluate side-chains
  63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0870
   chunk 31 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.4762

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
A 652 HIS
A 689 ASN
A 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.119789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.095638 restraints weight = 6446.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.098721 restraints weight = 4196.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.100838 restraints weight = 3085.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3349  Z= 0.222
  Angle     :  0.625   6.968   4544  Z= 0.314
  Chirality :  0.045   0.188    531
  Planarity :  0.004   0.046    588
  Dihedral  :  8.695  48.639    526
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.93 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.38), residues: 428
  helix:  0.11 (0.36), residues: 190
  sheet: -2.95 (0.54), residues: 59
  loop : -2.56 (0.43), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 
 PHE   0.014   0.002   PHE A 642 
 TYR   0.005   0.001   TYR A 654 
 ARG   0.003   0.000   ARG A 544 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8703 (m-40) cc_final: 0.8344 (m110)
REVERT: A  392 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7397 (t0)
REVERT: A  497 HIS cc_start: 0.8395 (m90) cc_final: 0.8108 (t70)
REVERT: A  520 SER cc_start: 0.8900 (t) cc_final: 0.8655 (p)
REVERT: A  536 ASN cc_start: 0.8671 (t0) cc_final: 0.8213 (t0)
REVERT: A  556 GLN cc_start: 0.8024 (mt0) cc_final: 0.7622 (tt0)
REVERT: A  602 GLU cc_start: 0.8970 (pt0) cc_final: 0.8335 (mt-10)
REVERT: A  651 LYS cc_start: 0.8905 (mttt) cc_final: 0.8082 (tptt)
REVERT: A  652 HIS cc_start: 0.7740 (t-90) cc_final: 0.7147 (t-90)
REVERT: A  668 ASP cc_start: 0.7888 (t0) cc_final: 0.7503 (t0)
REVERT: A  712 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7667 (ttp-170)
  outliers start: 2
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1392
  time to fit residues: 14.9691
Evaluate side-chains
  63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.122160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.097722 restraints weight = 6398.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.100984 restraints weight = 4121.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103207 restraints weight = 2991.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3349  Z= 0.175
  Angle     :  0.620   9.748   4544  Z= 0.304
  Chirality :  0.044   0.154    531
  Planarity :  0.004   0.046    588
  Dihedral  :  8.171  50.648    526
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.40), residues: 428
  helix:  0.39 (0.37), residues: 196
  sheet: -2.62 (0.54), residues: 63
  loop : -2.10 (0.47), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 768 
 HIS   0.003   0.000   HIS A 673 
 PHE   0.009   0.001   PHE A 642 
 TYR   0.012   0.001   TYR A 573 
 ARG   0.003   0.000   ARG A 544 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 HIS cc_start: 0.8351 (m90) cc_final: 0.8049 (t70)
REVERT: A  536 ASN cc_start: 0.8688 (t0) cc_final: 0.8179 (t0)
REVERT: A  556 GLN cc_start: 0.8024 (mt0) cc_final: 0.7656 (tt0)
REVERT: A  651 LYS cc_start: 0.8682 (mttt) cc_final: 0.7931 (tptt)
REVERT: A  652 HIS cc_start: 0.7618 (t-90) cc_final: 0.7194 (t-90)
REVERT: A  668 ASP cc_start: 0.7843 (t0) cc_final: 0.7444 (t0)
REVERT: A  712 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7630 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1636
  time to fit residues: 17.4936
Evaluate side-chains
  61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   overall best weight:    2.3384

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.118469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.093788 restraints weight = 6616.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.096916 restraints weight = 4302.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099189 restraints weight = 3147.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3349  Z= 0.328
  Angle     :  0.697   9.267   4544  Z= 0.353
  Chirality :  0.046   0.169    531
  Planarity :  0.005   0.045    588
  Dihedral  :  8.451  52.572    526
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.39), residues: 428
  helix:  0.34 (0.37), residues: 194
  sheet: -2.54 (0.53), residues: 65
  loop : -2.29 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 768 
 HIS   0.003   0.001   HIS A 565 
 PHE   0.014   0.002   PHE A 642 
 TYR   0.005   0.001   TYR A 631 
 ARG   0.003   0.000   ARG A 718 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8723 (m-40) cc_final: 0.8388 (m-40)
REVERT: A  428 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: A  497 HIS cc_start: 0.8443 (m90) cc_final: 0.8144 (t70)
REVERT: A  536 ASN cc_start: 0.8694 (t0) cc_final: 0.8315 (t0)
REVERT: A  556 GLN cc_start: 0.8090 (mt0) cc_final: 0.7649 (tt0)
REVERT: A  602 GLU cc_start: 0.8894 (pt0) cc_final: 0.8497 (tt0)
REVERT: A  651 LYS cc_start: 0.8807 (mttt) cc_final: 0.8076 (tptt)
REVERT: A  652 HIS cc_start: 0.7569 (t-90) cc_final: 0.7053 (t-90)
REVERT: A  654 TYR cc_start: 0.7861 (m-80) cc_final: 0.7369 (m-80)
REVERT: A  668 ASP cc_start: 0.7917 (t0) cc_final: 0.7511 (t0)
REVERT: A  712 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7691 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1503
  time to fit residues: 14.5807
Evaluate side-chains
  62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    0.7980
   chunk 41 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.124856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.099686 restraints weight = 6435.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103229 restraints weight = 4001.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.105848 restraints weight = 2843.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3349  Z= 0.167
  Angle     :  0.611   7.835   4544  Z= 0.305
  Chirality :  0.044   0.152    531
  Planarity :  0.004   0.047    588
  Dihedral  :  7.905  52.431    526
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.41), residues: 428
  helix:  0.65 (0.38), residues: 196
  sheet: -2.42 (0.53), residues: 70
  loop : -1.75 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 748 
 HIS   0.004   0.001   HIS A 673 
 PHE   0.009   0.001   PHE A 719 
 TYR   0.009   0.001   TYR A 631 
 ARG   0.004   0.000   ARG A 718 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7936 (tm-30)
REVERT: A  497 HIS cc_start: 0.8441 (m90) cc_final: 0.8148 (t70)
REVERT: A  536 ASN cc_start: 0.8722 (t0) cc_final: 0.8237 (t0)
REVERT: A  553 ILE cc_start: 0.8628 (mm) cc_final: 0.8422 (mm)
REVERT: A  556 GLN cc_start: 0.8083 (mt0) cc_final: 0.7777 (tt0)
REVERT: A  651 LYS cc_start: 0.8746 (mttt) cc_final: 0.8175 (ptpp)
REVERT: A  668 ASP cc_start: 0.7896 (t0) cc_final: 0.7492 (t0)
REVERT: A  712 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7626 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1591
  time to fit residues: 17.3627
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 0 optimal weight:    9.9990
   chunk 39 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3622 r_free = 0.3622 target = 0.122824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.097976 restraints weight = 6317.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.101353 restraints weight = 4012.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.103833 restraints weight = 2892.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3349  Z= 0.206
  Angle     :  0.628   8.266   4544  Z= 0.317
  Chirality :  0.044   0.152    531
  Planarity :  0.004   0.045    588
  Dihedral  :  7.978  52.287    526
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.40), residues: 428
  helix:  0.64 (0.37), residues: 198
  sheet: -2.12 (0.54), residues: 69
  loop : -1.79 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 
 PHE   0.008   0.001   PHE A 466 
 TYR   0.008   0.001   TYR A 654 
 ARG   0.003   0.000   ARG A 411 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  536 ASN cc_start: 0.8743 (t0) cc_final: 0.8250 (t0)
REVERT: A  553 ILE cc_start: 0.8607 (mm) cc_final: 0.8407 (mm)
REVERT: A  556 GLN cc_start: 0.8178 (mt0) cc_final: 0.7870 (tt0)
REVERT: A  629 LYS cc_start: 0.8425 (pptt) cc_final: 0.7998 (pptt)
REVERT: A  651 LYS cc_start: 0.8702 (mttt) cc_final: 0.8172 (ptpp)
REVERT: A  668 ASP cc_start: 0.7885 (t0) cc_final: 0.7434 (t0)
REVERT: A  669 GLU cc_start: 0.7585 (tp30) cc_final: 0.7337 (tp30)
REVERT: A  712 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7632 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1410
  time to fit residues: 15.0804
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
A 637 ASN
A 652 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.126920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.101713 restraints weight = 6395.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.105401 restraints weight = 3951.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.107992 restraints weight = 2805.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3349  Z= 0.187
  Angle     :  0.606   8.666   4544  Z= 0.303
  Chirality :  0.043   0.146    531
  Planarity :  0.004   0.046    588
  Dihedral  :  7.887  52.707    526
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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: -0.86 (0.41), residues: 428
  helix:  0.83 (0.38), residues: 198
  sheet: -1.91 (0.56), residues: 69
  loop : -1.67 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 
 PHE   0.017   0.002   PHE A 387 
 TYR   0.009   0.001   TYR A 654 
 ARG   0.003   0.000   ARG A 411 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 HIS cc_start: 0.8349 (m-70) cc_final: 0.7988 (t70)
REVERT: A  536 ASN cc_start: 0.8693 (t0) cc_final: 0.8197 (t0)
REVERT: A  553 ILE cc_start: 0.8614 (mm) cc_final: 0.8410 (mm)
REVERT: A  556 GLN cc_start: 0.8088 (mt0) cc_final: 0.7822 (tt0)
REVERT: A  651 LYS cc_start: 0.8773 (mttt) cc_final: 0.8182 (ptpp)
REVERT: A  668 ASP cc_start: 0.7822 (t0) cc_final: 0.7429 (t0)
REVERT: A  669 GLU cc_start: 0.7471 (tp30) cc_final: 0.7252 (tp30)
REVERT: A  712 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7761 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1398
  time to fit residues: 15.0895
Evaluate side-chains
  65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 32 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.128174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.103439 restraints weight = 6454.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.106823 restraints weight = 4133.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.109303 restraints weight = 3016.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3349  Z= 0.176
  Angle     :  0.611   9.024   4544  Z= 0.306
  Chirality :  0.043   0.143    531
  Planarity :  0.004   0.046    588
  Dihedral  :  7.825  52.982    526
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.75 (0.41), residues: 428
  helix:  0.90 (0.38), residues: 198
  sheet: -1.79 (0.57), residues: 69
  loop : -1.62 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 
 PHE   0.008   0.001   PHE A 616 
 TYR   0.012   0.001   TYR A 573 
 ARG   0.002   0.000   ARG A 411 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  497 HIS cc_start: 0.8310 (m-70) cc_final: 0.7987 (t70)
REVERT: A  503 MET cc_start: 0.8751 (mmp) cc_final: 0.8548 (mmm)
REVERT: A  536 ASN cc_start: 0.8689 (t0) cc_final: 0.8181 (t0)
REVERT: A  553 ILE cc_start: 0.8617 (mm) cc_final: 0.8375 (mm)
REVERT: A  555 GLN cc_start: 0.8795 (mp10) cc_final: 0.8491 (pp30)
REVERT: A  556 GLN cc_start: 0.8113 (mt0) cc_final: 0.7832 (tt0)
REVERT: A  651 LYS cc_start: 0.8688 (mttt) cc_final: 0.8122 (ptpp)
REVERT: A  668 ASP cc_start: 0.7704 (t0) cc_final: 0.7316 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1601
  time to fit residues: 16.9520
Evaluate side-chains
  67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0980
   chunk 42 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.127539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.101988 restraints weight = 6354.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.105563 restraints weight = 3989.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.107965 restraints weight = 2874.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3349  Z= 0.212
  Angle     :  0.658   9.435   4544  Z= 0.333
  Chirality :  0.044   0.157    531
  Planarity :  0.004   0.045    588
  Dihedral  :  7.843  52.796    526
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.79 (0.41), residues: 428
  helix:  0.91 (0.38), residues: 198
  sheet: -1.75 (0.55), residues: 74
  loop : -1.71 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 565 
 PHE   0.009   0.001   PHE A 466 
 TYR   0.007   0.001   TYR A 631 
 ARG   0.002   0.000   ARG A 360 

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8430 (t80) cc_final: 0.8213 (t80)
REVERT: A  497 HIS cc_start: 0.8361 (m-70) cc_final: 0.8018 (t70)
REVERT: A  536 ASN cc_start: 0.8716 (t0) cc_final: 0.8226 (t0)
REVERT: A  553 ILE cc_start: 0.8609 (mm) cc_final: 0.8382 (mm)
REVERT: A  556 GLN cc_start: 0.8167 (mt0) cc_final: 0.7869 (tt0)
REVERT: A  629 LYS cc_start: 0.8401 (pptt) cc_final: 0.7947 (pptt)
REVERT: A  651 LYS cc_start: 0.8715 (mttt) cc_final: 0.8151 (ptpp)
REVERT: A  668 ASP cc_start: 0.7795 (t0) cc_final: 0.7398 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1477
  time to fit residues: 15.5641
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0980
   chunk 29 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 770 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.129348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.103826 restraints weight = 6324.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.107517 restraints weight = 3909.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.110239 restraints weight = 2774.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3349  Z= 0.171
  Angle     :  0.629   9.324   4544  Z= 0.312
  Chirality :  0.042   0.144    531
  Planarity :  0.004   0.047    588
  Dihedral  :  7.735  52.845    526
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.45 (0.42), residues: 428
  helix:  1.21 (0.39), residues: 198
  sheet: -1.50 (0.55), residues: 74
  loop : -1.63 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 768 
 HIS   0.004   0.001   HIS A 673 
 PHE   0.008   0.001   PHE A 466 
 TYR   0.013   0.001   TYR A 654 
 ARG   0.002   0.000   ARG A 360 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1345.76 seconds
wall clock time: 24 minutes 40.08 seconds (1480.08 seconds total)