Starting phenix.real_space_refine
on Wed Jun  4 17:04:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxg_32878/06_2025/7wxg_32878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxg_32878/06_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_32878/06_2025/7wxg_32878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxg_32878/06_2025/7wxg_32878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxg_32878/06_2025/7wxg_32878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxg_32878/06_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-5710/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: 3.13, per 1000 atoms: 0.95
  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: 1.07
  Conformation dependent library (CDL) restraints added in 474.9 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: 0.36
  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: 0.88

  Time building geometry restraints manager: 1.14 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:                  0.010
  Normalize map: mean=0, sd=1:             2.110
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.980
  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:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.450
-------------------------------------------------------------------------------
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= 0.580
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14431 (  149)
  hydrogen bonds       : angle       6.36880 (  435)
  covalent geometry    : bond        0.01169 ( 3349)
  covalent geometry    : angle       1.07303 ( 4544)

*********************** 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  : 0.362 
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: 0.1924
  time to fit residues: 19.3067
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  : 0.357 
-------------------------------------------------------------------------------
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 = 0.3621 r_free = 0.3621 target = 0.122477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.099338 restraints weight = 6402.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.102426 restraints weight = 4161.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.104707 restraints weight = 3054.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
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= 0.117
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03541 (  149)
  hydrogen bonds       : angle       4.85862 (  435)
  covalent geometry    : bond        0.00244 ( 3349)
  covalent geometry    : angle       0.63949 ( 4544)

*********************** 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  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 MET cc_start: 0.8960 (mtp) cc_final: 0.8741 (mtt)
REVERT: A  428 GLN cc_start: 0.8676 (mt0) cc_final: 0.8355 (tm-30)
REVERT: A  489 LEU cc_start: 0.9222 (mm) cc_final: 0.8950 (mm)
REVERT: A  497 HIS cc_start: 0.8352 (m90) cc_final: 0.8067 (t70)
REVERT: A  536 ASN cc_start: 0.8713 (t0) cc_final: 0.8387 (t0)
REVERT: A  556 GLN cc_start: 0.8052 (mt0) cc_final: 0.7779 (tt0)
REVERT: A  651 LYS cc_start: 0.8887 (mttt) cc_final: 0.8065 (tptt)
REVERT: A  668 ASP cc_start: 0.7824 (t0) cc_final: 0.7524 (t0)
REVERT: A  712 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7666 (ttp-170)
  outliers start: 2
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1572
  time to fit residues: 17.5029
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  : 0.354 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0980
   chunk 31 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    2.3586

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.116710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.092949 restraints weight = 6543.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.095799 restraints weight = 4309.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.097808 restraints weight = 3206.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3349  Z= 0.214
  Angle     :  0.681   7.200   4544  Z= 0.346
  Chirality :  0.046   0.215    531
  Planarity :  0.005   0.044    588
  Dihedral  :  9.189  49.121    526
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.38 %
    Favored  : 93.33 %
  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: -2.47 (0.38), residues: 428
  helix: -0.14 (0.36), residues: 190
  sheet: -3.07 (0.53), residues: 57
  loop : -2.79 (0.42), 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   0.019   0.002   PHE A 642 
 TYR   0.004   0.001   TYR A 654 
 ARG   0.004   0.000   ARG A 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  149)
  hydrogen bonds       : angle       4.92650 (  435)
  covalent geometry    : bond        0.00470 ( 3349)
  covalent geometry    : angle       0.68093 ( 4544)

*********************** 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
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 HIS cc_start: 0.8408 (m90) cc_final: 0.8105 (t70)
REVERT: A  536 ASN cc_start: 0.8683 (t0) cc_final: 0.8290 (t0)
REVERT: A  556 GLN cc_start: 0.8004 (mt0) cc_final: 0.7802 (mt0)
REVERT: A  602 GLU cc_start: 0.9038 (pt0) cc_final: 0.8392 (mt-10)
REVERT: A  651 LYS cc_start: 0.8955 (mttt) cc_final: 0.8158 (tptt)
REVERT: A  652 HIS cc_start: 0.7846 (t-90) cc_final: 0.7222 (t-90)
REVERT: A  668 ASP cc_start: 0.7882 (t0) cc_final: 0.7536 (t0)
REVERT: A  712 ARG cc_start: 0.8344 (tpp80) cc_final: 0.7744 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1610
  time to fit residues: 15.8815
Evaluate side-chains
  58 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0270
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.4046

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.094901 restraints weight = 6542.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.097969 restraints weight = 4263.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.100048 restraints weight = 3133.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3349  Z= 0.144
  Angle     :  0.655  10.882   4544  Z= 0.322
  Chirality :  0.045   0.171    531
  Planarity :  0.004   0.047    588
  Dihedral  :  8.596  50.553    526
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.93 %
    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: -1.85 (0.39), residues: 428
  helix:  0.33 (0.37), residues: 190
  sheet: -2.81 (0.53), residues: 63
  loop : -2.35 (0.45), residues: 175

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   0.011   0.002   PHE A 642 
 TYR   0.014   0.002   TYR A 573 
 ARG   0.003   0.000   ARG A 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03451 (  149)
  hydrogen bonds       : angle       4.60572 (  435)
  covalent geometry    : bond        0.00322 ( 3349)
  covalent geometry    : angle       0.65478 ( 4544)

*********************** 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: 1
    poor density    : 87
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7356 (tm-30)
REVERT: A  497 HIS cc_start: 0.8389 (m90) cc_final: 0.8086 (t70)
REVERT: A  536 ASN cc_start: 0.8732 (t0) cc_final: 0.8243 (t0)
REVERT: A  556 GLN cc_start: 0.8029 (mt0) cc_final: 0.7568 (tt0)
REVERT: A  602 GLU cc_start: 0.8827 (pt0) cc_final: 0.8157 (mt-10)
REVERT: A  651 LYS cc_start: 0.8810 (mttt) cc_final: 0.8034 (tptt)
REVERT: A  652 HIS cc_start: 0.7745 (t-90) cc_final: 0.6921 (t-90)
REVERT: A  668 ASP cc_start: 0.7869 (t0) cc_final: 0.7462 (t0)
REVERT: A  712 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7640 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1527
  time to fit residues: 16.4261
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  : 0.364 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    0.2980
   overall best weight:    1.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.120003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.095600 restraints weight = 6487.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.098675 restraints weight = 4211.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.100935 restraints weight = 3087.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3349  Z= 0.168
  Angle     :  0.668   9.530   4544  Z= 0.336
  Chirality :  0.045   0.193    531
  Planarity :  0.004   0.047    588
  Dihedral  :  8.424  53.561    526
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.40), residues: 428
  helix:  0.30 (0.37), residues: 197
  sheet: -2.66 (0.53), residues: 63
  loop : -2.06 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 681 
 PHE   0.012   0.002   PHE A 642 
 TYR   0.003   0.001   TYR A 631 
 ARG   0.003   0.000   ARG A 411 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  149)
  hydrogen bonds       : angle       4.60456 (  435)
  covalent geometry    : bond        0.00379 ( 3349)
  covalent geometry    : angle       0.66812 ( 4544)

*********************** 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  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8678 (m-40) cc_final: 0.8334 (m-40)
REVERT: A  428 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: A  497 HIS cc_start: 0.8380 (m90) cc_final: 0.8083 (t70)
REVERT: A  536 ASN cc_start: 0.8651 (t0) cc_final: 0.8236 (t0)
REVERT: A  556 GLN cc_start: 0.8055 (mt0) cc_final: 0.7598 (tt0)
REVERT: A  651 LYS cc_start: 0.8751 (mttt) cc_final: 0.8074 (tptt)
REVERT: A  652 HIS cc_start: 0.7328 (t-90) cc_final: 0.7067 (t-90)
REVERT: A  668 ASP cc_start: 0.7872 (t0) cc_final: 0.7448 (t0)
REVERT: A  712 ARG cc_start: 0.8215 (tpp80) cc_final: 0.7667 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1555
  time to fit residues: 15.1972
Evaluate side-chains
  56 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0770
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.123727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.098841 restraints weight = 6548.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.102199 restraints weight = 4134.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.104633 restraints weight = 2971.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3349  Z= 0.116
  Angle     :  0.620   7.750   4544  Z= 0.309
  Chirality :  0.044   0.155    531
  Planarity :  0.004   0.048    588
  Dihedral  :  7.978  53.866    526
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.41), residues: 428
  helix:  0.60 (0.38), residues: 196
  sheet: -2.42 (0.55), residues: 71
  loop : -1.78 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 748 
 HIS   0.004   0.001   HIS A 673 
 PHE   0.009   0.001   PHE A 719 
 TYR   0.008   0.001   TYR A 631 
 ARG   0.003   0.000   ARG A 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  149)
  hydrogen bonds       : angle       4.49569 (  435)
  covalent geometry    : bond        0.00258 ( 3349)
  covalent geometry    : angle       0.62031 ( 4544)

*********************** 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
  95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8145 (tt0)
REVERT: A  497 HIS cc_start: 0.8420 (m90) cc_final: 0.8104 (t70)
REVERT: A  536 ASN cc_start: 0.8710 (t0) cc_final: 0.8211 (t0)
REVERT: A  556 GLN cc_start: 0.8104 (mt0) cc_final: 0.7753 (tt0)
REVERT: A  651 LYS cc_start: 0.8712 (mttt) cc_final: 0.8155 (ptpp)
REVERT: A  652 HIS cc_start: 0.7477 (t-90) cc_final: 0.7268 (t70)
REVERT: A  668 ASP cc_start: 0.7840 (t0) cc_final: 0.7467 (t0)
REVERT: A  712 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7643 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1669
  time to fit residues: 19.2300
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  : 0.375 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 39 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.122982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.098176 restraints weight = 6276.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.101466 restraints weight = 3996.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.103906 restraints weight = 2887.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3349  Z= 0.138
  Angle     :  0.648   8.190   4544  Z= 0.322
  Chirality :  0.044   0.171    531
  Planarity :  0.004   0.046    588
  Dihedral  :  8.020  52.798    526
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  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: -1.09 (0.41), residues: 428
  helix:  0.67 (0.38), residues: 196
  sheet: -2.21 (0.55), residues: 71
  loop : -1.67 (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   0.005   0.001   TYR A 631 
 ARG   0.003   0.000   ARG A 411 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  149)
  hydrogen bonds       : angle       4.37424 (  435)
  covalent geometry    : bond        0.00314 ( 3349)
  covalent geometry    : angle       0.64841 ( 4544)

*********************** 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
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: A  497 HIS cc_start: 0.8376 (m90) cc_final: 0.8103 (t70)
REVERT: A  536 ASN cc_start: 0.8705 (t0) cc_final: 0.8213 (t0)
REVERT: A  556 GLN cc_start: 0.8060 (mt0) cc_final: 0.7798 (tt0)
REVERT: A  565 HIS cc_start: 0.6962 (p-80) cc_final: 0.6247 (p90)
REVERT: A  651 LYS cc_start: 0.8673 (mttt) cc_final: 0.8145 (ptpp)
REVERT: A  668 ASP cc_start: 0.7851 (t0) cc_final: 0.7425 (t0)
REVERT: A  712 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7647 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1368
  time to fit residues: 14.5683
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  : 0.342 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 39 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.124135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.099159 restraints weight = 6491.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.102356 restraints weight = 4156.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.104747 restraints weight = 3034.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3349  Z= 0.167
  Angle     :  0.657   8.802   4544  Z= 0.330
  Chirality :  0.045   0.197    531
  Planarity :  0.004   0.044    588
  Dihedral  :  8.168  53.448    526
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  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: -1.01 (0.41), residues: 428
  helix:  0.70 (0.37), residues: 195
  sheet: -2.12 (0.56), residues: 71
  loop : -1.60 (0.49), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 565 
 PHE   0.009   0.001   PHE A 719 
 TYR   0.006   0.001   TYR A 654 
 ARG   0.003   0.000   ARG A 411 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03447 (  149)
  hydrogen bonds       : angle       4.38045 (  435)
  covalent geometry    : bond        0.00377 ( 3349)
  covalent geometry    : angle       0.65701 ( 4544)

*********************** 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
  81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7380 (tm-30)
REVERT: A  497 HIS cc_start: 0.8366 (m90) cc_final: 0.8121 (m90)
REVERT: A  536 ASN cc_start: 0.8711 (t0) cc_final: 0.8238 (t0)
REVERT: A  556 GLN cc_start: 0.8075 (mt0) cc_final: 0.7755 (tt0)
REVERT: A  651 LYS cc_start: 0.8734 (mttt) cc_final: 0.8173 (ptpp)
REVERT: A  668 ASP cc_start: 0.7748 (t0) cc_final: 0.7361 (t0)
REVERT: A  712 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7934 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1341
  time to fit residues: 13.6096
Evaluate side-chains
  57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.126026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.100238 restraints weight = 6508.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103777 restraints weight = 4052.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.106284 restraints weight = 2904.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3349  Z= 0.133
  Angle     :  0.641   9.071   4544  Z= 0.318
  Chirality :  0.044   0.161    531
  Planarity :  0.004   0.046    588
  Dihedral  :  8.039  53.880    526
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.63
  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: -0.89 (0.41), residues: 428
  helix:  0.78 (0.38), residues: 197
  sheet: -1.83 (0.59), residues: 62
  loop : -1.71 (0.48), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 768 
 HIS   0.004   0.001   HIS A 565 
 PHE   0.009   0.001   PHE A 466 
 TYR   0.005   0.001   TYR A 631 
 ARG   0.002   0.000   ARG A 411 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  149)
  hydrogen bonds       : angle       4.32999 (  435)
  covalent geometry    : bond        0.00300 ( 3349)
  covalent geometry    : angle       0.64059 ( 4544)

*********************** 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
  84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8218 (tt0)
REVERT: A  497 HIS cc_start: 0.8424 (m90) cc_final: 0.8161 (t70)
REVERT: A  536 ASN cc_start: 0.8729 (t0) cc_final: 0.8246 (t0)
REVERT: A  556 GLN cc_start: 0.8129 (mt0) cc_final: 0.7865 (tt0)
REVERT: A  651 LYS cc_start: 0.8746 (mttt) cc_final: 0.8216 (ptpp)
REVERT: A  668 ASP cc_start: 0.7796 (t0) cc_final: 0.7398 (t0)
REVERT: A  712 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7878 (tpp80)
REVERT: A  724 GLU cc_start: 0.9098 (pp20) cc_final: 0.8576 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1601
  time to fit residues: 16.4349
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  : 0.396 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.127641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.102473 restraints weight = 6324.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.105980 restraints weight = 4011.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108518 restraints weight = 2894.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3349  Z= 0.123
  Angle     :  0.647   9.490   4544  Z= 0.321
  Chirality :  0.043   0.148    531
  Planarity :  0.004   0.048    588
  Dihedral  :  7.903  53.898    526
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  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: -0.70 (0.41), residues: 428
  helix:  0.91 (0.38), residues: 198
  sheet: -1.62 (0.59), residues: 62
  loop : -1.64 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 768 
 HIS   0.004   0.001   HIS A 565 
 PHE   0.016   0.001   PHE A 387 
 TYR   0.006   0.001   TYR A 654 
 ARG   0.002   0.000   ARG A 766 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03334 (  149)
  hydrogen bonds       : angle       4.28994 (  435)
  covalent geometry    : bond        0.00277 ( 3349)
  covalent geometry    : angle       0.64670 ( 4544)

********************** 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
  86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 HIS cc_start: 0.8446 (m90) cc_final: 0.8192 (t70)
REVERT: A  536 ASN cc_start: 0.8684 (t0) cc_final: 0.8194 (t0)
REVERT: A  556 GLN cc_start: 0.8099 (mt0) cc_final: 0.7887 (tt0)
REVERT: A  651 LYS cc_start: 0.8696 (mttt) cc_final: 0.8076 (ptpp)
REVERT: A  668 ASP cc_start: 0.7763 (t0) cc_final: 0.7383 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1590
  time to fit residues: 16.9243
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  : 0.388 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   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 = 0.3688 r_free = 0.3688 target = 0.127260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.102967 restraints weight = 6335.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.106214 restraints weight = 4084.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.108582 restraints weight = 2992.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3349  Z= 0.125
  Angle     :  0.662   9.399   4544  Z= 0.328
  Chirality :  0.044   0.152    531
  Planarity :  0.004   0.048    588
  Dihedral  :  7.879  53.742    526
  Min Nonbonded Distance : 2.351

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: -0.62 (0.41), residues: 428
  helix:  0.90 (0.37), residues: 198
  sheet: -1.37 (0.60), residues: 62
  loop : -1.60 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 768 
 HIS   0.005   0.001   HIS A 565 
 PHE   0.009   0.001   PHE A 466 
 TYR   0.004   0.001   TYR A 654 
 ARG   0.003   0.000   ARG A 712 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  149)
  hydrogen bonds       : angle       4.25388 (  435)
  covalent geometry    : bond        0.00286 ( 3349)
  covalent geometry    : angle       0.66210 ( 4544)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1505.98 seconds
wall clock time: 26 minutes 35.35 seconds (1595.35 seconds total)