Starting phenix.real_space_refine
on Wed Sep 17 03:56:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxg_32878/09_2025/7wxg_32878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxg_32878/09_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_32878/09_2025/7wxg_32878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxg_32878/09_2025/7wxg_32878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxg_32878/09_2025/7wxg_32878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxg_32878/09_2025/7wxg_32878.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.00, per 1000 atoms: 0.30
  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: 0.26
  Conformation dependent library (CDL) restraints added in 106.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.12
  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: 0.44

  Time building geometry restraints manager: 0.35 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:             1.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.990
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.310
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG A 370 
 TYR   0.010   0.002   TYR A 573 
 PHE   0.021   0.002   PHE A 642 
 TRP   0.014   0.003   TRP A 768 
 HIS   0.003   0.001   HIS A 681 

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

*********************** 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  : 0.128 
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: 0.0806
  time to fit residues: 8.0566
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0670
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.9922

-------------------------------------------------------------------------------
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 = 0.3595 r_free = 0.3595 target = 0.120507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096348 restraints weight = 6606.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.099607 restraints weight = 4191.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.101947 restraints weight = 3025.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.103628 restraints weight = 2394.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.104751 restraints weight = 2009.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1964

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= 0.132
  Angle     :  0.648   6.521   4544  Z= 0.326
  Chirality :  0.045   0.159    531
  Planarity :  0.005   0.043    588
  Dihedral  :  9.626  47.176    526
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.22 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.11 (0.36), residues: 428
  helix: -0.75 (0.35), residues: 191
  sheet: -3.47 (0.49), residues: 60
  loop : -2.98 (0.41), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 411 
 TYR   0.006   0.001   TYR A 631 
 PHE   0.013   0.001   PHE A 642 
 TRP   0.010   0.002   TRP A 748 
 HIS   0.004   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3349)
  covalent geometry    : angle       0.64781 ( 4544)
  hydrogen bonds       : bond        0.03613 (  149)
  hydrogen bonds       : angle       4.96312 (  435)

*********************** 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
  89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 MET cc_start: 0.8937 (mtp) cc_final: 0.8695 (mtt)
REVERT: A  428 GLN cc_start: 0.8685 (mt0) cc_final: 0.8348 (tm-30)
REVERT: A  481 MET cc_start: 0.7767 (ttm) cc_final: 0.7554 (ptm)
REVERT: A  489 LEU cc_start: 0.9247 (mm) cc_final: 0.8994 (mm)
REVERT: A  497 HIS cc_start: 0.8280 (m90) cc_final: 0.8036 (t70)
REVERT: A  536 ASN cc_start: 0.8690 (t0) cc_final: 0.8244 (t0)
REVERT: A  556 GLN cc_start: 0.8007 (mt0) cc_final: 0.7690 (tt0)
REVERT: A  573 TYR cc_start: 0.8771 (t80) cc_final: 0.8556 (t80)
REVERT: A  601 MET cc_start: 0.7875 (tmm) cc_final: 0.7655 (tmm)
REVERT: A  602 GLU cc_start: 0.8859 (pt0) cc_final: 0.8085 (mt-10)
REVERT: A  651 LYS cc_start: 0.8924 (mttt) cc_final: 0.8164 (tptt)
REVERT: A  652 HIS cc_start: 0.7622 (t-90) cc_final: 0.7334 (t-90)
REVERT: A  668 ASP cc_start: 0.7784 (t0) cc_final: 0.7489 (t0)
REVERT: A  712 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7661 (ttp80)
  outliers start: 2
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0746
  time to fit residues: 7.9176
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  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 16 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0670
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0070
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
A 689 ASN
A 770 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.123389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.100116 restraints weight = 6276.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.103511 restraints weight = 3932.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.105986 restraints weight = 2803.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.107590 restraints weight = 2181.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.108890 restraints weight = 1825.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3349  Z= 0.099
  Angle     :  0.591   6.822   4544  Z= 0.294
  Chirality :  0.044   0.150    531
  Planarity :  0.004   0.046    588
  Dihedral  :  8.327  47.594    526
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.40), residues: 428
  helix:  0.15 (0.37), residues: 196
  sheet: -2.81 (0.53), residues: 63
  loop : -2.15 (0.47), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 694 
 TYR   0.007   0.001   TYR A 631 
 PHE   0.009   0.001   PHE A 642 
 TRP   0.008   0.002   TRP A 748 
 HIS   0.004   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 3349)
  covalent geometry    : angle       0.59086 ( 4544)
  hydrogen bonds       : bond        0.03069 (  149)
  hydrogen bonds       : angle       4.50833 (  435)

*********************** 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
  98 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8634 (m-40) cc_final: 0.8307 (m-40)
REVERT: A  392 ASN cc_start: 0.7328 (OUTLIER) cc_final: 0.6647 (t0)
REVERT: A  497 HIS cc_start: 0.8227 (m90) cc_final: 0.7982 (t70)
REVERT: A  536 ASN cc_start: 0.8423 (t0) cc_final: 0.8075 (t0)
REVERT: A  556 GLN cc_start: 0.8020 (mt0) cc_final: 0.7791 (tt0)
REVERT: A  651 LYS cc_start: 0.8738 (mttt) cc_final: 0.8183 (ptpp)
REVERT: A  668 ASP cc_start: 0.7906 (t0) cc_final: 0.7472 (t0)
REVERT: A  712 ARG cc_start: 0.7957 (tpp80) cc_final: 0.7665 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0661
  time to fit residues: 7.9197
Evaluate side-chains
  65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 695 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.123762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099096 restraints weight = 6314.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.102539 restraints weight = 4009.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.105025 restraints weight = 2901.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.106785 restraints weight = 2282.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.108001 restraints weight = 1915.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3349  Z= 0.112
  Angle     :  0.599   8.341   4544  Z= 0.297
  Chirality :  0.044   0.155    531
  Planarity :  0.004   0.046    588
  Dihedral  :  7.878  48.602    526
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.41), residues: 428
  helix:  0.60 (0.37), residues: 197
  sheet: -2.49 (0.55), residues: 63
  loop : -1.88 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 411 
 TYR   0.010   0.001   TYR A 573 
 PHE   0.009   0.001   PHE A 616 
 TRP   0.006   0.001   TRP A 768 
 HIS   0.003   0.000   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3349)
  covalent geometry    : angle       0.59882 ( 4544)
  hydrogen bonds       : bond        0.03106 (  149)
  hydrogen bonds       : angle       4.47052 (  435)

*********************** 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
  92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7260 (tm-30)
REVERT: A  481 MET cc_start: 0.7379 (ttp) cc_final: 0.7168 (ptm)
REVERT: A  497 HIS cc_start: 0.8291 (m90) cc_final: 0.8034 (t70)
REVERT: A  536 ASN cc_start: 0.8417 (t0) cc_final: 0.7899 (t0)
REVERT: A  565 HIS cc_start: 0.6947 (p-80) cc_final: 0.6373 (p-80)
REVERT: A  651 LYS cc_start: 0.8770 (mttt) cc_final: 0.8204 (ptpp)
REVERT: A  652 HIS cc_start: 0.7626 (t-90) cc_final: 0.7378 (t-90)
REVERT: A  668 ASP cc_start: 0.7837 (t0) cc_final: 0.7404 (t0)
REVERT: A  669 GLU cc_start: 0.7514 (tp30) cc_final: 0.7301 (tp30)
REVERT: A  712 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7619 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0614
  time to fit residues: 6.9075
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  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 556 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.100215 restraints weight = 6271.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103679 restraints weight = 4013.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.106203 restraints weight = 2905.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.108020 restraints weight = 2286.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.109219 restraints weight = 1916.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3349  Z= 0.112
  Angle     :  0.628   8.323   4544  Z= 0.305
  Chirality :  0.044   0.167    531
  Planarity :  0.004   0.043    588
  Dihedral  :  7.777  49.377    526
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.41), residues: 428
  helix:  0.87 (0.38), residues: 197
  sheet: -2.25 (0.55), residues: 71
  loop : -1.73 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 718 
 TYR   0.006   0.001   TYR A 654 
 PHE   0.008   0.001   PHE A 616 
 TRP   0.007   0.001   TRP A 768 
 HIS   0.003   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 3349)
  covalent geometry    : angle       0.62788 ( 4544)
  hydrogen bonds       : bond        0.03259 (  149)
  hydrogen bonds       : angle       4.27885 (  435)

*********************** 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
  90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8681 (m-40) cc_final: 0.8397 (m110)
REVERT: A  419 LEU cc_start: 0.8851 (mm) cc_final: 0.8602 (mm)
REVERT: A  428 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: A  473 LEU cc_start: 0.8292 (tt) cc_final: 0.7981 (tp)
REVERT: A  497 HIS cc_start: 0.8306 (m90) cc_final: 0.8038 (t70)
REVERT: A  536 ASN cc_start: 0.8536 (t0) cc_final: 0.8171 (t0)
REVERT: A  555 GLN cc_start: 0.8865 (mp10) cc_final: 0.8516 (pp30)
REVERT: A  565 HIS cc_start: 0.6850 (p-80) cc_final: 0.6282 (p90)
REVERT: A  651 LYS cc_start: 0.8757 (mttt) cc_final: 0.8172 (ptpp)
REVERT: A  652 HIS cc_start: 0.7655 (t-90) cc_final: 0.7284 (t-90)
REVERT: A  668 ASP cc_start: 0.7837 (t0) cc_final: 0.7410 (t0)
REVERT: A  712 ARG cc_start: 0.7984 (tpp80) cc_final: 0.7637 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0694
  time to fit residues: 7.6107
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  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.123499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.098361 restraints weight = 6493.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.101793 restraints weight = 4169.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.104211 restraints weight = 3038.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.105940 restraints weight = 2414.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.107221 restraints weight = 2032.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3349  Z= 0.186
  Angle     :  0.662   7.616   4544  Z= 0.334
  Chirality :  0.045   0.186    531
  Planarity :  0.004   0.042    588
  Dihedral  :  8.127  51.590    526
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.40), residues: 428
  helix:  0.71 (0.36), residues: 194
  sheet: -2.33 (0.54), residues: 70
  loop : -1.92 (0.48), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 411 
 TYR   0.003   0.001   TYR A 631 
 PHE   0.009   0.001   PHE A 642 
 TRP   0.013   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3349)
  covalent geometry    : angle       0.66179 ( 4544)
  hydrogen bonds       : bond        0.03491 (  149)
  hydrogen bonds       : angle       4.48507 (  435)

*********************** 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
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: A  536 ASN cc_start: 0.8644 (t0) cc_final: 0.8160 (t0)
REVERT: A  555 GLN cc_start: 0.8894 (mp10) cc_final: 0.8658 (pp30)
REVERT: A  602 GLU cc_start: 0.8901 (pt0) cc_final: 0.8525 (tt0)
REVERT: A  651 LYS cc_start: 0.8766 (mttt) cc_final: 0.8157 (ptpp)
REVERT: A  652 HIS cc_start: 0.7456 (t-90) cc_final: 0.7194 (t-90)
REVERT: A  668 ASP cc_start: 0.7749 (t0) cc_final: 0.7361 (t0)
REVERT: A  712 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7562 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0675
  time to fit residues: 6.6918
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  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0060
   chunk 26 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.125782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.100817 restraints weight = 6293.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.104219 restraints weight = 3961.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.106692 restraints weight = 2839.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.108333 restraints weight = 2222.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.109637 restraints weight = 1872.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3349  Z= 0.108
  Angle     :  0.612   8.216   4544  Z= 0.303
  Chirality :  0.043   0.147    531
  Planarity :  0.004   0.042    588
  Dihedral  :  7.721  50.932    526
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.41), residues: 428
  helix:  0.80 (0.38), residues: 196
  sheet: -1.95 (0.56), residues: 69
  loop : -1.71 (0.50), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 411 
 TYR   0.007   0.001   TYR A 631 
 PHE   0.014   0.001   PHE A 387 
 TRP   0.008   0.002   TRP A 748 
 HIS   0.004   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3349)
  covalent geometry    : angle       0.61231 ( 4544)
  hydrogen bonds       : bond        0.03203 (  149)
  hydrogen bonds       : angle       4.41732 (  435)

*********************** 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
  91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  521 LEU cc_start: 0.8500 (mm) cc_final: 0.8242 (mm)
REVERT: A  536 ASN cc_start: 0.8642 (t0) cc_final: 0.8119 (t0)
REVERT: A  553 ILE cc_start: 0.8602 (mm) cc_final: 0.8399 (mm)
REVERT: A  555 GLN cc_start: 0.8910 (mp10) cc_final: 0.8611 (pp30)
REVERT: A  629 LYS cc_start: 0.8226 (pptt) cc_final: 0.7836 (pptt)
REVERT: A  651 LYS cc_start: 0.8735 (mttt) cc_final: 0.8212 (ptpp)
REVERT: A  652 HIS cc_start: 0.7606 (t-90) cc_final: 0.7397 (t70)
REVERT: A  668 ASP cc_start: 0.7831 (t0) cc_final: 0.7439 (t0)
REVERT: A  669 GLU cc_start: 0.7462 (tp30) cc_final: 0.7220 (tp30)
REVERT: A  712 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7706 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0650
  time to fit residues: 7.2556
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  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 41 optimal weight:    0.3980
   chunk 5 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0000
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0570
   chunk 42 optimal weight:    7.9990
   overall best weight:    0.8504

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.127692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.102350 restraints weight = 6642.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.106027 restraints weight = 4109.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.108674 restraints weight = 2922.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.110533 restraints weight = 2278.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111708 restraints weight = 1901.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3960

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= 0.119
  Angle     :  0.616   8.520   4544  Z= 0.305
  Chirality :  0.042   0.143    531
  Planarity :  0.004   0.043    588
  Dihedral  :  7.660  49.515    526
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.41), residues: 428
  helix:  0.95 (0.38), residues: 197
  sheet: -1.94 (0.54), residues: 74
  loop : -1.80 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 411 
 TYR   0.007   0.001   TYR A 654 
 PHE   0.016   0.001   PHE A 387 
 TRP   0.007   0.001   TRP A 768 
 HIS   0.003   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3349)
  covalent geometry    : angle       0.61637 ( 4544)
  hydrogen bonds       : bond        0.03134 (  149)
  hydrogen bonds       : angle       4.28408 (  435)

*********************** 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  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  536 ASN cc_start: 0.8635 (t0) cc_final: 0.8115 (t0)
REVERT: A  553 ILE cc_start: 0.8554 (mm) cc_final: 0.8236 (mm)
REVERT: A  555 GLN cc_start: 0.8882 (mp10) cc_final: 0.8557 (pp30)
REVERT: A  651 LYS cc_start: 0.8756 (mttt) cc_final: 0.8171 (ptpp)
REVERT: A  652 HIS cc_start: 0.7571 (t-90) cc_final: 0.7313 (t-90)
REVERT: A  668 ASP cc_start: 0.7756 (t0) cc_final: 0.7323 (t0)
REVERT: A  669 GLU cc_start: 0.7368 (tp30) cc_final: 0.7148 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0574
  time to fit residues: 6.2560
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  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.126823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.101521 restraints weight = 6566.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.105054 restraints weight = 4098.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.107628 restraints weight = 2932.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.109500 restraints weight = 2300.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.110821 restraints weight = 1914.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3914

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= 0.133
  Angle     :  0.632   8.992   4544  Z= 0.313
  Chirality :  0.043   0.134    531
  Planarity :  0.004   0.042    588
  Dihedral  :  7.748  50.500    526
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.41), residues: 428
  helix:  0.97 (0.38), residues: 197
  sheet: -1.70 (0.57), residues: 69
  loop : -1.79 (0.48), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 718 
 TYR   0.003   0.001   TYR A 654 
 PHE   0.017   0.002   PHE A 387 
 TRP   0.009   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3349)
  covalent geometry    : angle       0.63232 ( 4544)
  hydrogen bonds       : bond        0.03217 (  149)
  hydrogen bonds       : angle       4.34253 (  435)

*********************** 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
  83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  536 ASN cc_start: 0.8662 (t0) cc_final: 0.8137 (t0)
REVERT: A  553 ILE cc_start: 0.8561 (mm) cc_final: 0.8233 (mm)
REVERT: A  555 GLN cc_start: 0.8872 (mp10) cc_final: 0.8510 (pp30)
REVERT: A  602 GLU cc_start: 0.8893 (pt0) cc_final: 0.8521 (tt0)
REVERT: A  651 LYS cc_start: 0.8759 (mttt) cc_final: 0.8194 (ptpp)
REVERT: A  668 ASP cc_start: 0.7742 (t0) cc_final: 0.7337 (t0)
REVERT: A  724 GLU cc_start: 0.9111 (pp20) cc_final: 0.8893 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0611
  time to fit residues: 6.3603
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3652 r_free = 0.3652 target = 0.125212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.100949 restraints weight = 6609.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.104365 restraints weight = 4170.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.106814 restraints weight = 3004.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.108538 restraints weight = 2360.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.109835 restraints weight = 1977.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3349  Z= 0.148
  Angle     :  0.649   9.324   4544  Z= 0.325
  Chirality :  0.044   0.147    531
  Planarity :  0.004   0.043    588
  Dihedral  :  7.874  51.835    526
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.41), residues: 428
  helix:  1.01 (0.38), residues: 198
  sheet: -1.96 (0.54), residues: 74
  loop : -1.76 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 718 
 TYR   0.003   0.001   TYR A 631 
 PHE   0.019   0.002   PHE A 387 
 TRP   0.010   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3349)
  covalent geometry    : angle       0.64935 ( 4544)
  hydrogen bonds       : bond        0.03299 (  149)
  hydrogen bonds       : angle       4.36830 (  435)

********************** 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
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  521 LEU cc_start: 0.8364 (mm) cc_final: 0.8138 (mm)
REVERT: A  536 ASN cc_start: 0.8635 (t0) cc_final: 0.8119 (t0)
REVERT: A  555 GLN cc_start: 0.8888 (mp10) cc_final: 0.8527 (pp30)
REVERT: A  602 GLU cc_start: 0.8893 (pt0) cc_final: 0.8574 (tt0)
REVERT: A  651 LYS cc_start: 0.8799 (mttt) cc_final: 0.8174 (ptpp)
REVERT: A  668 ASP cc_start: 0.7727 (t0) cc_final: 0.7314 (t0)
REVERT: A  724 GLU cc_start: 0.9113 (pp20) cc_final: 0.8894 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0589
  time to fit residues: 5.9810
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  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 39 optimal weight:    0.1980
   chunk 3 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 7 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.128177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.103955 restraints weight = 6543.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.107596 restraints weight = 3997.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.110176 restraints weight = 2813.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111863 restraints weight = 2173.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.113286 restraints weight = 1810.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3349  Z= 0.107
  Angle     :  0.610   9.269   4544  Z= 0.300
  Chirality :  0.042   0.132    531
  Planarity :  0.004   0.045    588
  Dihedral  :  7.725  51.051    526
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.42), residues: 428
  helix:  1.19 (0.39), residues: 198
  sheet: -1.50 (0.58), residues: 69
  loop : -1.63 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 718 
 TYR   0.003   0.001   TYR A 677 
 PHE   0.019   0.002   PHE A 387 
 TRP   0.007   0.002   TRP A 768 
 HIS   0.004   0.001   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 3349)
  covalent geometry    : angle       0.60966 ( 4544)
  hydrogen bonds       : bond        0.02982 (  149)
  hydrogen bonds       : angle       4.22609 (  435)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 763.27 seconds
wall clock time: 13 minutes 50.09 seconds (830.09 seconds total)