Starting phenix.real_space_refine
on Fri Aug 22 17:20:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e29_27829/08_2025/8e29_27829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e29_27829/08_2025/8e29_27829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2025/8e29_27829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2025/8e29_27829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2025/8e29_27829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2025/8e29_27829.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      33      5.49       5
     S      31      5.16       5
     C    3821      2.51       5
     N    1053      2.21       5
     O    1259      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6197
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 692, 5511
          Classifications: {'peptide': 692}
          Link IDs: {'PTRANS': 41, 'TRANS': 650}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 686
          Classifications: {'RNA': 33}
          Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 5, 'rna3p': 27}
  Time building chain proxies: 1.63, per 1000 atoms: 0.26
  Number of scatterers: 6197
  At special positions: 0
  Unit cell: (77.05, 87.1, 105.19, 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      31     16.00
     P      33     15.00
     O    1259      8.00
     N    1053      7.00
     C    3821      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: 0.69
  Conformation dependent library (CDL) restraints added in 338.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1322

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 9 sheets defined
      30.8% alpha, 23.6% beta
      8 base pairs and 17 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 66
    Processing helix  chain 'A' and resid 329 through 341
    Processing helix  chain 'A' and resid 348 through 353
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 3.734A  pdb=" N   PHE A 368 " --> pdb=" O   PRO A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 430
      removed outlier: 3.538A  pdb=" N   ARG A 430 " --> pdb=" O   VAL A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'A' and resid 495 through 502
    Processing helix  chain 'A' and resid 509 through 513
      removed outlier: 3.645A  pdb=" N   GLU A 512 " --> pdb=" O   PRO A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 547
      removed outlier: 3.795A  pdb=" N   VAL A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLN A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 601
      removed outlier: 3.759A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLU A 583 " --> pdb=" O   ASN A 579 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 627
      removed outlier: 3.709A  pdb=" N   ASP A 620 " --> pdb=" O   ARG A 616 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLN A 627 " --> pdb=" O   GLU A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 649
      removed outlier: 4.166A  pdb=" N   PHE A 648 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLY A 649 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 666
    Processing helix  chain 'A' and resid 706 through 719
    Processing helix  chain 'A' and resid 728 through 765
      removed outlier: 3.586A  pdb=" N   LEU A 732 " --> pdb=" O   ALA A 728 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLN A 733 " --> pdb=" O   PRO A 729 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72
      removed outlier: 7.096A  pdb=" N   LEU A 110 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LYS A 114 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   VAL A 235 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ASP A  97 " --> pdb=" O   ALA A 233 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   VAL A 235 " --> pdb=" O   ASP A  97 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 252
      removed outlier: 6.791A  pdb=" N   LEU A 319 " --> pdb=" O   PRO A 281 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LEU A 316 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ILE A 302 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   SER A 322 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   LEU A 300 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 373
      removed outlier: 3.822A  pdb=" N   ASP A 478 " --> pdb=" O   THR A 469 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382
      removed outlier: 6.365A  pdb=" N   THR A 381 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 435
    Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 560
      removed outlier: 6.459A  pdb=" N   ALA A 557 " --> pdb=" O   CYS A 570 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   CYS A 570 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   THR A 559 " --> pdb=" O   GLN A 568 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 609
    Processing sheet with id=AA8, first strand: chain 'A' and resid 792 through 796
      removed outlier: 7.095A  pdb=" N   ALA A 781 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   ILE A 777 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ASP A 783 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 802 through 810

    235 hydrogen bonds defined for protein.
    669 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      23 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      17 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1300
        1.33 -     1.45: 1510
        1.45 -     1.57: 3468
        1.57 -     1.69: 65
        1.69 -     1.81: 47
  Bond restraints: 6390
  Sorted by residual:
  bond pdb=" CG  LEU A 691 "
       pdb=" CD1 LEU A 691 "
    ideal  model  delta    sigma   weight residual
    1.521  1.428  0.093 3.30e-02 9.18e+02 7.91e+00
  bond pdb=" CG  LEU A 691 "
       pdb=" CD2 LEU A 691 "
    ideal  model  delta    sigma   weight residual
    1.521  1.429  0.092 3.30e-02 9.18e+02 7.77e+00
  bond pdb=" CB  TRP A 468 "
       pdb=" CG  TRP A 468 "
    ideal  model  delta    sigma   weight residual
    1.498  1.424  0.074 3.10e-02 1.04e+03 5.69e+00
  bond pdb=" CA  SER A 465 "
       pdb=" CB  SER A 465 "
    ideal  model  delta    sigma   weight residual
    1.536  1.476  0.060 2.53e-02 1.56e+03 5.60e+00
  bond pdb=" CG  LEU A 455 "
       pdb=" CD2 LEU A 455 "
    ideal  model  delta    sigma   weight residual
    1.521  1.449  0.072 3.30e-02 9.18e+02 4.71e+00
  ... (remaining 6385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 8116
        1.87 -     3.75: 546
        3.75 -     5.62: 105
        5.62 -     7.50: 21
        7.50 -     9.37: 10
  Bond angle restraints: 8798
  Sorted by residual:
  angle pdb=" N   ARG A 104 "
        pdb=" CA  ARG A 104 "
        pdb=" CB  ARG A 104 "
      ideal   model   delta    sigma   weight residual
     111.84  106.31    5.53 1.49e+00 4.50e-01 1.38e+01
  angle pdb=" N   HIS A 688 "
        pdb=" CA  HIS A 688 "
        pdb=" C   HIS A 688 "
      ideal   model   delta    sigma   weight residual
     109.46  103.34    6.12 1.66e+00 3.63e-01 1.36e+01
  angle pdb=" CA  GLU A 512 "
        pdb=" CB  GLU A 512 "
        pdb=" CG  GLU A 512 "
      ideal   model   delta    sigma   weight residual
     114.10  121.40   -7.30 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" C   CYS A 449 "
        pdb=" N   GLU A 450 "
        pdb=" CA  GLU A 450 "
      ideal   model   delta    sigma   weight residual
     122.60  117.02    5.58 1.56e+00 4.11e-01 1.28e+01
  angle pdb=" N   SER A 701 "
        pdb=" CA  SER A 701 "
        pdb=" C   SER A 701 "
      ideal   model   delta    sigma   weight residual
     109.81  117.59   -7.78 2.21e+00 2.05e-01 1.24e+01
  ... (remaining 8793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.48: 3567
       21.48 -    42.96: 310
       42.96 -    64.43: 100
       64.43 -    85.91: 18
       85.91 -   107.39: 2
  Dihedral angle restraints: 3997
    sinusoidal: 1967
      harmonic: 2030
  Sorted by residual:
  dihedral pdb=" O4'   U B  30 "
           pdb=" C1'   U B  30 "
           pdb=" N1    U B  30 "
           pdb=" C2    U B  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -105.96  -54.04     1      1.50e+01 4.44e-03 1.76e+01
  dihedral pdb=" CA  ARG A 277 "
           pdb=" C   ARG A 277 "
           pdb=" N   ILE A 278 "
           pdb=" CA  ILE A 278 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.56  -20.44     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  MET A 617 "
           pdb=" C   MET A 617 "
           pdb=" N   LEU A 618 "
           pdb=" CA  LEU A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.52   19.48     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 3994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 672
       0.060 -    0.119: 248
       0.119 -    0.179: 86
       0.179 -    0.238: 11
       0.238 -    0.298: 3
  Chirality restraints: 1020
  Sorted by residual:
  chirality pdb=" CB  VAL A 113 "
            pdb=" CA  VAL A 113 "
            pdb=" CG1 VAL A 113 "
            pdb=" CG2 VAL A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CG  LEU A 560 "
            pdb=" CB  LEU A 560 "
            pdb=" CD1 LEU A 560 "
            pdb=" CD2 LEU A 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ILE A  75 "
            pdb=" N   ILE A  75 "
            pdb=" C   ILE A  75 "
            pdb=" CB  ILE A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1017 not shown)

  Planarity restraints: 1019
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 708 "    0.025 2.00e-02 2.50e+03   5.08e-02 2.58e+01
        pdb=" CG  ASP A 708 "   -0.088 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 708 "    0.030 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 708 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 743 "    0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   ARG A 743 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   ARG A 743 "    0.022 2.00e-02 2.50e+03
        pdb=" N   MET A 744 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 583 "   -0.017 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        pdb=" C   GLU A 583 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLU A 583 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A 584 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1016 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1796
        2.82 -     3.34: 4911
        3.34 -     3.86: 9644
        3.86 -     4.38: 10585
        4.38 -     4.90: 19143
  Nonbonded interactions: 46079
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 575 "
            pdb=" OE1 GLU A 583 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   THR A 835 "
            pdb=" OG  SER A 838 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OH  TYR A 653 "
            pdb=" O   PHE A 837 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   THR A 386 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" NH1 ARG A 388 "
            pdb=" OE2 GLU A 450 "
     model   vdw
     2.372 3.120
  ... (remaining 46074 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.880
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.720
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
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   0.101   6390  Z= 0.501
  Angle     :  1.137   9.374   8798  Z= 0.630
  Chirality :  0.069   0.298   1020
  Planarity :  0.008   0.058   1019
  Dihedral  : 17.732 107.388   2675
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.90 %
    Favored  : 92.45 %
  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: -1.55 (0.29), residues: 686
  helix: -1.02 (0.32), residues: 205
  sheet:  0.18 (0.41), residues: 155
  loop : -1.61 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 104 
 TYR   0.028   0.005   TYR A 853 
 PHE   0.049   0.004   PHE A 699 
 TRP   0.024   0.005   TRP A 468 
 HIS   0.017   0.002   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.01231 ( 6390)
  covalent geometry    : angle       1.13719 ( 8798)
  hydrogen bonds       : bond        0.16817 (  258)
  hydrogen bonds       : angle       6.09197 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  424 ASP cc_start: 0.8112 (t70) cc_final: 0.7877 (t0)
REVERT: A  726 ASP cc_start: 0.7801 (p0) cc_final: 0.7515 (t0)
REVERT: A  851 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7078 (mp)
  outliers start: 4
  outliers final: 2
  residues processed: 73
  average time/residue: 0.0924
  time to fit residues: 8.7898
Evaluate side-chains
  57 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  775 MET
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0030
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0670
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5328

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.182998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.131678 restraints weight = 6524.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.68
r_work: 0.3429 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6390  Z= 0.113
  Angle     :  0.571   7.931   8798  Z= 0.292
  Chirality :  0.040   0.136   1020
  Planarity :  0.005   0.040   1019
  Dihedral  : 17.440 108.387   1295
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.66 %
    Favored  : 87.52 %
  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: -0.48 (0.31), residues: 686
  helix:  0.71 (0.37), residues: 214
  sheet:  0.34 (0.40), residues: 168
  loop : -1.46 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 803 
 TYR   0.011   0.001   TYR A 653 
 PHE   0.014   0.001   PHE A 699 
 TRP   0.016   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6390)
  covalent geometry    : angle       0.57088 ( 8798)
  hydrogen bonds       : bond        0.05127 (  258)
  hydrogen bonds       : angle       4.54939 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   58 ASP cc_start: 0.8014 (t70) cc_final: 0.7751 (t0)
REVERT: A   63 LEU cc_start: 0.6319 (tp) cc_final: 0.6043 (tp)
REVERT: A   82 GLU cc_start: 0.7377 (pt0) cc_final: 0.6571 (mt-10)
REVERT: A  726 ASP cc_start: 0.8241 (p0) cc_final: 0.7832 (t0)
REVERT: A  803 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7478 (ttp-110)
REVERT: A  851 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6878 (mp)
  outliers start: 5
  outliers final: 1
  residues processed: 67
  average time/residue: 0.0748
  time to fit residues: 6.9620
Evaluate side-chains
  61 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 70 optimal weight:   30.0000
   chunk 54 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.176094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.120403 restraints weight = 6398.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.98
r_work: 0.3323 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6390  Z= 0.127
  Angle     :  0.536   7.152   8798  Z= 0.273
  Chirality :  0.039   0.142   1020
  Planarity :  0.004   0.038   1019
  Dihedral  : 17.293 108.574   1290
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 13.46 %
    Favored  : 85.39 %
  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: -0.15 (0.32), residues: 686
  helix:  1.16 (0.37), residues: 213
  sheet:  0.48 (0.40), residues: 172
  loop : -1.39 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 277 
 TYR   0.011   0.001   TYR A 674 
 PHE   0.014   0.001   PHE A 699 
 TRP   0.014   0.001   TRP A 468 
 HIS   0.005   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6390)
  covalent geometry    : angle       0.53607 ( 8798)
  hydrogen bonds       : bond        0.05037 (  258)
  hydrogen bonds       : angle       4.32989 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   63 LEU cc_start: 0.6039 (tp) cc_final: 0.5812 (tp)
REVERT: A  726 ASP cc_start: 0.8344 (p0) cc_final: 0.7922 (t0)
REVERT: A  803 ARG cc_start: 0.7629 (ttp80) cc_final: 0.7349 (ttp-110)
REVERT: A  851 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6664 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 68
  average time/residue: 0.0811
  time to fit residues: 7.3598
Evaluate side-chains
  61 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.176179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.120172 restraints weight = 6471.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.99
r_work: 0.3314 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6390  Z= 0.115
  Angle     :  0.509   6.696   8798  Z= 0.259
  Chirality :  0.039   0.140   1020
  Planarity :  0.004   0.036   1019
  Dihedral  : 17.208 106.595   1290
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.11 %
    Favored  : 83.25 %
  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:  0.08 (0.32), residues: 686
  helix:  1.47 (0.38), residues: 210
  sheet:  0.58 (0.40), residues: 172
  loop : -1.31 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 277 
 TYR   0.010   0.001   TYR A 674 
 PHE   0.011   0.001   PHE A 699 
 TRP   0.014   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6390)
  covalent geometry    : angle       0.50928 ( 8798)
  hydrogen bonds       : bond        0.04592 (  258)
  hydrogen bonds       : angle       4.17276 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   58 ASP cc_start: 0.7997 (t70) cc_final: 0.7735 (t0)
REVERT: A  726 ASP cc_start: 0.8314 (p0) cc_final: 0.7909 (t0)
REVERT: A  803 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7108 (ttp-110)
REVERT: A  851 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6547 (mp)
  outliers start: 10
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0697
  time to fit residues: 6.3865
Evaluate side-chains
  63 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 56 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.171008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.114937 restraints weight = 6579.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.00
r_work: 0.3246 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6390  Z= 0.212
  Angle     :  0.591   6.989   8798  Z= 0.301
  Chirality :  0.041   0.152   1020
  Planarity :  0.005   0.040   1019
  Dihedral  : 17.270 104.853   1290
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.76 %
    Favored  : 82.10 %
  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: -0.15 (0.32), residues: 686
  helix:  1.15 (0.37), residues: 213
  sheet:  0.56 (0.40), residues: 172
  loop : -1.44 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.013   0.002   TYR A 340 
 PHE   0.016   0.002   PHE A 782 
 TRP   0.014   0.002   TRP A 468 
 HIS   0.008   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 6390)
  covalent geometry    : angle       0.59142 ( 8798)
  hydrogen bonds       : bond        0.06039 (  258)
  hydrogen bonds       : angle       4.40429 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   58 ASP cc_start: 0.8010 (t70) cc_final: 0.7764 (t0)
REVERT: A  726 ASP cc_start: 0.8279 (p0) cc_final: 0.7868 (t0)
REVERT: A  803 ARG cc_start: 0.7535 (ttp80) cc_final: 0.7238 (ttp-110)
REVERT: A  851 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6722 (mp)
  outliers start: 13
  outliers final: 8
  residues processed: 69
  average time/residue: 0.0708
  time to fit residues: 6.7149
Evaluate side-chains
  65 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0670
   chunk 66 optimal weight:    0.0370
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.177288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.121607 restraints weight = 6438.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.98
r_work: 0.3329 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6390  Z= 0.091
  Angle     :  0.478   6.289   8798  Z= 0.245
  Chirality :  0.037   0.138   1020
  Planarity :  0.004   0.034   1019
  Dihedral  : 17.102 102.819   1290
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.08 %
    Favored  : 81.12 %
  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:  0.27 (0.33), residues: 686
  helix:  1.71 (0.38), residues: 209
  sheet:  0.71 (0.41), residues: 170
  loop : -1.26 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 277 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.008   0.001   PHE A 757 
 TRP   0.016   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 6390)
  covalent geometry    : angle       0.47802 ( 8798)
  hydrogen bonds       : bond        0.04036 (  258)
  hydrogen bonds       : angle       4.08039 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   58 ASP cc_start: 0.8012 (t70) cc_final: 0.7767 (t0)
REVERT: A  319 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7938 (mp)
REVERT: A  657 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6789 (mtt90)
REVERT: A  726 ASP cc_start: 0.8273 (p0) cc_final: 0.7869 (t0)
REVERT: A  803 ARG cc_start: 0.7282 (ttp80) cc_final: 0.6978 (ttp-110)
REVERT: A  851 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6459 (mp)
  outliers start: 11
  outliers final: 5
  residues processed: 67
  average time/residue: 0.0691
  time to fit residues: 6.3645
Evaluate side-chains
  66 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0570
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.1904

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.174509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.118520 restraints weight = 6470.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 3.00
r_work: 0.3288 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6390  Z= 0.130
  Angle     :  0.516   6.065   8798  Z= 0.262
  Chirality :  0.039   0.146   1020
  Planarity :  0.004   0.036   1019
  Dihedral  : 16.993 100.930   1290
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.41 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.33), residues: 686
  helix:  1.59 (0.38), residues: 214
  sheet:  0.74 (0.41), residues: 170
  loop : -1.27 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.010   0.001   TYR A 674 
 PHE   0.012   0.001   PHE A 481 
 TRP   0.012   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6390)
  covalent geometry    : angle       0.51636 ( 8798)
  hydrogen bonds       : bond        0.04758 (  258)
  hydrogen bonds       : angle       4.12128 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A   58 ASP cc_start: 0.8025 (t70) cc_final: 0.7813 (t0)
REVERT: A  657 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6365 (mmt90)
REVERT: A  726 ASP cc_start: 0.8259 (p0) cc_final: 0.7836 (t0)
REVERT: A  803 ARG cc_start: 0.7305 (ttp80) cc_final: 0.7093 (ttp-110)
REVERT: A  851 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6465 (mp)
  outliers start: 12
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0841
  time to fit residues: 7.4794
Evaluate side-chains
  68 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.0870
   chunk 36 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.4980
   chunk 53 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.175489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.119050 restraints weight = 6538.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 3.08
r_work: 0.3297 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6390  Z= 0.094
  Angle     :  0.483   6.357   8798  Z= 0.244
  Chirality :  0.038   0.140   1020
  Planarity :  0.004   0.035   1019
  Dihedral  : 16.809  98.393   1290
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.57 %
    Favored  : 80.46 %
  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:  0.42 (0.34), residues: 686
  helix:  1.89 (0.38), residues: 209
  sheet:  0.82 (0.42), residues: 170
  loop : -1.22 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 277 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.008   0.001   PHE A 481 
 TRP   0.014   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 6390)
  covalent geometry    : angle       0.48308 ( 8798)
  hydrogen bonds       : bond        0.03894 (  258)
  hydrogen bonds       : angle       4.00324 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  657 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6317 (mmt90)
REVERT: A  726 ASP cc_start: 0.8253 (p0) cc_final: 0.7817 (t0)
REVERT: A  803 ARG cc_start: 0.7265 (ttp80) cc_final: 0.7048 (ttp-110)
  outliers start: 12
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0800
  time to fit residues: 7.7728
Evaluate side-chains
  64 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0770
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.177457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.119880 restraints weight = 6643.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 3.15
r_work: 0.3291 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6390  Z= 0.103
  Angle     :  0.499   6.901   8798  Z= 0.253
  Chirality :  0.038   0.144   1020
  Planarity :  0.004   0.034   1019
  Dihedral  : 16.691  96.284   1288
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.39 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.34), residues: 686
  helix:  1.86 (0.38), residues: 210
  sheet:  0.90 (0.42), residues: 170
  loop : -1.18 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 277 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.009   0.001   PHE A 481 
 TRP   0.012   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6390)
  covalent geometry    : angle       0.49878 ( 8798)
  hydrogen bonds       : bond        0.04005 (  258)
  hydrogen bonds       : angle       3.95842 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  657 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6336 (mmt90)
REVERT: A  726 ASP cc_start: 0.8259 (p0) cc_final: 0.7811 (t0)
REVERT: A  803 ARG cc_start: 0.7255 (ttp80) cc_final: 0.7031 (ttp-110)
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0703
  time to fit residues: 6.2296
Evaluate side-chains
  65 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.178658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.120984 restraints weight = 6589.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 3.14
r_work: 0.3308 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6390  Z= 0.098
  Angle     :  0.495   7.353   8798  Z= 0.250
  Chirality :  0.037   0.142   1020
  Planarity :  0.004   0.035   1019
  Dihedral  : 16.557  94.399   1288
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.06 %
    Favored  : 80.30 %
  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:  0.54 (0.34), residues: 686
  helix:  1.94 (0.38), residues: 210
  sheet:  0.94 (0.42), residues: 170
  loop : -1.15 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 277 
 TYR   0.008   0.001   TYR A 674 
 PHE   0.009   0.001   PHE A 481 
 TRP   0.013   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 6390)
  covalent geometry    : angle       0.49537 ( 8798)
  hydrogen bonds       : bond        0.03815 (  258)
  hydrogen bonds       : angle       3.90592 (  715)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  657 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6284 (mmt90)
REVERT: A  726 ASP cc_start: 0.8249 (p0) cc_final: 0.7775 (t0)
REVERT: A  803 ARG cc_start: 0.7242 (ttp80) cc_final: 0.7022 (ttp-110)
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0611
  time to fit residues: 5.3170
Evaluate side-chains
  64 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0030
   chunk 13 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0030
   overall best weight:    0.5202

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.179326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.121626 restraints weight = 6593.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 3.15
r_work: 0.3331 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6390  Z= 0.093
  Angle     :  0.484   7.220   8798  Z= 0.245
  Chirality :  0.037   0.141   1020
  Planarity :  0.004   0.033   1019
  Dihedral  : 16.475  95.846   1288
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.56 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.33), residues: 686
  helix:  1.98 (0.38), residues: 210
  sheet:  0.96 (0.41), residues: 170
  loop : -1.11 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 277 
 TYR   0.007   0.001   TYR A 674 
 PHE   0.008   0.001   PHE A 481 
 TRP   0.013   0.001   TRP A 468 
 HIS   0.002   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6390)
  covalent geometry    : angle       0.48436 ( 8798)
  hydrogen bonds       : bond        0.03642 (  258)
  hydrogen bonds       : angle       3.84930 (  715)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1532.73 seconds
wall clock time: 26 minutes 52.55 seconds (1612.55 seconds total)