Starting phenix.real_space_refine
on Tue Mar  3 14:12:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rxh_24731/03_2026/7rxh_24731_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rxh_24731/03_2026/7rxh_24731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rxh_24731/03_2026/7rxh_24731_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rxh_24731/03_2026/7rxh_24731_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rxh_24731/03_2026/7rxh_24731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rxh_24731/03_2026/7rxh_24731.map"
  }
  resolution = 2.3
  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=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P      15      5.49       5
     S      18      5.16       5
     C    3653      2.51       5
     N     849      2.21       5
     O    1046      1.98       5
     H      48      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5631
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 626, 5062
          Classifications: {'peptide': 626}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 30, 'TRANS': 595}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 90
          Unresolved non-hydrogen dihedrals: 65
          Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 52
    Chain: "A"
      Number of atoms: 569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 569
          Unusual residues: {' CA': 2, 'PGW': 16}
          Classifications: {'undetermined': 18, 'water': 24}
          Link IDs: {None: 41}
          Unresolved non-hydrogen bonds: 321
          Unresolved non-hydrogen angles: 338
          Unresolved non-hydrogen dihedrals: 357
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'PGW:plan-3': 10, 'PGW:plan-2': 1}
          Unresolved non-hydrogen planarities: 37
  Time building chain proxies: 1.37, per 1000 atoms: 0.24
  Number of scatterers: 5631
  At special positions: 0
  Unit cell: (72.7901, 85.5107, 98.938, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      2     19.99
     S      18     16.00
     P      15     15.00
     O    1046      8.00
     N     849      7.00
     C    3653      6.00
     H      48      1.00
    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: 0.39
  Conformation dependent library (CDL) restraints added in 221.0 milliseconds
  

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1200

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 3 sheets defined
      73.3% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 46
    Processing helix  chain 'A' and resid 68 through 86
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 103 through 117
    Processing helix  chain 'A' and resid 118 through 122
    Processing helix  chain 'A' and resid 144 through 156
    Processing helix  chain 'A' and resid 162 through 174
    Processing helix  chain 'A' and resid 174 through 191
    Processing helix  chain 'A' and resid 191 through 205
    Processing helix  chain 'A' and resid 209 through 238
    Processing helix  chain 'A' and resid 242 through 247
    Processing helix  chain 'A' and resid 272 through 281
    Processing helix  chain 'A' and resid 282 through 311
    Processing helix  chain 'A' and resid 317 through 350
      removed outlier: 4.462A  pdb=" N   ILE A 323 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      Proline residue:  A 324  - end of helix
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 354 through 384
      removed outlier: 3.980A  pdb=" N   VAL A 368 " --> pdb=" O   GLN A 364 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      Proline residue:  A 377  - end of helix
    Processing helix  chain 'A' and resid 392 through 398
      removed outlier: 4.124A  pdb=" N   ASP A 397 " --> pdb=" O   PRO A 394 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   VAL A 398 " --> pdb=" O   TYR A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 4.336A  pdb=" N   VAL A 403 " --> pdb=" O   PHE A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 414
    Processing helix  chain 'A' and resid 424 through 435
    Processing helix  chain 'A' and resid 435 through 463
      removed outlier: 4.735A  pdb=" N   VAL A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      Proline residue:  A 449  - end of helix
    Processing helix  chain 'A' and resid 490 through 501
    Processing helix  chain 'A' and resid 507 through 526
      removed outlier: 4.054A  pdb=" N   ASP A 511 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 529
      No H-bonds generated for 'chain 'A' and resid 527 through 529'
    Processing helix  chain 'A' and resid 531 through 554
      removed outlier: 3.787A  pdb=" N   ARG A 545 " --> pdb=" O   TRP A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 591
      removed outlier: 4.419A  pdb=" N   ASP A 571 " --> pdb=" O   GLY A 567 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 582 " --> pdb=" O   TRP A 578 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 634
      removed outlier: 3.528A  pdb=" N   LYS A 634 " --> pdb=" O   SER A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 658
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 54
      removed outlier: 3.764A  pdb=" N   ALA A 138 " --> pdb=" O   ARG A  21 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ASN A  23 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   VAL A 136 " --> pdb=" O   ASN A  23 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261
      removed outlier: 4.119A  pdb=" N   GLU A 266 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505
      removed outlier: 6.672A  pdb=" N   GLU A 504 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    347 hydrogen bonds defined for protein.
    1011 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: 0.90

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 48
        1.03 -     1.22: 33
        1.22 -     1.42: 2317
        1.42 -     1.61: 3274
        1.61 -     1.81: 52
  Bond restraints: 5724
  Sorted by residual:
  bond pdb=" C1  PGW A 810 "
       pdb=" O01 PGW A 810 "
    ideal  model  delta    sigma   weight residual
    1.332  1.426 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" C1  PGW A 807 "
       pdb=" O01 PGW A 807 "
    ideal  model  delta    sigma   weight residual
    1.332  1.422 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C1  PGW A 809 "
       pdb=" O01 PGW A 809 "
    ideal  model  delta    sigma   weight residual
    1.332  1.422 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C1  PGW A 817 "
       pdb=" O01 PGW A 817 "
    ideal  model  delta    sigma   weight residual
    1.332  1.421 -0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" C1  PGW A 814 "
       pdb=" O01 PGW A 814 "
    ideal  model  delta    sigma   weight residual
    1.332  1.420 -0.088 2.00e-02 2.50e+03 1.93e+01
  ... (remaining 5719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 7127
        2.29 -     4.58: 342
        4.58 -     6.87: 124
        6.87 -     9.16: 20
        9.16 -    11.45: 39
  Bond angle restraints: 7652
  Sorted by residual:
  angle pdb=" N   ARG A 404 "
        pdb=" CA  ARG A 404 "
        pdb=" C   ARG A 404 "
      ideal   model   delta    sigma   weight residual
     113.16  119.81   -6.65 1.42e+00 4.96e-01 2.19e+01
  angle pdb=" N   GLU A 418 "
        pdb=" CA  GLU A 418 "
        pdb=" C   GLU A 418 "
      ideal   model   delta    sigma   weight residual
     109.96  103.92    6.04 1.50e+00 4.44e-01 1.62e+01
  angle pdb=" C   ARG A 404 "
        pdb=" N   PRO A 405 "
        pdb=" CA  PRO A 405 "
      ideal   model   delta    sigma   weight residual
     119.84  114.93    4.91 1.25e+00 6.40e-01 1.54e+01
  angle pdb=" O11 PGW A 807 "
        pdb=" P   PGW A 807 "
        pdb=" O12 PGW A 807 "
      ideal   model   delta    sigma   weight residual
      98.90  110.35  -11.45 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" N   ILE A 421 "
        pdb=" CA  ILE A 421 "
        pdb=" C   ILE A 421 "
      ideal   model   delta    sigma   weight residual
     109.51  114.97   -5.46 1.43e+00 4.89e-01 1.46e+01
  ... (remaining 7647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.98: 3238
       34.98 -    69.95: 182
       69.95 -   104.93: 35
      104.93 -   139.90: 8
      139.90 -   174.87: 11
  Dihedral angle restraints: 3474
    sinusoidal: 1624
      harmonic: 1850
  Sorted by residual:
  dihedral pdb=" CA  ALA A 389 "
           pdb=" C   ALA A 389 "
           pdb=" N   SER A 390 "
           pdb=" CA  SER A 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.91   26.09     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" O01 PGW A 810 "
           pdb=" C01 PGW A 810 "
           pdb=" C02 PGW A 810 "
           pdb=" O03 PGW A 810 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.30 -115.57  174.87     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C03 PGW A 810 "
           pdb=" C01 PGW A 810 "
           pdb=" C02 PGW A 810 "
           pdb=" O03 PGW A 810 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.35  121.86  173.49     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 3471 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 707
       0.068 -    0.136: 88
       0.136 -    0.203: 16
       0.203 -    0.271: 0
       0.271 -    0.339: 1
  Chirality restraints: 812
  Sorted by residual:
  chirality pdb=" CA  ARG A 404 "
            pdb=" N   ARG A 404 "
            pdb=" C   ARG A 404 "
            pdb=" CB  ARG A 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CA  ILE A 421 "
            pdb=" N   ILE A 421 "
            pdb=" C   ILE A 421 "
            pdb=" CB  ILE A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.25    0.19 2.00e-01 2.50e+01 8.65e-01
  chirality pdb=" C02 PGW A 813 "
            pdb=" C01 PGW A 813 "
            pdb=" C03 PGW A 813 "
            pdb=" O01 PGW A 813 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.54   -0.18 2.00e-01 2.50e+01 8.11e-01
  ... (remaining 809 not shown)

  Planarity restraints: 930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 352 "   -0.010 2.00e-02 2.50e+03   1.92e-02 3.70e+00
        pdb=" C   TYR A 352 "    0.033 2.00e-02 2.50e+03
        pdb=" O   TYR A 352 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A 353 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 393 "    0.030 5.00e-02 4.00e+02   4.52e-02 3.26e+00
        pdb=" N   PRO A 394 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 394 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 394 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 526 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.98e+00
        pdb=" N   PRO A 527 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 527 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 527 "    0.024 5.00e-02 4.00e+02
  ... (remaining 927 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 30
        2.30 -     2.87: 2026
        2.87 -     3.45: 6618
        3.45 -     4.02: 11498
        4.02 -     4.60: 16821
  Nonbonded interactions: 36993
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 546 "
            pdb=" H1  HOH A2702 "
     model   vdw
     1.723 2.450
  nonbonded pdb=" O   LYS A 556 "
            pdb=" H1  HOH A2709 "
     model   vdw
     1.739 2.450
  nonbonded pdb=" OH  TYR A 621 "
            pdb=" H1  HOH A2704 "
     model   vdw
     1.740 2.450
  nonbonded pdb=" OG1 THR A 116 "
            pdb=" H1  HOH A2705 "
     model   vdw
     1.769 2.450
  nonbonded pdb=" OD2 ASP A 233 "
            pdb=" H1  HOH A2703 "
     model   vdw
     1.778 2.450
  ... (remaining 36988 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.640
  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:             0.050
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.770
  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:             0.000
  Load rotamer database and sin/cos tables:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
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      :  0.009   0.094   5676  Z= 0.433
  Angle     :  1.403  11.447   7628  Z= 0.571
  Chirality :  0.050   0.339    812
  Planarity :  0.005   0.045    930
  Dihedral  : 24.726 174.875   2274
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.73 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  2.22 %
    Favored  : 97.22 %
  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 are not related in a simple way.
  whole: -0.87 (0.31), residues: 622
  helix:  0.09 (0.22), residues: 424
  sheet: -0.80 (0.80), residues: 27
  loop : -2.04 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 496 
 TYR   0.013   0.002   TYR A 352 
 PHE   0.018   0.002   PHE A 388 
 TRP   0.028   0.003   TRP A 155 
 HIS   0.008   0.002   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00872 ( 5676)
  covalent geometry    : angle       1.40329 ( 7628)
  hydrogen bonds       : bond        0.10973 (  347)
  hydrogen bonds       : angle       5.47823 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.211 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 92
  average time/residue: 0.6381
  time to fit residues: 61.0776
Evaluate side-chains
  51 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   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  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  78 GLN
** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
A 171 ASN
A 283 GLN
A 370 ASN
A 438 GLN
A 453 GLN
A 539 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.103173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.073928 restraints weight = 8269.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.03
r_work: 0.2707 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5676  Z= 0.162
  Angle     :  0.595   6.367   7628  Z= 0.294
  Chirality :  0.039   0.162    812
  Planarity :  0.004   0.035    930
  Dihedral  : 24.640 170.298   1100
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.56 %
    Favored  : 87.41 %
  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 are not related in a simple way.
  whole:  0.87 (0.33), residues: 622
  helix:  1.45 (0.24), residues: 426
  sheet:  0.03 (1.00), residues: 22
  loop : -1.55 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 562 
 TYR   0.016   0.001   TYR A 180 
 PHE   0.011   0.001   PHE A 193 
 TRP   0.032   0.002   TRP A 155 
 HIS   0.004   0.001   HIS A 400 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5676)
  covalent geometry    : angle       0.59483 ( 7628)
  hydrogen bonds       : bond        0.04589 (  347)
  hydrogen bonds       : angle       4.31175 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.7818 (t0) cc_final: 0.7024 (t0)
REVERT: A  104 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7778 (tt0)
REVERT: A  305 GLU cc_start: 0.8603 (tp30) cc_final: 0.8389 (tp30)
REVERT: A  647 ARG cc_start: 0.7349 (tpt170) cc_final: 0.6931 (ttp80)
  outliers start: 11
  outliers final: 5
  residues processed: 57
  average time/residue: 0.5830
  time to fit residues: 34.7935
Evaluate side-chains
  44 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  592 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  54 GLN
A 113 HIS
A 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.096033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.066236 restraints weight = 8229.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 2.04
r_work: 0.2563 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2419 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.5476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5676  Z= 0.204
  Angle     :  0.540   5.540   7628  Z= 0.290
  Chirality :  0.041   0.167    812
  Planarity :  0.004   0.034    930
  Dihedral  : 21.667 174.427   1100
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.74 %
    Favored  : 87.04 %
  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 are not related in a simple way.
  whole:  1.63 (0.34), residues: 622
  helix:  2.00 (0.25), residues: 425
  sheet:  0.01 (0.99), residues: 24
  loop : -1.13 (0.47), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 642 
 TYR   0.021   0.002   TYR A 212 
 PHE   0.017   0.002   PHE A 193 
 TRP   0.036   0.002   TRP A 155 
 HIS   0.008   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 5676)
  covalent geometry    : angle       0.54029 ( 7628)
  hydrogen bonds       : bond        0.05550 (  347)
  hydrogen bonds       : angle       4.34613 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8562 (p0) cc_final: 0.8340 (p0)
REVERT: A   28 ASP cc_start: 0.8006 (t0) cc_final: 0.7509 (t0)
REVERT: A  104 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8251 (tt0)
REVERT: A  146 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8621 (tp30)
REVERT: A  211 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8857 (tp)
REVERT: A  647 ARG cc_start: 0.7471 (tpt170) cc_final: 0.7049 (ttp80)
  outliers start: 12
  outliers final: 3
  residues processed: 50
  average time/residue: 0.6110
  time to fit residues: 31.9172
Evaluate side-chains
  41 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  658 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.096657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.067053 restraints weight = 8299.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 2.05
r_work: 0.2580 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work: 0.2434 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.5646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5676  Z= 0.153
  Angle     :  0.447   4.714   7628  Z= 0.242
  Chirality :  0.038   0.146    812
  Planarity :  0.003   0.031    930
  Dihedral  : 20.056 178.382   1098
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.19 %
    Favored  : 88.15 %
  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 are not related in a simple way.
  whole:  2.06 (0.35), residues: 622
  helix:  2.32 (0.25), residues: 424
  sheet:  0.79 (1.07), residues: 22
  loop : -1.00 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 268 
 TYR   0.011   0.001   TYR A 212 
 PHE   0.010   0.001   PHE A 193 
 TRP   0.030   0.002   TRP A 155 
 HIS   0.004   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5676)
  covalent geometry    : angle       0.44688 ( 7628)
  hydrogen bonds       : bond        0.04613 (  347)
  hydrogen bonds       : angle       4.09572 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8650 (p0) cc_final: 0.8414 (p0)
REVERT: A   28 ASP cc_start: 0.7856 (t0) cc_final: 0.7092 (t0)
REVERT: A  104 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8197 (tt0)
REVERT: A  211 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8774 (tp)
REVERT: A  420 SER cc_start: 0.8048 (t) cc_final: 0.7590 (p)
REVERT: A  454 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7381 (tpt170)
REVERT: A  647 ARG cc_start: 0.7481 (tpt170) cc_final: 0.7060 (ttp80)
  outliers start: 9
  outliers final: 4
  residues processed: 44
  average time/residue: 0.6615
  time to fit residues: 30.3675
Evaluate side-chains
  44 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** 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 = 0.3264 r_free = 0.3264 target = 0.093885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.064624 restraints weight = 8386.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.2696 rms_B_bonded: 2.02
r_work: 0.2526 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2383 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.5925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5676  Z= 0.237
  Angle     :  0.511   5.293   7628  Z= 0.280
  Chirality :  0.041   0.172    812
  Planarity :  0.004   0.029    930
  Dihedral  : 19.223 179.747   1098
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  :  9.63 %
    Favored  : 87.59 %
  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 are not related in a simple way.
  whole:  1.95 (0.35), residues: 622
  helix:  2.19 (0.25), residues: 423
  sheet:  0.42 (1.05), residues: 24
  loop : -0.87 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 642 
 TYR   0.017   0.002   TYR A 212 
 PHE   0.016   0.002   PHE A 193 
 TRP   0.033   0.002   TRP A 155 
 HIS   0.008   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 5676)
  covalent geometry    : angle       0.51110 ( 7628)
  hydrogen bonds       : bond        0.05424 (  347)
  hydrogen bonds       : angle       4.31953 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8791 (p0) cc_final: 0.8562 (p0)
REVERT: A   28 ASP cc_start: 0.8062 (t0) cc_final: 0.7614 (t0)
REVERT: A  104 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8232 (tt0)
REVERT: A  211 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8842 (tp)
REVERT: A  454 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7495 (tpt170)
REVERT: A  647 ARG cc_start: 0.7484 (tpt170) cc_final: 0.7051 (ttp80)
  outliers start: 15
  outliers final: 4
  residues processed: 52
  average time/residue: 0.7148
  time to fit residues: 38.4799
Evaluate side-chains
  42 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0270
   chunk 28 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.097319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.068347 restraints weight = 8246.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 2.03
r_work: 0.2599 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2458 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.6033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5676  Z= 0.111
  Angle     :  0.414   5.360   7628  Z= 0.225
  Chirality :  0.037   0.134    812
  Planarity :  0.003   0.029    930
  Dihedral  : 17.681 176.382   1098
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.30 %
    Favored  : 87.41 %
  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 are not related in a simple way.
  whole:  2.35 (0.36), residues: 622
  helix:  2.54 (0.26), residues: 424
  sheet:  0.92 (1.13), residues: 22
  loop : -0.89 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 268 
 TYR   0.010   0.001   TYR A 180 
 PHE   0.005   0.001   PHE A 181 
 TRP   0.024   0.002   TRP A 155 
 HIS   0.003   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 5676)
  covalent geometry    : angle       0.41378 ( 7628)
  hydrogen bonds       : bond        0.04166 (  347)
  hydrogen bonds       : angle       3.99903 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8811 (p0) cc_final: 0.8551 (p0)
REVERT: A   28 ASP cc_start: 0.7976 (t0) cc_final: 0.7529 (t0)
REVERT: A  104 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8107 (tt0)
REVERT: A  137 ASP cc_start: 0.8834 (t0) cc_final: 0.8464 (t0)
REVERT: A  211 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8715 (tp)
REVERT: A  420 SER cc_start: 0.7966 (t) cc_final: 0.7539 (p)
REVERT: A  454 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7481 (mmt-90)
REVERT: A  647 ARG cc_start: 0.7459 (tpt170) cc_final: 0.7044 (ttp80)
  outliers start: 7
  outliers final: 3
  residues processed: 49
  average time/residue: 0.7358
  time to fit residues: 37.3979
Evaluate side-chains
  49 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0270
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0060
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.6060

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.094071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.065356 restraints weight = 8362.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 1.99
r_work: 0.2539 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2395 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8827
moved from start:          0.6094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5676  Z= 0.217
  Angle     :  0.487   5.772   7628  Z= 0.265
  Chirality :  0.040   0.163    812
  Planarity :  0.003   0.028    930
  Dihedral  : 17.720 176.441   1098
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.67 %
    Favored  : 86.85 %
  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 are not related in a simple way.
  whole:  2.27 (0.35), residues: 622
  helix:  2.44 (0.25), residues: 423
  sheet:  0.55 (1.06), residues: 24
  loop : -0.76 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 492 
 TYR   0.015   0.001   TYR A 212 
 PHE   0.013   0.001   PHE A 193 
 TRP   0.027   0.002   TRP A 155 
 HIS   0.007   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 5676)
  covalent geometry    : angle       0.48687 ( 7628)
  hydrogen bonds       : bond        0.05055 (  347)
  hydrogen bonds       : angle       4.18247 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8877 (p0) cc_final: 0.8608 (p0)
REVERT: A   28 ASP cc_start: 0.8103 (t0) cc_final: 0.7644 (t0)
REVERT: A  104 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8223 (tt0)
REVERT: A  211 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8836 (tp)
REVERT: A  454 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7556 (mmt-90)
REVERT: A  647 ARG cc_start: 0.7535 (tpt170) cc_final: 0.7112 (ttp80)
  outliers start: 8
  outliers final: 3
  residues processed: 49
  average time/residue: 0.7504
  time to fit residues: 38.1526
Evaluate side-chains
  45 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.095038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.066115 restraints weight = 8278.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.2731 rms_B_bonded: 2.02
r_work: 0.2561 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2417 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.6186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5676  Z= 0.180
  Angle     :  0.460   6.012   7628  Z= 0.250
  Chirality :  0.039   0.153    812
  Planarity :  0.003   0.027    930
  Dihedral  : 16.976 173.517   1098
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.85 %
    Favored  : 86.67 %
  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 are not related in a simple way.
  whole:  2.33 (0.35), residues: 622
  helix:  2.50 (0.26), residues: 424
  sheet:  0.64 (1.08), residues: 24
  loop : -0.79 (0.51), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 492 
 TYR   0.012   0.001   TYR A 212 
 PHE   0.010   0.001   PHE A 193 
 TRP   0.023   0.002   TRP A 155 
 HIS   0.006   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5676)
  covalent geometry    : angle       0.45999 ( 7628)
  hydrogen bonds       : bond        0.04703 (  347)
  hydrogen bonds       : angle       4.11593 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8897 (p0) cc_final: 0.8635 (p0)
REVERT: A   28 ASP cc_start: 0.8151 (t0) cc_final: 0.7720 (t0)
REVERT: A  104 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8170 (tt0)
REVERT: A  211 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8777 (tp)
REVERT: A  420 SER cc_start: 0.8157 (t) cc_final: 0.7732 (p)
REVERT: A  454 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7603 (mmt-90)
REVERT: A  647 ARG cc_start: 0.7523 (tpt170) cc_final: 0.7085 (ttp80)
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.7222
  time to fit residues: 34.5548
Evaluate side-chains
  48 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  659 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.093334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.064567 restraints weight = 8179.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.2714 rms_B_bonded: 1.98
r_work: 0.2540 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2395 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.6243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5676  Z= 0.204
  Angle     :  0.489   6.150   7628  Z= 0.267
  Chirality :  0.040   0.158    812
  Planarity :  0.003   0.027    930
  Dihedral  : 16.563 171.280   1098
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.67 %
    Favored  : 86.67 %
  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 are not related in a simple way.
  whole:  2.19 (0.35), residues: 622
  helix:  2.43 (0.25), residues: 423
  sheet:  0.64 (1.06), residues: 24
  loop : -0.96 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 492 
 TYR   0.016   0.001   TYR A 212 
 PHE   0.012   0.001   PHE A 193 
 TRP   0.026   0.002   TRP A 155 
 HIS   0.006   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 5676)
  covalent geometry    : angle       0.48895 ( 7628)
  hydrogen bonds       : bond        0.05061 (  347)
  hydrogen bonds       : angle       4.20030 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8930 (p0) cc_final: 0.8670 (p0)
REVERT: A   28 ASP cc_start: 0.8197 (t0) cc_final: 0.7793 (t0)
REVERT: A  104 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8211 (tt0)
REVERT: A  211 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8795 (tp)
REVERT: A  454 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7633 (mmt-90)
REVERT: A  647 ARG cc_start: 0.7523 (tpt170) cc_final: 0.7083 (ttp80)
  outliers start: 9
  outliers final: 5
  residues processed: 49
  average time/residue: 0.7404
  time to fit residues: 37.6535
Evaluate side-chains
  48 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  659 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0170
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.096425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.067938 restraints weight = 8274.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 1.99
r_work: 0.2595 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2453 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.6305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5676  Z= 0.120
  Angle     :  0.424   6.570   7628  Z= 0.230
  Chirality :  0.037   0.139    812
  Planarity :  0.003   0.028    930
  Dihedral  : 15.602 165.337   1098
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.41 %
    Favored  : 86.48 %
  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 are not related in a simple way.
  whole:  2.44 (0.36), residues: 622
  helix:  2.59 (0.26), residues: 425
  sheet:  0.66 (1.09), residues: 24
  loop : -0.82 (0.51), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 492 
 TYR   0.010   0.001   TYR A 180 
 PHE   0.006   0.001   PHE A 525 
 TRP   0.021   0.002   TRP A 155 
 HIS   0.004   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5676)
  covalent geometry    : angle       0.42417 ( 7628)
  hydrogen bonds       : bond        0.04230 (  347)
  hydrogen bonds       : angle       4.00416 ( 1011)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.8903 (p0) cc_final: 0.8644 (p0)
REVERT: A   28 ASP cc_start: 0.8117 (t0) cc_final: 0.7713 (t0)
REVERT: A  104 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8129 (tt0)
REVERT: A  211 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8712 (tp)
REVERT: A  420 SER cc_start: 0.8076 (t) cc_final: 0.7664 (p)
REVERT: A  454 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7603 (mmt-90)
REVERT: A  647 ARG cc_start: 0.7493 (tpt170) cc_final: 0.7067 (ttp80)
  outliers start: 6
  outliers final: 3
  residues processed: 47
  average time/residue: 0.6570
  time to fit residues: 32.1140
Evaluate side-chains
  47 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  454 ARG
Chi-restraints excluded: chain A residue  611 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0010
   chunk 56 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.096293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.067342 restraints weight = 8107.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 2.01
r_work: 0.2597 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2453 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.6355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5676  Z= 0.122
  Angle     :  0.427   6.373   7628  Z= 0.232
  Chirality :  0.037   0.137    812
  Planarity :  0.003   0.027    930
  Dihedral  : 14.660 155.939   1098
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.04 %
    Favored  : 86.67 %
  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 are not related in a simple way.
  whole:  2.59 (0.36), residues: 622
  helix:  2.70 (0.26), residues: 427
  sheet:  0.75 (1.09), residues: 24
  loop : -0.81 (0.51), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 492 
 TYR   0.011   0.001   TYR A 212 
 PHE   0.008   0.001   PHE A 193 
 TRP   0.023   0.002   TRP A 155 
 HIS   0.005   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5676)
  covalent geometry    : angle       0.42730 ( 7628)
  hydrogen bonds       : bond        0.04210 (  347)
  hydrogen bonds       : angle       3.94333 ( 1011)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2341.48 seconds
wall clock time: 40 minutes 30.90 seconds (2430.90 seconds total)