Starting phenix.real_space_refine
on Tue Mar  3 11:52:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wsm_32760/03_2026/7wsm_32760.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsm_32760/03_2026/7wsm_32760.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wsm_32760/03_2026/7wsm_32760.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsm_32760/03_2026/7wsm_32760.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsm_32760/03_2026/7wsm_32760.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsm_32760/03_2026/7wsm_32760.cif"
  }
  resolution = 3.25
  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=  -0.003 sd=   0.090
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: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2359      2.51       5
     N     582      2.21       5
     O     622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 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: 3577
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3514
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 24, 'TRANS': 439}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'5RH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.00, per 1000 atoms: 0.28
  Number of scatterers: 3577
  At special positions: 0
  Unit cell: (86.6, 56.29, 83.3525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     622      8.00
     N     582      7.00
     C    2359      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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A  57 "
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 96.1 milliseconds
  

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  830

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      88.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 44
    Processing helix  chain 'A' and resid 48 through 65
      removed outlier: 4.084A  pdb=" N   GLN A  54 " --> pdb=" O   LYS A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 68
      No H-bonds generated for 'chain 'A' and resid 66 through 68'
    Processing helix  chain 'A' and resid 73 through 99
      removed outlier: 4.162A  pdb=" N   PHE A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   PHE A  97 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 107
    Processing helix  chain 'A' and resid 108 through 128
    Processing helix  chain 'A' and resid 129 through 133
    Processing helix  chain 'A' and resid 135 through 164
      Proline residue:  A 157  - end of helix
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 3.795A  pdb=" N   THR A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 190
      removed outlier: 3.853A  pdb=" N   ILE A 180 " --> pdb=" O   ASN A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 209
      removed outlier: 4.057A  pdb=" N   LEU A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 206 " --> pdb=" O   TRP A 202 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 220
      removed outlier: 4.265A  pdb=" N   ALA A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 223
      No H-bonds generated for 'chain 'A' and resid 221 through 223'
    Processing helix  chain 'A' and resid 226 through 233
    Processing helix  chain 'A' and resid 237 through 249
    Processing helix  chain 'A' and resid 253 through 270
      removed outlier: 3.613A  pdb=" N   ASP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 280
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 284 through 300
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.640A  pdb=" N   VAL A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER A 310 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   SER A 312 " --> pdb=" O   TYR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 344
      removed outlier: 3.514A  pdb=" N   ALA A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 347
      No H-bonds generated for 'chain 'A' and resid 345 through 347'
    Processing helix  chain 'A' and resid 349 through 373
    Processing helix  chain 'A' and resid 379 through 398
      removed outlier: 3.947A  pdb=" N   VAL A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 411
      removed outlier: 3.562A  pdb=" N   PHE A 405 " --> pdb=" O   PRO A 401 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 411 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 446
      removed outlier: 5.858A  pdb=" N   GLN A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   TYR A 440 " --> pdb=" O   MET A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 468
    Processing helix  chain 'A' and resid 475 through 483

    279 hydrogen bonds defined for protein.
    831 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: 0.60

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 550
        1.32 -     1.44: 969
        1.44 -     1.56: 2116
        1.56 -     1.69: 0
        1.69 -     1.81: 25
  Bond restraints: 3660
  Sorted by residual:
  bond pdb=" C   TRP A  60 "
       pdb=" O   TRP A  60 "
    ideal  model  delta    sigma   weight residual
    1.236  1.196  0.040 1.29e-02 6.01e+03 9.64e+00
  bond pdb=" C   TRP A  60 "
       pdb=" N   LEU A  61 "
    ideal  model  delta    sigma   weight residual
    1.333  1.290  0.043 1.45e-02 4.76e+03 8.81e+00
  bond pdb=" CA  ALA A 364 "
       pdb=" CB  ALA A 364 "
    ideal  model  delta    sigma   weight residual
    1.528  1.479  0.049 1.66e-02 3.63e+03 8.69e+00
  bond pdb=" N   ILE A 365 "
       pdb=" CA  ILE A 365 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.33e-02 5.65e+03 6.58e+00
  bond pdb=" N   ILE A 479 "
       pdb=" CA  ILE A 479 "
    ideal  model  delta    sigma   weight residual
    1.462  1.491 -0.029 1.14e-02 7.69e+03 6.30e+00
  ... (remaining 3655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 4803
        1.92 -     3.85: 159
        3.85 -     5.77: 19
        5.77 -     7.69: 4
        7.69 -     9.61: 5
  Bond angle restraints: 4990
  Sorted by residual:
  angle pdb=" N   LEU A  61 "
        pdb=" CA  LEU A  61 "
        pdb=" C   LEU A  61 "
      ideal   model   delta    sigma   weight residual
     112.45  103.58    8.87 1.39e+00 5.18e-01 4.07e+01
  angle pdb=" N   PHE A 476 "
        pdb=" CA  PHE A 476 "
        pdb=" C   PHE A 476 "
      ideal   model   delta    sigma   weight residual
     111.75  103.68    8.07 1.28e+00 6.10e-01 3.98e+01
  angle pdb=" N   LEU A 366 "
        pdb=" CA  LEU A 366 "
        pdb=" C   LEU A 366 "
      ideal   model   delta    sigma   weight residual
     111.14  104.95    6.19 1.08e+00 8.57e-01 3.28e+01
  angle pdb=" N   GLY A  62 "
        pdb=" CA  GLY A  62 "
        pdb=" C   GLY A  62 "
      ideal   model   delta    sigma   weight residual
     113.27  106.78    6.49 1.33e+00 5.65e-01 2.38e+01
  angle pdb=" C   TRP A  60 "
        pdb=" N   LEU A  61 "
        pdb=" CA  LEU A  61 "
      ideal   model   delta    sigma   weight residual
     121.64  112.03    9.61 2.13e+00 2.20e-01 2.04e+01
  ... (remaining 4985 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 2156
       35.97 -    71.93: 43
       71.93 -   107.90: 4
      107.90 -   143.87: 0
      143.87 -   179.83: 2
  Dihedral angle restraints: 2205
    sinusoidal: 899
      harmonic: 1306
  Sorted by residual:
  dihedral pdb=" C19 5RH A 601 "
           pdb=" C17 5RH A 601 "
           pdb=" C18 5RH A 601 "
           pdb=" O3  5RH A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -166.95   12.88 -179.83     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C19 5RH A 601 "
           pdb=" C17 5RH A 601 "
           pdb=" C18 5RH A 601 "
           pdb=" O2  5RH A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      11.42 -166.96  178.38     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CA  PRO A 401 "
           pdb=" C   PRO A 401 "
           pdb=" N   ILE A 402 "
           pdb=" CA  ILE A 402 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.64  -18.36     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 2202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 487
       0.053 -    0.106: 102
       0.106 -    0.160: 11
       0.160 -    0.213: 2
       0.213 -    0.266: 2
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.67    0.27 2.00e-02 2.50e+03 1.77e+02
  chirality pdb=" CA  LEU A 366 "
            pdb=" N   LEU A 366 "
            pdb=" C   LEU A 366 "
            pdb=" CB  LEU A 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  LEU A  61 "
            pdb=" N   LEU A  61 "
            pdb=" C   LEU A  61 "
            pdb=" CB  LEU A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 601 not shown)

  Planarity restraints: 619
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  57 "   -0.096 2.00e-02 2.50e+03   1.03e-01 1.34e+02
        pdb=" CG  ASN A  57 "    0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  57 "    0.034 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  57 "    0.159 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.129 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C17 5RH A 601 "   -0.029 2.00e-02 2.50e+03   5.23e-02 2.73e+01
        pdb=" C18 5RH A 601 "    0.068 2.00e-02 2.50e+03
        pdb=" C19 5RH A 601 "   -0.068 2.00e-02 2.50e+03
        pdb=" C20 5RH A 601 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   5RH A 601 "    0.041 2.00e-02 2.50e+03   2.65e-02 8.76e+00
        pdb=" C15 5RH A 601 "    0.003 2.00e-02 2.50e+03
        pdb=" C16 5RH A 601 "    0.013 2.00e-02 2.50e+03
        pdb=" C7  5RH A 601 "   -0.033 2.00e-02 2.50e+03
        pdb=" O1  5RH A 601 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 616 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 951
        2.78 -     3.31: 4008
        3.31 -     3.84: 5987
        3.84 -     4.37: 6934
        4.37 -     4.90: 11613
  Nonbonded interactions: 29493
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  46 "
            pdb=" OG1 THR A 311 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   PRO A  69 "
            pdb=" OG  SER A  70 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   ALA A 423 "
            pdb=" OG  SER A 426 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG1 THR A  23 "
            pdb=" O   ARG A 246 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OE2 GLU A 225 "
            pdb=" N   SER A 226 "
     model   vdw
     2.347 3.120
  ... (remaining 29488 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:             0.640
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.270
  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:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
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      :  0.006   0.049   3662  Z= 0.313
  Angle     :  0.868  10.041   4996  Z= 0.507
  Chirality :  0.045   0.266    604
  Planarity :  0.006   0.052    618
  Dihedral  : 17.298 179.833   1375
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  1.35 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.39), residues: 462
  helix: -0.32 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -2.47 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 142 
 TYR   0.026   0.002   TYR A 148 
 PHE   0.021   0.002   PHE A 476 
 TRP   0.016   0.002   TRP A  60 
 HIS   0.002   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 3660)
  covalent geometry    : angle       0.84233 ( 4990)
  hydrogen bonds       : bond        0.16237 (  279)
  hydrogen bonds       : angle       7.91722 (  831)
  link_BETA1-4         : bond        0.00136 (    1)
  link_BETA1-4         : angle       6.79657 (    3)
  link_NAG-ASN         : bond        0.00318 (    1)
  link_NAG-ASN         : angle       5.39832 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A  389 PHE cc_start: 0.7591 (m-80) cc_final: 0.7005 (m-80)
REVERT: A  440 TYR cc_start: 0.8101 (m-80) cc_final: 0.7514 (m-80)
  outliers start: 3
  outliers final: 1
  residues processed: 76
  average time/residue: 0.0484
  time to fit residues: 4.8438
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 299 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.137992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.114615 restraints weight = 4974.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.07
r_work: 0.3267 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3662  Z= 0.175
  Angle     :  0.695   7.762   4996  Z= 0.345
  Chirality :  0.042   0.157    604
  Planarity :  0.006   0.065    618
  Dihedral  : 12.994 178.469    604
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.32 %
    Favored  : 86.52 %
  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 are not related in a simple way.
  whole:  0.99 (0.41), residues: 462
  helix:  1.26 (0.28), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.03 (0.63), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 246 
 TYR   0.011   0.002   TYR A 148 
 PHE   0.023   0.002   PHE A 336 
 TRP   0.013   0.001   TRP A  60 
 HIS   0.002   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3660)
  covalent geometry    : angle       0.69086 ( 4990)
  hydrogen bonds       : bond        0.05675 (  279)
  hydrogen bonds       : angle       4.76866 (  831)
  link_BETA1-4         : bond        0.00115 (    1)
  link_BETA1-4         : angle       1.84078 (    3)
  link_NAG-ASN         : bond        0.00100 (    1)
  link_NAG-ASN         : angle       2.81018 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  367 MET cc_start: 0.8002 (tpt) cc_final: 0.7784 (ttm)
REVERT: A  389 PHE cc_start: 0.8121 (m-80) cc_final: 0.7618 (m-80)
REVERT: A  440 TYR cc_start: 0.8501 (m-80) cc_final: 0.7778 (m-80)
REVERT: A  466 LEU cc_start: 0.8705 (pp) cc_final: 0.8284 (mp)
  outliers start: 8
  outliers final: 7
  residues processed: 72
  average time/residue: 0.0467
  time to fit residues: 4.3638
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0010
   chunk 1 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  37 GLN
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 439 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.142385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119398 restraints weight = 4946.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.08
r_work: 0.3313 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3662  Z= 0.142
  Angle     :  0.639   8.550   4996  Z= 0.313
  Chirality :  0.040   0.161    604
  Planarity :  0.005   0.067    618
  Dihedral  : 12.699 173.406    603
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.44 %
    Favored  : 81.13 %
  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:  1.50 (0.41), residues: 462
  helix:  1.58 (0.28), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.96 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 246 
 TYR   0.013   0.001   TYR A 148 
 PHE   0.010   0.001   PHE A 395 
 TRP   0.010   0.001   TRP A  60 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3660)
  covalent geometry    : angle       0.63391 ( 4990)
  hydrogen bonds       : bond        0.04607 (  279)
  hydrogen bonds       : angle       4.38210 (  831)
  link_BETA1-4         : bond        0.00249 (    1)
  link_BETA1-4         : angle       1.76970 (    3)
  link_NAG-ASN         : bond        0.00213 (    1)
  link_NAG-ASN         : angle       2.91584 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  367 MET cc_start: 0.7878 (tpt) cc_final: 0.7637 (ttm)
REVERT: A  389 PHE cc_start: 0.7933 (m-80) cc_final: 0.7695 (m-80)
REVERT: A  440 TYR cc_start: 0.8399 (m-80) cc_final: 0.7595 (m-80)
REVERT: A  476 PHE cc_start: 0.7827 (t80) cc_final: 0.7541 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0571
  time to fit residues: 5.4022
Evaluate side-chains
  62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  339 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0970
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0670
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.5318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.142784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.119538 restraints weight = 4900.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.10
r_work: 0.3320 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
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      :  0.003   0.039   3662  Z= 0.137
  Angle     :  0.637  13.871   4996  Z= 0.306
  Chirality :  0.040   0.153    604
  Planarity :  0.005   0.068    618
  Dihedral  : 12.597 171.733    603
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.52 %
    Favored  : 79.25 %
  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 are not related in a simple way.
  whole:  1.57 (0.40), residues: 462
  helix:  1.63 (0.27), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.89 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 271 
 TYR   0.015   0.001   TYR A 148 
 PHE   0.008   0.001   PHE A 438 
 TRP   0.008   0.001   TRP A  60 
 HIS   0.002   0.000   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3660)
  covalent geometry    : angle       0.63299 ( 4990)
  hydrogen bonds       : bond        0.04413 (  279)
  hydrogen bonds       : angle       4.33390 (  831)
  link_BETA1-4         : bond        0.00220 (    1)
  link_BETA1-4         : angle       1.57327 (    3)
  link_NAG-ASN         : bond        0.00318 (    1)
  link_NAG-ASN         : angle       2.79580 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  367 MET cc_start: 0.7898 (tpt) cc_final: 0.7646 (ttm)
REVERT: A  440 TYR cc_start: 0.8415 (m-80) cc_final: 0.7608 (m-80)
REVERT: A  476 PHE cc_start: 0.7808 (t80) cc_final: 0.7534 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0453
  time to fit residues: 3.9402
Evaluate side-chains
  62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  339 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   chunk 35 optimal weight:    0.1980
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.142918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119605 restraints weight = 4971.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.10
r_work: 0.3304 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3662  Z= 0.137
  Angle     :  0.638  13.895   4996  Z= 0.303
  Chirality :  0.040   0.148    604
  Planarity :  0.005   0.069    618
  Dihedral  : 12.558 170.758    603
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 18.87 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.40), residues: 462
  helix:  1.65 (0.27), residues: 385
  sheet:  None (None), residues: 0
  loop : -1.78 (0.63), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 271 
 TYR   0.011   0.001   TYR A 148 
 PHE   0.017   0.001   PHE A 432 
 TRP   0.007   0.001   TRP A  60 
 HIS   0.001   0.000   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3660)
  covalent geometry    : angle       0.63424 ( 4990)
  hydrogen bonds       : bond        0.04344 (  279)
  hydrogen bonds       : angle       4.25229 (  831)
  link_BETA1-4         : bond        0.00348 (    1)
  link_BETA1-4         : angle       1.60114 (    3)
  link_NAG-ASN         : bond        0.00209 (    1)
  link_NAG-ASN         : angle       2.50998 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  440 TYR cc_start: 0.8411 (m-80) cc_final: 0.7641 (m-80)
REVERT: A  476 PHE cc_start: 0.7892 (t80) cc_final: 0.7530 (m-80)
  outliers start: 17
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0493
  time to fit residues: 4.5013
Evaluate side-chains
  65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  339 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0980
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0770
   chunk 44 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 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 = 0.3701 r_free = 0.3701 target = 0.143383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120328 restraints weight = 4943.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.08
r_work: 0.3327 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3662  Z= 0.132
  Angle     :  0.625  14.728   4996  Z= 0.298
  Chirality :  0.039   0.148    604
  Planarity :  0.005   0.068    618
  Dihedral  : 12.472 169.610    603
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.02 %
    Favored  : 75.74 %
  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:  1.66 (0.40), residues: 462
  helix:  1.66 (0.27), residues: 385
  sheet:  None (None), residues: 0
  loop : -1.75 (0.63), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 148 
 PHE   0.012   0.001   PHE A 432 
 TRP   0.005   0.001   TRP A  60 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3660)
  covalent geometry    : angle       0.62183 ( 4990)
  hydrogen bonds       : bond        0.04198 (  279)
  hydrogen bonds       : angle       4.27595 (  831)
  link_BETA1-4         : bond        0.00269 (    1)
  link_BETA1-4         : angle       1.42398 (    3)
  link_NAG-ASN         : bond        0.00207 (    1)
  link_NAG-ASN         : angle       2.45780 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  440 TYR cc_start: 0.8519 (m-80) cc_final: 0.7733 (m-80)
REVERT: A  476 PHE cc_start: 0.7845 (t80) cc_final: 0.7559 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 68
  average time/residue: 0.0484
  time to fit residues: 4.3068
Evaluate side-chains
  65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  332 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0010
   chunk 32 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0270
   overall best weight:    0.3844

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.145025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.122014 restraints weight = 4975.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.09
r_work: 0.3349 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3662  Z= 0.125
  Angle     :  0.623  14.928   4996  Z= 0.295
  Chirality :  0.039   0.146    604
  Planarity :  0.005   0.068    618
  Dihedral  : 12.292 167.507    603
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.37 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.40), residues: 462
  helix:  1.72 (0.27), residues: 385
  sheet:  None (None), residues: 0
  loop : -1.76 (0.63), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.008   0.001   TYR A 148 
 PHE   0.013   0.001   PHE A 336 
 TRP   0.005   0.001   TRP A  60 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3660)
  covalent geometry    : angle       0.62021 ( 4990)
  hydrogen bonds       : bond        0.04063 (  279)
  hydrogen bonds       : angle       4.19220 (  831)
  link_BETA1-4         : bond        0.00302 (    1)
  link_BETA1-4         : angle       1.32137 (    3)
  link_NAG-ASN         : bond        0.00109 (    1)
  link_NAG-ASN         : angle       2.36524 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  440 TYR cc_start: 0.8451 (m-80) cc_final: 0.7757 (m-80)
REVERT: A  476 PHE cc_start: 0.7823 (t80) cc_final: 0.7581 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 72
  average time/residue: 0.0480
  time to fit residues: 4.5655
Evaluate side-chains
  65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  294 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.143225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.119679 restraints weight = 5013.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.11
r_work: 0.3326 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3662  Z= 0.144
  Angle     :  0.641  14.566   4996  Z= 0.307
  Chirality :  0.041   0.185    604
  Planarity :  0.005   0.067    618
  Dihedral  : 12.387 168.732    603
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.18 %
    Favored  : 73.58 %
  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:  1.80 (0.40), residues: 462
  helix:  1.75 (0.27), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.63 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 271 
 TYR   0.008   0.001   TYR A 148 
 PHE   0.014   0.001   PHE A 336 
 TRP   0.005   0.001   TRP A 404 
 HIS   0.002   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3660)
  covalent geometry    : angle       0.63682 ( 4990)
  hydrogen bonds       : bond        0.04249 (  279)
  hydrogen bonds       : angle       4.19738 (  831)
  link_BETA1-4         : bond        0.00513 (    1)
  link_BETA1-4         : angle       1.14417 (    3)
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       2.72915 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  440 TYR cc_start: 0.8534 (m-80) cc_final: 0.7756 (m-80)
REVERT: A  476 PHE cc_start: 0.7788 (t80) cc_final: 0.7570 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0521
  time to fit residues: 4.4747
Evaluate side-chains
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  332 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.142247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.118987 restraints weight = 4904.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.08
r_work: 0.3315 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3662  Z= 0.151
  Angle     :  0.655  14.131   4996  Z= 0.317
  Chirality :  0.041   0.148    604
  Planarity :  0.005   0.067    618
  Dihedral  : 12.471 169.740    603
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.91 %
    Favored  : 73.85 %
  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:  1.79 (0.40), residues: 462
  helix:  1.74 (0.27), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.60 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.008   0.001   TYR A 148 
 PHE   0.015   0.001   PHE A 336 
 TRP   0.007   0.001   TRP A 404 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3660)
  covalent geometry    : angle       0.65290 ( 4990)
  hydrogen bonds       : bond        0.04395 (  279)
  hydrogen bonds       : angle       4.31311 (  831)
  link_BETA1-4         : bond        0.00388 (    1)
  link_BETA1-4         : angle       1.26511 (    3)
  link_NAG-ASN         : bond        0.00015 (    1)
  link_NAG-ASN         : angle       2.21414 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  440 TYR cc_start: 0.8515 (m-80) cc_final: 0.7735 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 65
  average time/residue: 0.0485
  time to fit residues: 4.1769
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  332 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.141952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.118380 restraints weight = 5023.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.12
r_work: 0.3301 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3662  Z= 0.151
  Angle     :  0.655  14.120   4996  Z= 0.316
  Chirality :  0.041   0.149    604
  Planarity :  0.005   0.067    618
  Dihedral  : 12.506 170.159    603
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.45 %
    Favored  : 73.32 %
  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:  1.76 (0.40), residues: 462
  helix:  1.72 (0.27), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.58 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.008   0.001   TYR A 148 
 PHE   0.016   0.001   PHE A 336 
 TRP   0.007   0.001   TRP A 404 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3660)
  covalent geometry    : angle       0.65225 ( 4990)
  hydrogen bonds       : bond        0.04419 (  279)
  hydrogen bonds       : angle       4.31309 (  831)
  link_BETA1-4         : bond        0.00279 (    1)
  link_BETA1-4         : angle       1.26631 (    3)
  link_NAG-ASN         : bond        0.00068 (    1)
  link_NAG-ASN         : angle       2.11993 (    3)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A  440 TYR cc_start: 0.8524 (m-80) cc_final: 0.7750 (m-80)
  outliers start: 12
  outliers final: 12
  residues processed: 69
  average time/residue: 0.0508
  time to fit residues: 4.6163
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  471 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.142327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.118873 restraints weight = 4909.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.10
r_work: 0.3307 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3662  Z= 0.143
  Angle     :  0.649  11.704   4996  Z= 0.313
  Chirality :  0.041   0.149    604
  Planarity :  0.005   0.068    618
  Dihedral  : 12.459 169.559    603
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.45 %
    Favored  : 73.58 %
  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:  1.79 (0.40), residues: 462
  helix:  1.73 (0.27), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.55 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.008   0.001   TYR A 148 
 PHE   0.016   0.001   PHE A 336 
 TRP   0.006   0.001   TRP A 404 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3660)
  covalent geometry    : angle       0.64709 ( 4990)
  hydrogen bonds       : bond        0.04331 (  279)
  hydrogen bonds       : angle       4.29444 (  831)
  link_BETA1-4         : bond        0.00389 (    1)
  link_BETA1-4         : angle       1.23323 (    3)
  link_NAG-ASN         : bond        0.00052 (    1)
  link_NAG-ASN         : angle       1.79889 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 976.14 seconds
wall clock time: 17 minutes 22.71 seconds (1042.71 seconds total)