Starting phenix.real_space_refine
on Tue Mar  3 13:36:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wxv_66358/03_2026/9wxv_66358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wxv_66358/03_2026/9wxv_66358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wxv_66358/03_2026/9wxv_66358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wxv_66358/03_2026/9wxv_66358.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wxv_66358/03_2026/9wxv_66358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wxv_66358/03_2026/9wxv_66358.map"
  }
  resolution = 4.4
  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=   0.006 sd=   0.065
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      31      5.16       5
     C    3423      2.51       5
     N     820      2.21       5
     O     878      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 5152
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 626, 5096
          Classifications: {'peptide': 626}
          Link IDs: {'PTRANS': 22, 'TRANS': 603}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.28, per 1000 atoms: 0.25
  Number of scatterers: 5152
  At special positions: 0
  Unit cell: (87.98, 95.45, 92.96, 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      31     16.00
     O     878      8.00
     N     820      7.00
     C    3423      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 335.3 milliseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1198

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 1 sheets defined
      65.7% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 19
      removed outlier: 4.325A  pdb=" N   SER A  16 " --> pdb=" O   SER A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 71
    Processing helix  chain 'A' and resid 133 through 167
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 191 through 218
    Processing helix  chain 'A' and resid 247 through 252
    Processing helix  chain 'A' and resid 268 through 287
    Processing helix  chain 'A' and resid 321 through 349
      removed outlier: 4.066A  pdb=" N   LYS A 328 " --> pdb=" O   TYR A 324 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ASP A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLU A 339 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
    Processing helix  chain 'A' and resid 363 through 372
      removed outlier: 4.362A  pdb=" N   PHE A 367 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 446
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 460 through 465
    Processing helix  chain 'A' and resid 465 through 478
      removed outlier: 3.597A  pdb=" N   THR A 469 " --> pdb=" O   GLN A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 490
    Processing helix  chain 'A' and resid 494 through 534
      Proline residue:  A 518  - end of helix
    Processing helix  chain 'A' and resid 553 through 574
    Processing helix  chain 'A' and resid 574 through 587
      removed outlier: 6.426A  pdb=" N   LEU A 580 " --> pdb=" O   PRO A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 601
    Processing helix  chain 'A' and resid 606 through 624
      removed outlier: 3.889A  pdb=" N   TYR A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 653
      removed outlier: 3.705A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 637 " --> pdb=" O   PRO A 633 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   TYR A 651 " --> pdb=" O   ARG A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 689
      removed outlier: 4.070A  pdb=" N   PHE A 665 " --> pdb=" O   LYS A 661 " (cutoff:3.500A)
      Proline residue:  A 675  - end of helix
    Processing helix  chain 'A' and resid 694 through 716
    Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 238
      removed outlier: 4.335A  pdb=" N   ASP A 238 " --> pdb=" O   GLU A 356 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   GLU A 356 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1

    301 hydrogen bonds defined for protein.
    903 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: 0.61

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1538
        1.35 -     1.46: 1388
        1.46 -     1.58: 2322
        1.58 -     1.70: 0
        1.70 -     1.82: 46
  Bond restraints: 5294
  Sorted by residual:
  bond pdb=" C   PHE A 652 "
       pdb=" N   VAL A 653 "
    ideal  model  delta    sigma   weight residual
    1.332  1.344 -0.013 5.60e-03 3.19e+04 5.06e+00
  bond pdb=" C23 CLR A 901 "
       pdb=" C24 CLR A 901 "
    ideal  model  delta    sigma   weight residual
    1.525  1.497  0.028 2.00e-02 2.50e+03 1.98e+00
  bond pdb=" C   TYR A 252 "
       pdb=" N   PRO A 253 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.60e+00
  bond pdb=" C22 CLR A 901 "
       pdb=" C23 CLR A 901 "
    ideal  model  delta    sigma   weight residual
    1.525  1.500  0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C22 CLR A 902 "
       pdb=" C23 CLR A 902 "
    ideal  model  delta    sigma   weight residual
    1.525  1.504  0.021 2.00e-02 2.50e+03 1.06e+00
  ... (remaining 5289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.81: 7185
        5.81 -    11.63: 7
       11.63 -    17.44: 2
       17.44 -    23.25: 0
       23.25 -    29.07: 6
  Bond angle restraints: 7200
  Sorted by residual:
  angle pdb=" C19 CLR A 901 "
        pdb=" C10 CLR A 901 "
        pdb=" C9  CLR A 901 "
      ideal   model   delta    sigma   weight residual
     111.86   82.79   29.07 3.00e+00 1.11e-01 9.39e+01
  angle pdb=" C19 CLR A 902 "
        pdb=" C10 CLR A 902 "
        pdb=" C9  CLR A 902 "
      ideal   model   delta    sigma   weight residual
     111.86   82.89   28.97 3.00e+00 1.11e-01 9.32e+01
  angle pdb=" C1  CLR A 901 "
        pdb=" C10 CLR A 901 "
        pdb=" C19 CLR A 901 "
      ideal   model   delta    sigma   weight residual
     109.60   83.51   26.09 3.00e+00 1.11e-01 7.56e+01
  angle pdb=" C1  CLR A 902 "
        pdb=" C10 CLR A 902 "
        pdb=" C19 CLR A 902 "
      ideal   model   delta    sigma   weight residual
     109.60   83.81   25.79 3.00e+00 1.11e-01 7.39e+01
  angle pdb=" C19 CLR A 902 "
        pdb=" C10 CLR A 902 "
        pdb=" C5  CLR A 902 "
      ideal   model   delta    sigma   weight residual
     108.37   84.08   24.29 3.00e+00 1.11e-01 6.55e+01
  ... (remaining 7195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.90: 3112
       34.90 -    69.81: 55
       69.81 -   104.71: 6
      104.71 -   139.62: 0
      139.62 -   174.52: 10
  Dihedral angle restraints: 3183
    sinusoidal: 1336
      harmonic: 1847
  Sorted by residual:
  dihedral pdb=" CA  ASP A  77 "
           pdb=" C   ASP A  77 "
           pdb=" N   TYR A  78 "
           pdb=" CA  TYR A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.45  -30.55     0      5.00e+00 4.00e-02 3.73e+01
  dihedral pdb=" CA  TYR A  31 "
           pdb=" C   TYR A  31 "
           pdb=" N   CYS A  32 "
           pdb=" CA  CYS A  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.59   26.41     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  MET A 513 "
           pdb=" C   MET A 513 "
           pdb=" N   VAL A 514 "
           pdb=" CA  VAL A 514 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.83  -23.17     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 3180 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.357: 828
       0.357 -    0.714: 0
       0.714 -    1.071: 0
       1.071 -    1.427: 0
       1.427 -    1.784: 2
  Chirality restraints: 830
  Sorted by residual:
  chirality pdb=" C10 CLR A 902 "
            pdb=" C1  CLR A 902 "
            pdb=" C5  CLR A 902 "
            pdb=" C9  CLR A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -1.06   -1.78 2.00e-01 2.50e+01 7.96e+01
  chirality pdb=" C10 CLR A 901 "
            pdb=" C1  CLR A 901 "
            pdb=" C5  CLR A 901 "
            pdb=" C9  CLR A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -1.08   -1.77 2.00e-01 2.50e+01 7.82e+01
  chirality pdb=" CA  PHE A 199 "
            pdb=" N   PHE A 199 "
            pdb=" C   PHE A 199 "
            pdb=" CB  PHE A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.87e-01
  ... (remaining 827 not shown)

  Planarity restraints: 866
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 513 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   MET A 513 "    0.055 2.00e-02 2.50e+03
        pdb=" O   MET A 513 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   VAL A 514 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 345 "   -0.046 5.00e-02 4.00e+02   7.07e-02 8.00e+00
        pdb=" N   PRO A 346 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 512 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.50e+00
        pdb=" C   PHE A 512 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   PHE A 512 "    0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 513 "    0.014 2.00e-02 2.50e+03
  ... (remaining 863 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1753
        2.83 -     3.35: 5757
        3.35 -     3.87: 8386
        3.87 -     4.38: 9728
        4.38 -     4.90: 15442
  Nonbonded interactions: 41066
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 242 "
            pdb=" OG1 THR A 243 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OH  TYR A  78 "
            pdb=" O   LEU A 573 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" O   GLU A 339 "
            pdb=" OE1 GLN A 343 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" O   TYR A 391 "
            pdb=" OG1 THR A 392 "
     model   vdw
     2.434 3.040
  nonbonded pdb=" O   GLU A 242 "
            pdb=" OE2 GLU A 245 "
     model   vdw
     2.436 3.040
  ... (remaining 41061 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.450
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6629
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      :  0.003   0.035   5294  Z= 0.166
  Angle     :  1.061  29.067   7200  Z= 0.463
  Chirality :  0.095   1.784    830
  Planarity :  0.006   0.071    866
  Dihedral  : 18.738 174.522   1985
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.12 %
    Favored  : 85.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -2.52 (0.33), residues: 616
  helix: -0.22 (0.26), residues: 384
  sheet: -6.64 (0.64), residues: 7
  loop : -4.22 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 689 
 TYR   0.012   0.002   TYR A  31 
 PHE   0.017   0.001   PHE A 512 
 TRP   0.007   0.001   TRP A 419 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5294)
  covalent geometry    : angle       1.06115 ( 7200)
  hydrogen bonds       : bond        0.09954 (  301)
  hydrogen bonds       : angle       7.19860 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.8718 (m90) cc_final: 0.8259 (m90)
REVERT: A  185 ASN cc_start: 0.8886 (m-40) cc_final: 0.7813 (p0)
REVERT: A  190 ASN cc_start: 0.7341 (m110) cc_final: 0.6239 (m110)
REVERT: A  193 LEU cc_start: 0.8874 (mt) cc_final: 0.8535 (mt)
REVERT: A  220 TYR cc_start: 0.7296 (p90) cc_final: 0.7018 (p90)
REVERT: A  255 CYS cc_start: 0.7686 (p) cc_final: 0.7214 (p)
REVERT: A  262 LEU cc_start: 0.8182 (pt) cc_final: 0.7886 (pt)
REVERT: A  271 TYR cc_start: 0.8280 (t80) cc_final: 0.7956 (t80)
REVERT: A  273 CYS cc_start: 0.9513 (p) cc_final: 0.9251 (p)
REVERT: A  340 ARG cc_start: 0.9447 (mmt180) cc_final: 0.8816 (ptt180)
REVERT: A  349 MET cc_start: 0.9230 (ppp) cc_final: 0.8952 (ppp)
REVERT: A  352 VAL cc_start: 0.8127 (t) cc_final: 0.7871 (p)
REVERT: A  363 ILE cc_start: 0.9135 (mm) cc_final: 0.8877 (mm)
REVERT: A  367 PHE cc_start: 0.8487 (m-80) cc_final: 0.8284 (m-80)
REVERT: A  489 LEU cc_start: 0.8679 (mt) cc_final: 0.8476 (mt)
REVERT: A  490 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7536 (mt-10)
REVERT: A  499 ASN cc_start: 0.9218 (m110) cc_final: 0.8861 (m110)
REVERT: A  502 MET cc_start: 0.9127 (mtp) cc_final: 0.8591 (mmt)
REVERT: A  534 ASP cc_start: 0.8779 (t0) cc_final: 0.8562 (m-30)
REVERT: A  548 PHE cc_start: 0.7972 (t80) cc_final: 0.7259 (t80)
REVERT: A  570 MET cc_start: 0.8609 (mmm) cc_final: 0.8119 (mmm)
REVERT: A  578 LEU cc_start: 0.8581 (tp) cc_final: 0.8354 (tp)
REVERT: A  587 MET cc_start: 0.8109 (mmt) cc_final: 0.7804 (mmp)
REVERT: A  598 LYS cc_start: 0.8767 (pttt) cc_final: 0.8442 (pttm)
REVERT: A  677 LEU cc_start: 0.8868 (mt) cc_final: 0.8584 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.0511
  time to fit residues: 15.4302
Evaluate side-chains
  198 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0050
   chunk 26 optimal weight:    0.0980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0060
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.4214

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
A 604 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.160745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.116022 restraints weight = 9616.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122327 restraints weight = 5459.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.126818 restraints weight = 3649.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.130020 restraints weight = 2700.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.132225 restraints weight = 2146.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5294  Z= 0.154
  Angle     :  1.103  31.115   7200  Z= 0.459
  Chirality :  0.099   1.849    830
  Planarity :  0.005   0.074    866
  Dihedral  : 20.362 173.783    805
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.99 %
    Favored  : 87.01 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.74 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -2.10 (0.34), residues: 616
  helix:  0.06 (0.26), residues: 390
  sheet: -5.67 (1.26), residues: 5
  loop : -4.09 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  18 
 TYR   0.023   0.002   TYR A 286 
 PHE   0.011   0.001   PHE A 512 
 TRP   0.008   0.001   TRP A 681 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5294)
  covalent geometry    : angle       1.10274 ( 7200)
  hydrogen bonds       : bond        0.04858 (  301)
  hydrogen bonds       : angle       6.10296 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.8758 (m-40) cc_final: 0.7783 (p0)
REVERT: A  190 ASN cc_start: 0.7740 (m110) cc_final: 0.6910 (m110)
REVERT: A  193 LEU cc_start: 0.8985 (mt) cc_final: 0.8692 (mt)
REVERT: A  255 CYS cc_start: 0.7697 (p) cc_final: 0.7269 (p)
REVERT: A  271 TYR cc_start: 0.8244 (t80) cc_final: 0.7849 (t80)
REVERT: A  273 CYS cc_start: 0.9505 (p) cc_final: 0.9089 (p)
REVERT: A  277 LYS cc_start: 0.9576 (tppt) cc_final: 0.9191 (tmtt)
REVERT: A  340 ARG cc_start: 0.9250 (mmt180) cc_final: 0.8795 (ptt180)
REVERT: A  349 MET cc_start: 0.9106 (ppp) cc_final: 0.8856 (ppp)
REVERT: A  352 VAL cc_start: 0.8255 (t) cc_final: 0.7996 (p)
REVERT: A  405 ASP cc_start: 0.8360 (t70) cc_final: 0.8109 (t70)
REVERT: A  446 MET cc_start: 0.8576 (ptp) cc_final: 0.8192 (ptp)
REVERT: A  489 LEU cc_start: 0.8758 (mt) cc_final: 0.8541 (mt)
REVERT: A  490 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7604 (mt-10)
REVERT: A  499 ASN cc_start: 0.9282 (m110) cc_final: 0.8988 (m110)
REVERT: A  502 MET cc_start: 0.9209 (mtp) cc_final: 0.8735 (mtp)
REVERT: A  534 ASP cc_start: 0.8863 (t0) cc_final: 0.8655 (m-30)
REVERT: A  548 PHE cc_start: 0.7857 (t80) cc_final: 0.7241 (t80)
REVERT: A  570 MET cc_start: 0.8818 (mmm) cc_final: 0.8241 (mmm)
REVERT: A  572 LEU cc_start: 0.9315 (tt) cc_final: 0.9086 (tt)
REVERT: A  598 LYS cc_start: 0.8778 (pttt) cc_final: 0.8550 (pttp)
  outliers start: 1
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0535
  time to fit residues: 16.0755
Evaluate side-chains
  202 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 29 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 143 GLN
A 604 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.159595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.114250 restraints weight = 9942.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.120067 restraints weight = 5725.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.124325 restraints weight = 3892.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.127394 restraints weight = 2937.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.129492 restraints weight = 2373.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5294  Z= 0.161
  Angle     :  1.099  31.366   7200  Z= 0.457
  Chirality :  0.096   1.789    830
  Planarity :  0.006   0.066    866
  Dihedral  : 20.317 177.688    805
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.28 %
    Favored  : 95.54 %
  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: -1.92 (0.34), residues: 616
  helix:  0.17 (0.26), residues: 393
  sheet: -5.74 (1.36), residues: 7
  loop : -3.98 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 574 
 TYR   0.021   0.002   TYR A 286 
 PHE   0.014   0.001   PHE A  68 
 TRP   0.006   0.001   TRP A 419 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 5294)
  covalent geometry    : angle       1.09860 ( 7200)
  hydrogen bonds       : bond        0.04612 (  301)
  hydrogen bonds       : angle       5.78851 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.8772 (m-40) cc_final: 0.7848 (p0)
REVERT: A  186 LEU cc_start: 0.8175 (tt) cc_final: 0.7542 (tt)
REVERT: A  190 ASN cc_start: 0.7843 (m110) cc_final: 0.7037 (m110)
REVERT: A  193 LEU cc_start: 0.8974 (mt) cc_final: 0.8735 (mt)
REVERT: A  255 CYS cc_start: 0.7741 (p) cc_final: 0.7298 (p)
REVERT: A  262 LEU cc_start: 0.8163 (pt) cc_final: 0.7946 (pt)
REVERT: A  271 TYR cc_start: 0.8179 (t80) cc_final: 0.7800 (t80)
REVERT: A  273 CYS cc_start: 0.9480 (p) cc_final: 0.9150 (p)
REVERT: A  340 ARG cc_start: 0.9354 (mmt180) cc_final: 0.8944 (ptt180)
REVERT: A  349 MET cc_start: 0.9005 (ppp) cc_final: 0.8792 (ppp)
REVERT: A  367 PHE cc_start: 0.8540 (m-80) cc_final: 0.8307 (m-80)
REVERT: A  405 ASP cc_start: 0.8356 (t70) cc_final: 0.8097 (t70)
REVERT: A  446 MET cc_start: 0.8519 (ptp) cc_final: 0.8183 (ptp)
REVERT: A  487 THR cc_start: 0.9229 (m) cc_final: 0.8713 (m)
REVERT: A  489 LEU cc_start: 0.8765 (mt) cc_final: 0.8562 (mt)
REVERT: A  490 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: A  499 ASN cc_start: 0.9285 (m110) cc_final: 0.8930 (m110)
REVERT: A  502 MET cc_start: 0.9284 (mtp) cc_final: 0.8463 (mmt)
REVERT: A  548 PHE cc_start: 0.7799 (t80) cc_final: 0.7302 (t80)
REVERT: A  568 ASN cc_start: 0.9069 (m110) cc_final: 0.8772 (m110)
REVERT: A  570 MET cc_start: 0.8873 (mmm) cc_final: 0.8331 (mmm)
REVERT: A  578 LEU cc_start: 0.8363 (tp) cc_final: 0.8130 (tp)
REVERT: A  598 LYS cc_start: 0.8777 (pttt) cc_final: 0.8524 (pttp)
REVERT: A  621 ILE cc_start: 0.9287 (mt) cc_final: 0.9056 (mt)
REVERT: A  625 SER cc_start: 0.9356 (p) cc_final: 0.9144 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0502
  time to fit residues: 14.7948
Evaluate side-chains
  187 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN
A 568 ASN
** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.154022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.108374 restraints weight = 9978.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113904 restraints weight = 5669.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.117863 restraints weight = 3856.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.120848 restraints weight = 2927.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.122779 restraints weight = 2378.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090   5294  Z= 0.252
  Angle     :  1.160  32.088   7200  Z= 0.498
  Chirality :  0.097   1.749    830
  Planarity :  0.006   0.064    866
  Dihedral  : 20.448 179.981    805
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.77 %
    Favored  : 85.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  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: -1.92 (0.33), residues: 616
  helix:  0.17 (0.25), residues: 391
  sheet: -6.06 (1.45), residues: 7
  loop : -3.93 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 574 
 TYR   0.024   0.002   TYR A 611 
 PHE   0.019   0.002   PHE A 512 
 TRP   0.035   0.002   TRP A 681 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 5294)
  covalent geometry    : angle       1.16003 ( 7200)
  hydrogen bonds       : bond        0.05224 (  301)
  hydrogen bonds       : angle       5.79412 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.8812 (m-40) cc_final: 0.8117 (p0)
REVERT: A  186 LEU cc_start: 0.8302 (tt) cc_final: 0.7723 (tp)
REVERT: A  190 ASN cc_start: 0.7848 (m110) cc_final: 0.6833 (m110)
REVERT: A  255 CYS cc_start: 0.7782 (p) cc_final: 0.7318 (p)
REVERT: A  265 ASN cc_start: 0.8484 (m110) cc_final: 0.8117 (m110)
REVERT: A  271 TYR cc_start: 0.8232 (t80) cc_final: 0.7862 (t80)
REVERT: A  273 CYS cc_start: 0.9468 (p) cc_final: 0.9141 (p)
REVERT: A  277 LYS cc_start: 0.9531 (tppt) cc_final: 0.9100 (tmtt)
REVERT: A  340 ARG cc_start: 0.9350 (mmt180) cc_final: 0.8929 (pmt170)
REVERT: A  349 MET cc_start: 0.9029 (ppp) cc_final: 0.8755 (ppp)
REVERT: A  367 PHE cc_start: 0.8634 (m-10) cc_final: 0.8397 (m-80)
REVERT: A  405 ASP cc_start: 0.8354 (t70) cc_final: 0.8120 (t70)
REVERT: A  416 LEU cc_start: 0.9023 (tp) cc_final: 0.8814 (tp)
REVERT: A  446 MET cc_start: 0.8700 (ptp) cc_final: 0.8305 (ptp)
REVERT: A  487 THR cc_start: 0.9288 (m) cc_final: 0.8758 (m)
REVERT: A  489 LEU cc_start: 0.8900 (mt) cc_final: 0.8688 (mt)
REVERT: A  490 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7742 (mt-10)
REVERT: A  499 ASN cc_start: 0.9342 (m110) cc_final: 0.8969 (m110)
REVERT: A  502 MET cc_start: 0.9296 (mtp) cc_final: 0.8611 (mmt)
REVERT: A  513 MET cc_start: 0.8370 (ttm) cc_final: 0.7866 (tmm)
REVERT: A  517 LEU cc_start: 0.9128 (mm) cc_final: 0.8918 (mm)
REVERT: A  533 PHE cc_start: 0.8657 (t80) cc_final: 0.8335 (t80)
REVERT: A  534 ASP cc_start: 0.9111 (m-30) cc_final: 0.8693 (m-30)
REVERT: A  541 SER cc_start: 0.8643 (m) cc_final: 0.8427 (m)
REVERT: A  548 PHE cc_start: 0.8763 (t80) cc_final: 0.8321 (t80)
REVERT: A  570 MET cc_start: 0.8931 (mmm) cc_final: 0.8370 (mmm)
REVERT: A  598 LYS cc_start: 0.8663 (pttt) cc_final: 0.8409 (pttm)
REVERT: A  679 LEU cc_start: 0.8431 (mt) cc_final: 0.8224 (mt)
REVERT: A  692 MET cc_start: 0.9427 (ppp) cc_final: 0.9078 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0508
  time to fit residues: 14.5334
Evaluate side-chains
  173 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 44 optimal weight:    0.0570
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 19 optimal weight:   30.0000
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 714 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.162491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116331 restraints weight = 9590.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122735 restraints weight = 5284.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.127245 restraints weight = 3500.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.130464 restraints weight = 2586.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.132802 restraints weight = 2055.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.3706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5294  Z= 0.152
  Angle     :  1.101  30.870   7200  Z= 0.456
  Chirality :  0.099   1.810    830
  Planarity :  0.005   0.063    866
  Dihedral  : 20.274 175.477    805
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.01 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  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: -1.65 (0.34), residues: 616
  helix:  0.36 (0.26), residues: 393
  sheet:  None (None), residues: 0
  loop : -3.92 (0.37), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 334 
 TYR   0.023   0.002   TYR A 286 
 PHE   0.015   0.001   PHE A 434 
 TRP   0.032   0.002   TRP A 681 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5294)
  covalent geometry    : angle       1.10126 ( 7200)
  hydrogen bonds       : bond        0.04396 (  301)
  hydrogen bonds       : angle       5.40499 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.8735 (m90) cc_final: 0.8185 (m90)
REVERT: A  185 ASN cc_start: 0.8774 (m-40) cc_final: 0.8001 (p0)
REVERT: A  190 ASN cc_start: 0.7853 (m110) cc_final: 0.6933 (m110)
REVERT: A  255 CYS cc_start: 0.7898 (p) cc_final: 0.7478 (p)
REVERT: A  271 TYR cc_start: 0.8121 (t80) cc_final: 0.7731 (t80)
REVERT: A  273 CYS cc_start: 0.9479 (p) cc_final: 0.9218 (p)
REVERT: A  277 LYS cc_start: 0.9516 (tppt) cc_final: 0.9127 (tmtt)
REVERT: A  340 ARG cc_start: 0.9347 (mmt180) cc_final: 0.8930 (ptt180)
REVERT: A  367 PHE cc_start: 0.8619 (m-10) cc_final: 0.8396 (m-80)
REVERT: A  405 ASP cc_start: 0.8293 (t70) cc_final: 0.8031 (t70)
REVERT: A  410 ASN cc_start: 0.9386 (m-40) cc_final: 0.9128 (m-40)
REVERT: A  446 MET cc_start: 0.8492 (ptp) cc_final: 0.8157 (ptp)
REVERT: A  479 LEU cc_start: 0.9459 (mp) cc_final: 0.9237 (mp)
REVERT: A  487 THR cc_start: 0.9292 (m) cc_final: 0.8760 (m)
REVERT: A  489 LEU cc_start: 0.8901 (mt) cc_final: 0.8691 (mt)
REVERT: A  490 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7577 (mt-10)
REVERT: A  493 TRP cc_start: 0.6391 (m-10) cc_final: 0.6140 (m-90)
REVERT: A  499 ASN cc_start: 0.9300 (m110) cc_final: 0.8981 (m110)
REVERT: A  502 MET cc_start: 0.9188 (mtp) cc_final: 0.8408 (mmt)
REVERT: A  510 LEU cc_start: 0.9156 (mm) cc_final: 0.8955 (mm)
REVERT: A  513 MET cc_start: 0.8130 (ttm) cc_final: 0.7769 (tmm)
REVERT: A  533 PHE cc_start: 0.8578 (t80) cc_final: 0.8165 (t80)
REVERT: A  534 ASP cc_start: 0.9030 (m-30) cc_final: 0.8587 (m-30)
REVERT: A  539 GLU cc_start: 0.7935 (tp30) cc_final: 0.7583 (pt0)
REVERT: A  548 PHE cc_start: 0.8437 (t80) cc_final: 0.7929 (t80)
REVERT: A  568 ASN cc_start: 0.9239 (m-40) cc_final: 0.8968 (m-40)
REVERT: A  570 MET cc_start: 0.8784 (mmm) cc_final: 0.8316 (mmp)
REVERT: A  578 LEU cc_start: 0.8351 (tp) cc_final: 0.8124 (tp)
REVERT: A  598 LYS cc_start: 0.8591 (pttt) cc_final: 0.8342 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0466
  time to fit residues: 13.8790
Evaluate side-chains
  187 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   chunk 29 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 ASN
A 649 ASN
A 714 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.163104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.116823 restraints weight = 9711.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.123053 restraints weight = 5410.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.127550 restraints weight = 3634.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.130658 restraints weight = 2717.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.132763 restraints weight = 2183.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5294  Z= 0.157
  Angle     :  1.116  30.943   7200  Z= 0.462
  Chirality :  0.098   1.809    830
  Planarity :  0.005   0.064    866
  Dihedral  : 20.257 176.704    805
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.15 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  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: -1.61 (0.34), residues: 616
  helix:  0.40 (0.26), residues: 393
  sheet: -5.42 (1.75), residues: 8
  loop : -3.82 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 334 
 TYR   0.021   0.002   TYR A 286 
 PHE   0.015   0.001   PHE A 607 
 TRP   0.033   0.002   TRP A 681 
 HIS   0.003   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5294)
  covalent geometry    : angle       1.11568 ( 7200)
  hydrogen bonds       : bond        0.04405 (  301)
  hydrogen bonds       : angle       5.38202 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ASP cc_start: 0.7833 (p0) cc_final: 0.7558 (p0)
REVERT: A  185 ASN cc_start: 0.8770 (m-40) cc_final: 0.8146 (p0)
REVERT: A  186 LEU cc_start: 0.8468 (tt) cc_final: 0.7844 (tp)
REVERT: A  190 ASN cc_start: 0.7572 (m110) cc_final: 0.6782 (m110)
REVERT: A  193 LEU cc_start: 0.8928 (mm) cc_final: 0.8594 (mp)
REVERT: A  216 GLN cc_start: 0.9379 (tp-100) cc_final: 0.9043 (tm-30)
REVERT: A  255 CYS cc_start: 0.7901 (p) cc_final: 0.7470 (p)
REVERT: A  271 TYR cc_start: 0.8150 (t80) cc_final: 0.7766 (t80)
REVERT: A  349 MET cc_start: 0.8638 (ppp) cc_final: 0.8365 (ppp)
REVERT: A  368 ASN cc_start: 0.9574 (m110) cc_final: 0.9211 (p0)
REVERT: A  405 ASP cc_start: 0.8228 (t70) cc_final: 0.7984 (t70)
REVERT: A  410 ASN cc_start: 0.9427 (m-40) cc_final: 0.9192 (m-40)
REVERT: A  446 MET cc_start: 0.8512 (ptp) cc_final: 0.8144 (ptp)
REVERT: A  479 LEU cc_start: 0.9462 (mp) cc_final: 0.9250 (mp)
REVERT: A  487 THR cc_start: 0.9282 (m) cc_final: 0.8736 (m)
REVERT: A  489 LEU cc_start: 0.8922 (mt) cc_final: 0.8715 (mt)
REVERT: A  490 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7515 (mt-10)
REVERT: A  493 TRP cc_start: 0.6411 (m-10) cc_final: 0.6122 (m-90)
REVERT: A  499 ASN cc_start: 0.9334 (m110) cc_final: 0.9009 (m110)
REVERT: A  502 MET cc_start: 0.9170 (mtp) cc_final: 0.8389 (mmt)
REVERT: A  513 MET cc_start: 0.8161 (ttm) cc_final: 0.7668 (tmm)
REVERT: A  533 PHE cc_start: 0.8738 (t80) cc_final: 0.8364 (t80)
REVERT: A  534 ASP cc_start: 0.9061 (m-30) cc_final: 0.8583 (m-30)
REVERT: A  539 GLU cc_start: 0.7999 (tp30) cc_final: 0.7664 (pt0)
REVERT: A  548 PHE cc_start: 0.8513 (t80) cc_final: 0.8014 (t80)
REVERT: A  568 ASN cc_start: 0.9213 (m-40) cc_final: 0.8947 (m-40)
REVERT: A  570 MET cc_start: 0.8769 (mmm) cc_final: 0.8328 (mmp)
REVERT: A  578 LEU cc_start: 0.8370 (tp) cc_final: 0.8125 (tp)
REVERT: A  598 LYS cc_start: 0.8560 (pttt) cc_final: 0.8346 (pttp)
REVERT: A  692 MET cc_start: 0.9517 (ppp) cc_final: 0.9017 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.0486
  time to fit residues: 14.4528
Evaluate side-chains
  190 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 345 GLN
A 714 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.157869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112632 restraints weight = 10424.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.118412 restraints weight = 5952.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122395 restraints weight = 4058.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.125157 restraints weight = 3073.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.127351 restraints weight = 2513.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   5294  Z= 0.196
  Angle     :  1.146  30.980   7200  Z= 0.482
  Chirality :  0.098   1.792    830
  Planarity :  0.005   0.062    866
  Dihedral  : 20.280 177.669    805
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.33), residues: 616
  helix:  0.40 (0.26), residues: 389
  sheet: -5.42 (1.72), residues: 8
  loop : -3.86 (0.36), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.019   0.002   TYR A 286 
 PHE   0.015   0.001   PHE A 512 
 TRP   0.034   0.002   TRP A 681 
 HIS   0.002   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 5294)
  covalent geometry    : angle       1.14637 ( 7200)
  hydrogen bonds       : bond        0.04598 (  301)
  hydrogen bonds       : angle       5.37829 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.8736 (m-40) cc_final: 0.8094 (p0)
REVERT: A  186 LEU cc_start: 0.8553 (tt) cc_final: 0.7990 (tp)
REVERT: A  190 ASN cc_start: 0.7524 (m110) cc_final: 0.6590 (m110)
REVERT: A  193 LEU cc_start: 0.9021 (mm) cc_final: 0.8820 (mm)
REVERT: A  216 GLN cc_start: 0.9408 (tp-100) cc_final: 0.9086 (tm-30)
REVERT: A  271 TYR cc_start: 0.8210 (t80) cc_final: 0.7756 (t80)
REVERT: A  340 ARG cc_start: 0.9107 (mmm160) cc_final: 0.8779 (ptt180)
REVERT: A  349 MET cc_start: 0.8621 (ppp) cc_final: 0.8395 (ppp)
REVERT: A  405 ASP cc_start: 0.8318 (t70) cc_final: 0.8073 (t70)
REVERT: A  410 ASN cc_start: 0.9471 (m-40) cc_final: 0.9214 (m110)
REVERT: A  487 THR cc_start: 0.9271 (m) cc_final: 0.8738 (m)
REVERT: A  489 LEU cc_start: 0.8966 (mt) cc_final: 0.8756 (mt)
REVERT: A  490 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7625 (mt-10)
REVERT: A  499 ASN cc_start: 0.9416 (m110) cc_final: 0.9085 (m110)
REVERT: A  502 MET cc_start: 0.9199 (mtp) cc_final: 0.8482 (mmt)
REVERT: A  513 MET cc_start: 0.8221 (ttm) cc_final: 0.7725 (tmm)
REVERT: A  533 PHE cc_start: 0.8828 (t80) cc_final: 0.8513 (t80)
REVERT: A  534 ASP cc_start: 0.9066 (m-30) cc_final: 0.8471 (m-30)
REVERT: A  539 GLU cc_start: 0.7999 (tp30) cc_final: 0.7696 (pt0)
REVERT: A  548 PHE cc_start: 0.8611 (t80) cc_final: 0.8119 (t80)
REVERT: A  568 ASN cc_start: 0.9293 (m-40) cc_final: 0.9088 (m-40)
REVERT: A  570 MET cc_start: 0.8843 (mmm) cc_final: 0.8422 (mmp)
REVERT: A  598 LYS cc_start: 0.8609 (pttt) cc_final: 0.8383 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0528
  time to fit residues: 15.2522
Evaluate side-chains
  183 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 714 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.159707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.114852 restraints weight = 10340.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.120911 restraints weight = 5876.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.125018 restraints weight = 3979.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.127980 restraints weight = 2991.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.130097 restraints weight = 2414.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   5294  Z= 0.180
  Angle     :  1.153  30.931   7200  Z= 0.482
  Chirality :  0.099   1.802    830
  Planarity :  0.005   0.063    866
  Dihedral  : 20.246 176.837    805
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  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: -1.64 (0.33), residues: 616
  helix:  0.41 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop : -3.92 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 574 
 TYR   0.017   0.002   TYR A  78 
 PHE   0.025   0.002   PHE A 685 
 TRP   0.041   0.002   TRP A 681 
 HIS   0.003   0.001   HIS A 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 5294)
  covalent geometry    : angle       1.15312 ( 7200)
  hydrogen bonds       : bond        0.04646 (  301)
  hydrogen bonds       : angle       5.35118 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 THR cc_start: 0.9395 (p) cc_final: 0.9165 (t)
REVERT: A  185 ASN cc_start: 0.8778 (m-40) cc_final: 0.8142 (p0)
REVERT: A  186 LEU cc_start: 0.8540 (tt) cc_final: 0.8002 (tp)
REVERT: A  190 ASN cc_start: 0.7506 (m110) cc_final: 0.6525 (m110)
REVERT: A  216 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9108 (tm-30)
REVERT: A  271 TYR cc_start: 0.8204 (t80) cc_final: 0.7784 (t80)
REVERT: A  340 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8747 (ptt180)
REVERT: A  367 PHE cc_start: 0.8527 (m-80) cc_final: 0.8222 (m-80)
REVERT: A  368 ASN cc_start: 0.9591 (m110) cc_final: 0.9220 (p0)
REVERT: A  405 ASP cc_start: 0.8272 (t70) cc_final: 0.8018 (t70)
REVERT: A  446 MET cc_start: 0.8166 (ptm) cc_final: 0.7922 (ptm)
REVERT: A  487 THR cc_start: 0.9291 (m) cc_final: 0.8725 (m)
REVERT: A  490 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7544 (mt-10)
REVERT: A  499 ASN cc_start: 0.9432 (m110) cc_final: 0.9052 (m110)
REVERT: A  502 MET cc_start: 0.9132 (mtp) cc_final: 0.8360 (mmt)
REVERT: A  510 LEU cc_start: 0.9165 (mm) cc_final: 0.8959 (mm)
REVERT: A  513 MET cc_start: 0.8224 (ttm) cc_final: 0.7715 (tmm)
REVERT: A  533 PHE cc_start: 0.8878 (t80) cc_final: 0.8554 (t80)
REVERT: A  534 ASP cc_start: 0.8927 (m-30) cc_final: 0.8450 (m-30)
REVERT: A  539 GLU cc_start: 0.8115 (tp30) cc_final: 0.7807 (pt0)
REVERT: A  548 PHE cc_start: 0.8495 (t80) cc_final: 0.8024 (t80)
REVERT: A  568 ASN cc_start: 0.9222 (m-40) cc_final: 0.9012 (m-40)
REVERT: A  570 MET cc_start: 0.8767 (mmm) cc_final: 0.8358 (mmp)
REVERT: A  598 LYS cc_start: 0.8559 (pttt) cc_final: 0.8341 (pttp)
REVERT: A  658 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8503 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0527
  time to fit residues: 14.7927
Evaluate side-chains
  188 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 20 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 714 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.161502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.117714 restraints weight = 9658.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.123769 restraints weight = 5428.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.128137 restraints weight = 3643.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.131291 restraints weight = 2716.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.133151 restraints weight = 2166.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.5241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   5294  Z= 0.160
  Angle     :  1.151  30.447   7200  Z= 0.480
  Chirality :  0.100   1.818    830
  Planarity :  0.005   0.062    866
  Dihedral  : 20.183 175.526    805
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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 (0.33), residues: 616
  helix:  0.54 (0.26), residues: 389
  sheet:  None (None), residues: 0
  loop : -3.91 (0.35), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 334 
 TYR   0.016   0.002   TYR A  78 
 PHE   0.022   0.001   PHE A 434 
 TRP   0.037   0.002   TRP A 681 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5294)
  covalent geometry    : angle       1.15077 ( 7200)
  hydrogen bonds       : bond        0.04503 (  301)
  hydrogen bonds       : angle       5.25769 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.8741 (m-40) cc_final: 0.8118 (p0)
REVERT: A  186 LEU cc_start: 0.8579 (tt) cc_final: 0.8036 (tp)
REVERT: A  190 ASN cc_start: 0.7380 (m110) cc_final: 0.6414 (m110)
REVERT: A  216 GLN cc_start: 0.9426 (tp-100) cc_final: 0.9090 (tm-30)
REVERT: A  271 TYR cc_start: 0.8154 (t80) cc_final: 0.7736 (t80)
REVERT: A  340 ARG cc_start: 0.9084 (mmm160) cc_final: 0.8746 (ptt180)
REVERT: A  367 PHE cc_start: 0.8524 (m-80) cc_final: 0.8238 (m-80)
REVERT: A  368 ASN cc_start: 0.9605 (m110) cc_final: 0.9207 (p0)
REVERT: A  405 ASP cc_start: 0.8233 (t70) cc_final: 0.7990 (t70)
REVERT: A  410 ASN cc_start: 0.9357 (m110) cc_final: 0.8956 (m110)
REVERT: A  490 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7456 (mt-10)
REVERT: A  493 TRP cc_start: 0.6149 (m-10) cc_final: 0.5911 (m-90)
REVERT: A  499 ASN cc_start: 0.9414 (m110) cc_final: 0.8802 (m110)
REVERT: A  502 MET cc_start: 0.9109 (mtp) cc_final: 0.8326 (mmt)
REVERT: A  503 MET cc_start: 0.9398 (ptp) cc_final: 0.8721 (ptp)
REVERT: A  513 MET cc_start: 0.8137 (ttm) cc_final: 0.7601 (tmm)
REVERT: A  533 PHE cc_start: 0.8796 (t80) cc_final: 0.8536 (t80)
REVERT: A  534 ASP cc_start: 0.8943 (m-30) cc_final: 0.8587 (m-30)
REVERT: A  539 GLU cc_start: 0.8117 (tp30) cc_final: 0.7802 (pt0)
REVERT: A  548 PHE cc_start: 0.8572 (t80) cc_final: 0.8109 (t80)
REVERT: A  570 MET cc_start: 0.8714 (mmm) cc_final: 0.8318 (mmp)
REVERT: A  596 ASN cc_start: 0.9496 (m110) cc_final: 0.9277 (m110)
REVERT: A  598 LYS cc_start: 0.8609 (pttt) cc_final: 0.8376 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0515
  time to fit residues: 14.4972
Evaluate side-chains
  187 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 58 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 714 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.162881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.117315 restraints weight = 9831.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.123489 restraints weight = 5612.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.127874 restraints weight = 3795.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.131124 restraints weight = 2849.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.133432 restraints weight = 2280.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.5561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5294  Z= 0.157
  Angle     :  1.152  30.338   7200  Z= 0.482
  Chirality :  0.100   1.825    830
  Planarity :  0.005   0.071    866
  Dihedral  : 20.156 175.303    805
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 11.69 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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: -1.45 (0.33), residues: 616
  helix:  0.56 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop : -3.84 (0.36), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 334 
 TYR   0.031   0.002   TYR A  78 
 PHE   0.023   0.001   PHE A 699 
 TRP   0.075   0.002   TRP A 681 
 HIS   0.003   0.001   HIS A 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5294)
  covalent geometry    : angle       1.15232 ( 7200)
  hydrogen bonds       : bond        0.04488 (  301)
  hydrogen bonds       : angle       5.27448 (  903)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 SER cc_start: 0.9144 (t) cc_final: 0.8924 (p)
REVERT: A  164 VAL cc_start: 0.9379 (t) cc_final: 0.9167 (t)
REVERT: A  177 SER cc_start: 0.8879 (t) cc_final: 0.8587 (p)
REVERT: A  185 ASN cc_start: 0.8777 (m-40) cc_final: 0.8093 (p0)
REVERT: A  186 LEU cc_start: 0.8563 (tt) cc_final: 0.7974 (tp)
REVERT: A  190 ASN cc_start: 0.7317 (m110) cc_final: 0.6571 (m110)
REVERT: A  216 GLN cc_start: 0.9436 (tp-100) cc_final: 0.8922 (tm-30)
REVERT: A  255 CYS cc_start: 0.7859 (p) cc_final: 0.7448 (p)
REVERT: A  340 ARG cc_start: 0.9057 (mmm160) cc_final: 0.8733 (ptt180)
REVERT: A  367 PHE cc_start: 0.8520 (m-80) cc_final: 0.8229 (m-80)
REVERT: A  368 ASN cc_start: 0.9605 (m110) cc_final: 0.9198 (p0)
REVERT: A  405 ASP cc_start: 0.8259 (t70) cc_final: 0.8019 (t70)
REVERT: A  410 ASN cc_start: 0.9317 (m110) cc_final: 0.8926 (m110)
REVERT: A  490 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7576 (mt-10)
REVERT: A  493 TRP cc_start: 0.6161 (m-10) cc_final: 0.5948 (m-90)
REVERT: A  499 ASN cc_start: 0.9425 (m110) cc_final: 0.9030 (m110)
REVERT: A  502 MET cc_start: 0.9043 (mtp) cc_final: 0.8212 (mmt)
REVERT: A  534 ASP cc_start: 0.8889 (m-30) cc_final: 0.8429 (m-30)
REVERT: A  539 GLU cc_start: 0.8070 (tp30) cc_final: 0.7816 (pt0)
REVERT: A  548 PHE cc_start: 0.8364 (t80) cc_final: 0.7912 (t80)
REVERT: A  570 MET cc_start: 0.8681 (mmm) cc_final: 0.8255 (mmp)
REVERT: A  596 ASN cc_start: 0.9494 (m110) cc_final: 0.9241 (m110)
REVERT: A  598 LYS cc_start: 0.8641 (pttt) cc_final: 0.8431 (pttp)
REVERT: A  599 GLN cc_start: 0.7917 (mt0) cc_final: 0.7091 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0495
  time to fit residues: 14.7292
Evaluate side-chains
  182 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
A 714 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.164405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.119041 restraints weight = 9903.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.125392 restraints weight = 5598.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.129890 restraints weight = 3758.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.133075 restraints weight = 2794.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135450 restraints weight = 2237.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.5789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   5294  Z= 0.156
  Angle     :  1.152  30.204   7200  Z= 0.483
  Chirality :  0.100   1.827    830
  Planarity :  0.005   0.061    866
  Dihedral  : 20.151 175.285    805
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 11.36 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -1.22 (0.34), residues: 616
  helix:  0.71 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -3.73 (0.37), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 334 
 TYR   0.023   0.002   TYR A 176 
 PHE   0.020   0.001   PHE A 685 
 TRP   0.026   0.002   TRP A 681 
 HIS   0.002   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5294)
  covalent geometry    : angle       1.15192 ( 7200)
  hydrogen bonds       : bond        0.04312 (  301)
  hydrogen bonds       : angle       5.22211 (  903)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1001.04 seconds
wall clock time: 17 minutes 58.15 seconds (1078.15 seconds total)