Starting phenix.real_space_refine
on Fri Aug 22 14:11:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xoo_33354/08_2025/7xoo_33354.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xoo_33354/08_2025/7xoo_33354.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xoo_33354/08_2025/7xoo_33354.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xoo_33354/08_2025/7xoo_33354.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xoo_33354/08_2025/7xoo_33354.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xoo_33354/08_2025/7xoo_33354.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      20      5.16       5
     C    2397      2.51       5
     N     665      2.21       5
     O     773      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3855
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
  Time building chain proxies: 1.25, per 1000 atoms: 0.32
  Number of scatterers: 3855
  At special positions: 0
  Unit cell: (69.6, 73.95, 85.26, 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      20     16.00
     O     773      8.00
     N     665      7.00
     C    2397      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: 0.29
  Conformation dependent library (CDL) restraints added in 128.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  948

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 7 sheets defined
      59.4% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 29
      removed outlier: 4.116A  pdb=" N   VAL B  29 " --> pdb=" O   ASP B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 64 through 86
    Processing helix  chain 'B' and resid 88 through 109
    Processing helix  chain 'B' and resid 112 through 135
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 155 through 170
      removed outlier: 3.598A  pdb=" N   GLY B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 205
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 256 through 268
    Processing helix  chain 'B' and resid 282 through 297
    Processing helix  chain 'B' and resid 338 through 355
      removed outlier: 3.812A  pdb=" N   ILE B 342 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 375
      removed outlier: 4.218A  pdb=" N   GLY B 375 " --> pdb=" O   LYS B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 409
    Processing helix  chain 'B' and resid 416 through 427
    Processing helix  chain 'B' and resid 433 through 459
      Proline residue:  B 450  - end of helix
    Processing helix  chain 'B' and resid 461 through 472
    Processing helix  chain 'B' and resid 488 through 492
    Processing helix  chain 'B' and resid 497 through 516
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 8
    Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40
    Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 179
      removed outlier: 6.423A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ILE B 379 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   THR B 176 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   VAL B 381 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   GLU B 178 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 195
      removed outlier: 6.373A  pdb=" N   GLY B 335 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA B 320 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL B 323 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 195
      removed outlier: 6.373A  pdb=" N   GLY B 335 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA B 320 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   PHE B 219 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ILE B 250 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 247 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   ILE B 249 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 413
    Processing sheet with id=AA7, first strand: chain 'B' and resid 476 through 479

    270 hydrogen bonds defined for protein.
    771 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: 0.56

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1339
        1.34 -     1.46: 414
        1.46 -     1.57: 2093
        1.57 -     1.69: 0
        1.69 -     1.80: 37
  Bond restraints: 3883
  Sorted by residual:
  bond pdb=" CB  THR B 522 "
       pdb=" CG2 THR B 522 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.54e+00
  bond pdb=" CB  MET B  16 "
       pdb=" CG  MET B  16 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 6.87e-01
  bond pdb=" CB  MET B 520 "
       pdb=" CG  MET B 520 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.52e-01
  bond pdb=" CA  ALA B 449 "
       pdb=" C   ALA B 449 "
    ideal  model  delta    sigma   weight residual
    1.520  1.530 -0.010 1.23e-02 6.61e+03 6.46e-01
  bond pdb=" C   GLY B  70 "
       pdb=" O   GLY B  70 "
    ideal  model  delta    sigma   weight residual
    1.234  1.243 -0.010 1.21e-02 6.83e+03 6.31e-01
  ... (remaining 3878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 5108
        1.17 -     2.34: 102
        2.34 -     3.52: 29
        3.52 -     4.69: 1
        4.69 -     5.86: 3
  Bond angle restraints: 5243
  Sorted by residual:
  angle pdb=" N   GLY B 306 "
        pdb=" CA  GLY B 306 "
        pdb=" C   GLY B 306 "
      ideal   model   delta    sigma   weight residual
     113.18  119.04   -5.86 2.37e+00 1.78e-01 6.12e+00
  angle pdb=" N   SER B 228 "
        pdb=" CA  SER B 228 "
        pdb=" C   SER B 228 "
      ideal   model   delta    sigma   weight residual
     113.18  110.26    2.92 1.33e+00 5.65e-01 4.83e+00
  angle pdb=" N   ALA B 449 "
        pdb=" CA  ALA B 449 "
        pdb=" C   ALA B 449 "
      ideal   model   delta    sigma   weight residual
     112.75  115.46   -2.71 1.36e+00 5.41e-01 3.98e+00
  angle pdb=" N   GLN B 351 "
        pdb=" CA  GLN B 351 "
        pdb=" CB  GLN B 351 "
      ideal   model   delta    sigma   weight residual
     110.12  112.90   -2.78 1.47e+00 4.63e-01 3.58e+00
  angle pdb=" CB  MET B  69 "
        pdb=" CG  MET B  69 "
        pdb=" SD  MET B  69 "
      ideal   model   delta    sigma   weight residual
     112.70  107.32    5.38 3.00e+00 1.11e-01 3.21e+00
  ... (remaining 5238 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.66: 2218
       15.66 -    31.31: 151
       31.31 -    46.97: 35
       46.97 -    62.62: 3
       62.62 -    78.28: 5
  Dihedral angle restraints: 2412
    sinusoidal: 934
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CA  GLU B 338 "
           pdb=" C   GLU B 338 "
           pdb=" N   GLU B 339 "
           pdb=" CA  GLU B 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.71  -15.29     0      5.00e+00 4.00e-02 9.35e+00
  dihedral pdb=" CG  ARG B 421 "
           pdb=" CD  ARG B 421 "
           pdb=" NE  ARG B 421 "
           pdb=" CZ  ARG B 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -138.97  -41.03     2      1.50e+01 4.44e-03 9.19e+00
  dihedral pdb=" CG  LYS B 132 "
           pdb=" CD  LYS B 132 "
           pdb=" CE  LYS B 132 "
           pdb=" NZ  LYS B 132 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.83   47.83     3      1.50e+01 4.44e-03 8.55e+00
  ... (remaining 2409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 395
       0.028 -    0.057: 154
       0.057 -    0.085: 50
       0.085 -    0.114: 34
       0.114 -    0.142: 5
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  GLU B 102 "
            pdb=" N   GLU B 102 "
            pdb=" C   GLU B 102 "
            pdb=" CB  GLU B 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.04e-01
  chirality pdb=" CA  ILE B 332 "
            pdb=" N   ILE B 332 "
            pdb=" C   ILE B 332 "
            pdb=" CB  ILE B 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  PRO B 462 "
            pdb=" N   PRO B 462 "
            pdb=" C   PRO B 462 "
            pdb=" CB  PRO B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.54e-01
  ... (remaining 635 not shown)

  Planarity restraints: 687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  98 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.56e+00
        pdb=" C   ALA B  98 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ALA B  98 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE B  99 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 233 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.19e+00
        pdb=" C   MET B 233 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   MET B 233 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LEU B 234 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 449 "   -0.015 5.00e-02 4.00e+02   2.26e-02 8.20e-01
        pdb=" N   PRO B 450 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B 450 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B 450 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 684 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1284
        2.85 -     3.36: 4021
        3.36 -     3.87: 6325
        3.87 -     4.39: 6853
        4.39 -     4.90: 12172
  Nonbonded interactions: 30655
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 479 "
            pdb=" OG1 THR B 482 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER B 135 "
            pdb=" OG1 THR B 497 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OE2 GLU B 339 "
            pdb=" NE2 GLN B 343 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" O   PHE B 219 "
            pdb=" N   LEU B 248 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OD1 ASN B 229 "
            pdb=" N   ILE B 230 "
     model   vdw
     2.431 3.120
  ... (remaining 30650 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.220
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.690
  Find NCS groups from input model:        0.010
  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:7.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
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   0.041   3883  Z= 0.146
  Angle     :  0.461   5.862   5243  Z= 0.255
  Chirality :  0.039   0.142    638
  Planarity :  0.002   0.023    687
  Dihedral  : 11.952  78.277   1464
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.36), residues: 522
  helix:  2.86 (0.29), residues: 297
  sheet:  0.25 (0.54), residues: 88
  loop :  0.10 (0.51), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 404 
 TYR   0.008   0.001   TYR B 199 
 PHE   0.007   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3883)
  covalent geometry    : angle       0.46054 ( 5243)
  hydrogen bonds       : bond        0.13644 (  262)
  hydrogen bonds       : angle       5.39877 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B  288 MET cc_start: 0.8613 (mtt) cc_final: 0.8396 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.8419
  time to fit residues: 23.3576
Evaluate side-chains
  20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0010
   overall best weight:    3.7994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.078000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.052999 restraints weight = 9610.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.89
r_work: 0.2681 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3883  Z= 0.189
  Angle     :  0.493   6.036   5243  Z= 0.268
  Chirality :  0.041   0.152    638
  Planarity :  0.003   0.024    687
  Dihedral  :  3.677  14.408    552
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  5.45 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.36), residues: 522
  helix:  2.83 (0.29), residues: 302
  sheet:  0.16 (0.58), residues: 80
  loop : -0.21 (0.48), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 404 
 TYR   0.007   0.001   TYR B 360 
 PHE   0.013   0.001   PHE B 195 
 HIS   0.001   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 3883)
  covalent geometry    : angle       0.49328 ( 5243)
  hydrogen bonds       : bond        0.04793 (  262)
  hydrogen bonds       : angle       4.39291 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.163 
Fit side-chains
REVERT: B  111 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8613 (mtp)
REVERT: B  518 GLU cc_start: 0.6612 (pt0) cc_final: 0.5803 (pt0)
  outliers start: 4
  outliers final: 1
  residues processed: 21
  average time/residue: 0.7329
  time to fit residues: 16.0009
Evaluate side-chains
  21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  522 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.077678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.052669 restraints weight = 9396.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 2.87
r_work: 0.2670 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3883  Z= 0.177
  Angle     :  0.478   6.600   5243  Z= 0.259
  Chirality :  0.040   0.144    638
  Planarity :  0.002   0.024    687
  Dihedral  :  3.678  15.902    552
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  7.92 %
    Favored  : 91.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.36), residues: 522
  helix:  2.81 (0.28), residues: 302
  sheet:  0.22 (0.60), residues: 80
  loop : -0.30 (0.48), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 404 
 TYR   0.006   0.001   TYR B 476 
 PHE   0.012   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3883)
  covalent geometry    : angle       0.47810 ( 5243)
  hydrogen bonds       : bond        0.04624 (  262)
  hydrogen bonds       : angle       4.26990 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.172 
Fit side-chains
REVERT: B  111 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8625 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 20
  average time/residue: 0.7042
  time to fit residues: 14.7478
Evaluate side-chains
  19 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 33 optimal weight:   20.0000
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0870
   overall best weight:    2.9162

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.078035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.053288 restraints weight = 9484.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.84
r_work: 0.2695 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3883  Z= 0.153
  Angle     :  0.459   6.988   5243  Z= 0.245
  Chirality :  0.040   0.142    638
  Planarity :  0.002   0.023    687
  Dihedral  :  3.635  16.257    552
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.66 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.36), residues: 522
  helix:  2.85 (0.29), residues: 302
  sheet:  0.17 (0.57), residues: 88
  loop : -0.36 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 404 
 TYR   0.006   0.001   TYR B 476 
 PHE   0.012   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3883)
  covalent geometry    : angle       0.45895 ( 5243)
  hydrogen bonds       : bond        0.04323 (  262)
  hydrogen bonds       : angle       4.15164 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: B  111 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8633 (mtp)
  outliers start: 4
  outliers final: 0
  residues processed: 21
  average time/residue: 0.7093
  time to fit residues: 15.5086
Evaluate side-chains
  20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0370
   overall best weight:    1.1460

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.079757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.055396 restraints weight = 9280.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 2.83
r_work: 0.2742 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3883  Z= 0.101
  Angle     :  0.429   8.258   5243  Z= 0.227
  Chirality :  0.038   0.138    638
  Planarity :  0.002   0.023    687
  Dihedral  :  3.508  14.037    552
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.41 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.36), residues: 522
  helix:  2.90 (0.28), residues: 304
  sheet:  0.29 (0.56), residues: 88
  loop : -0.36 (0.48), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 421 
 TYR   0.007   0.001   TYR B 476 
 PHE   0.012   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 3883)
  covalent geometry    : angle       0.42854 ( 5243)
  hydrogen bonds       : bond        0.03694 (  262)
  hydrogen bonds       : angle       3.97800 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 25
  average time/residue: 0.6900
  time to fit residues: 17.8884
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   54 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   overall best weight:    3.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.052988 restraints weight = 9741.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.86
r_work: 0.2681 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3883  Z= 0.161
  Angle     :  0.473   8.877   5243  Z= 0.248
  Chirality :  0.039   0.140    638
  Planarity :  0.002   0.024    687
  Dihedral  :  3.593  15.164    552
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.15 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.37), residues: 522
  helix:  2.93 (0.29), residues: 302
  sheet:  0.35 (0.57), residues: 88
  loop : -0.38 (0.48), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 368 
 TYR   0.006   0.001   TYR B 476 
 PHE   0.011   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3883)
  covalent geometry    : angle       0.47252 ( 5243)
  hydrogen bonds       : bond        0.04325 (  262)
  hydrogen bonds       : angle       4.09370 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 25
  average time/residue: 0.6380
  time to fit residues: 16.6139
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  169 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   chunk 27 optimal weight:   30.0000
   chunk 45 optimal weight:    0.3980
   chunk 50 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    3.0788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.077714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.052772 restraints weight = 9786.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 2.90
r_work: 0.2677 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3883  Z= 0.158
  Angle     :  0.470   9.846   5243  Z= 0.247
  Chirality :  0.039   0.140    638
  Planarity :  0.002   0.025    687
  Dihedral  :  3.606  14.428    552
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.64 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.37), residues: 522
  helix:  2.90 (0.29), residues: 302
  sheet:  0.38 (0.58), residues: 88
  loop : -0.38 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 368 
 TYR   0.006   0.001   TYR B 476 
 PHE   0.010   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3883)
  covalent geometry    : angle       0.47046 ( 5243)
  hydrogen bonds       : bond        0.04277 (  262)
  hydrogen bonds       : angle       4.09550 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: B  193 MET cc_start: 0.9320 (ptp) cc_final: 0.9055 (ptt)
  outliers start: 4
  outliers final: 2
  residues processed: 23
  average time/residue: 0.6579
  time to fit residues: 15.7738
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  169 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 30 optimal weight:   30.0000
   chunk 28 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.079503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.054822 restraints weight = 9522.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.85
r_work: 0.2727 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3883  Z= 0.104
  Angle     :  0.462  10.864   5243  Z= 0.240
  Chirality :  0.038   0.138    638
  Planarity :  0.002   0.022    687
  Dihedral  :  3.488  12.993    552
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 11.14 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.37), residues: 522
  helix:  2.97 (0.29), residues: 304
  sheet:  0.40 (0.59), residues: 88
  loop : -0.35 (0.49), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 421 
 TYR   0.006   0.001   TYR B 476 
 PHE   0.011   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 3883)
  covalent geometry    : angle       0.46167 ( 5243)
  hydrogen bonds       : bond        0.03701 (  262)
  hydrogen bonds       : angle       3.98577 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.159 
Fit side-chains
REVERT: B  193 MET cc_start: 0.9270 (ptp) cc_final: 0.9001 (ptt)
  outliers start: 2
  outliers final: 2
  residues processed: 22
  average time/residue: 0.6246
  time to fit residues: 14.3239
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  169 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.075547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.050494 restraints weight = 9689.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.85
r_work: 0.2615 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8891
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   3883  Z= 0.297
  Angle     :  0.602  12.733   5243  Z= 0.312
  Chirality :  0.043   0.142    638
  Planarity :  0.003   0.026    687
  Dihedral  :  3.816  15.176    552
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.64 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.37 (0.37), residues: 522
  helix:  2.76 (0.29), residues: 301
  sheet:  0.23 (0.58), residues: 88
  loop : -0.27 (0.51), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  58 
 TYR   0.007   0.002   TYR B 199 
 PHE   0.008   0.001   PHE B 195 
 HIS   0.002   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 ( 3883)
  covalent geometry    : angle       0.60157 ( 5243)
  hydrogen bonds       : bond        0.05242 (  262)
  hydrogen bonds       : angle       4.33981 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 22
  average time/residue: 0.7152
  time to fit residues: 16.3076
Evaluate side-chains
  21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  351 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    2.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.053039 restraints weight = 9674.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 2.87
r_work: 0.2686 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3883  Z= 0.148
  Angle     :  0.518  12.750   5243  Z= 0.269
  Chirality :  0.039   0.140    638
  Planarity :  0.002   0.024    687
  Dihedral  :  3.646  13.954    552
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.63 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.37), residues: 522
  helix:  2.78 (0.29), residues: 302
  sheet:  0.27 (0.59), residues: 88
  loop : -0.39 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 268 
 TYR   0.005   0.001   TYR B 476 
 PHE   0.012   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3883)
  covalent geometry    : angle       0.51810 ( 5243)
  hydrogen bonds       : bond        0.04199 (  262)
  hydrogen bonds       : angle       4.13214 (  771)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: B  193 MET cc_start: 0.9396 (ptp) cc_final: 0.9077 (ptt)
  outliers start: 3
  outliers final: 3
  residues processed: 22
  average time/residue: 0.6412
  time to fit residues: 14.7279
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  351 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.077254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.052464 restraints weight = 9627.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 2.86
r_work: 0.2670 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3883  Z= 0.168
  Angle     :  0.529  13.698   5243  Z= 0.274
  Chirality :  0.040   0.140    638
  Planarity :  0.002   0.024    687
  Dihedral  :  3.636  13.775    552
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.88 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.37 (0.37), residues: 522
  helix:  2.75 (0.28), residues: 302
  sheet:  0.30 (0.59), residues: 88
  loop : -0.37 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 404 
 TYR   0.006   0.001   TYR B 476 
 PHE   0.011   0.001   PHE B 195 
 HIS   0.000   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3883)
  covalent geometry    : angle       0.52938 ( 5243)
  hydrogen bonds       : bond        0.04341 (  262)
  hydrogen bonds       : angle       4.14439 (  771)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1247.18 seconds
wall clock time: 22 minutes 10.10 seconds (1330.10 seconds total)