Starting phenix.real_space_refine
on Tue Mar  3 11:34:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wee_32448/03_2026/7wee_32448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wee_32448/03_2026/7wee_32448.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2026/7wee_32448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2026/7wee_32448.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2026/7wee_32448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2026/7wee_32448.map"
  }
  resolution = 4.0
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2139      2.51       5
     N     560      2.21       5
     O     637      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  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: 3350
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "H"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 938
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 7, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 800
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
  Time building chain proxies: 0.85, per 1000 atoms: 0.25
  Number of scatterers: 3350
  At special positions: 0
  Unit cell: (87.74, 66.34, 100.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     637      8.00
     N     560      7.00
     C    2139      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  91 " distance=2.04

  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: 0.20
  Conformation dependent library (CDL) restraints added in 136.5 milliseconds
  

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 8 sheets defined
      8.2% alpha, 31.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 349 through 353
      removed outlier: 3.842A  pdb=" N   TRP E 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 383 through 387
    Processing helix  chain 'E' and resid 405 through 407
      No H-bonds generated for 'chain 'E' and resid 405 through 407'
    Processing helix  chain 'E' and resid 438 through 443
      removed outlier: 3.911A  pdb=" N   SER E 443 " --> pdb=" O   ASN E 439 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 88 through 92
      removed outlier: 3.727A  pdb=" N   THR H  92 " --> pdb=" O   PRO H  89 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 86
    Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358
      removed outlier: 4.321A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   CYS E 361 " --> pdb=" O   CYS E 525 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358
      removed outlier: 4.321A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   GLU E 516 " --> pdb=" O   ASN E 394 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS E 432 " --> pdb=" O   LEU E 513 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.984A  pdb=" N   ALA H  51 " --> pdb=" O   TRP H  38 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ARG H  40 " --> pdb=" O   TRP H  49 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   TRP H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ARG H  60 " --> pdb=" O   LEU H  52 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 7.354A  pdb=" N   VAL L  11 " --> pdb=" O   LEU L 109 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   GLN L  40 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   LEU L  49 " --> pdb=" O   GLN L  40 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24

    97 hydrogen bonds defined for protein.
    228 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: 0.40

  Time building geometry restraints manager: 0.30 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: 1057
        1.34 -     1.46: 864
        1.46 -     1.58: 1503
        1.58 -     1.69: 1
        1.69 -     1.81: 16
  Bond restraints: 3441
  Sorted by residual:
  bond pdb=" CG  PRO H   9 "
       pdb=" CD  PRO H   9 "
    ideal  model  delta    sigma   weight residual
    1.503  1.344  0.159 3.40e-02 8.65e+02 2.18e+01
  bond pdb=" CB  PRO H   9 "
       pdb=" CG  PRO H   9 "
    ideal  model  delta    sigma   weight residual
    1.492  1.672 -0.180 5.00e-02 4.00e+02 1.30e+01
  bond pdb=" N   PRO H   9 "
       pdb=" CD  PRO H   9 "
    ideal  model  delta    sigma   weight residual
    1.473  1.509 -0.036 1.40e-02 5.10e+03 6.63e+00
  bond pdb=" N   PRO H   9 "
       pdb=" CA  PRO H   9 "
    ideal  model  delta    sigma   weight residual
    1.469  1.448  0.021 1.28e-02 6.10e+03 2.71e+00
  bond pdb=" CA  ASN H  86 "
       pdb=" CB  ASN H  86 "
    ideal  model  delta    sigma   weight residual
    1.527  1.542 -0.015 1.61e-02 3.86e+03 8.50e-01
  ... (remaining 3436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.22: 4664
        3.22 -     6.45: 21
        6.45 -     9.67: 2
        9.67 -    12.90: 1
       12.90 -    16.12: 2
  Bond angle restraints: 4690
  Sorted by residual:
  angle pdb=" CA  PRO H   9 "
        pdb=" N   PRO H   9 "
        pdb=" CD  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     112.00   95.88   16.12 1.40e+00 5.10e-01 1.33e+02
  angle pdb=" N   PRO H   9 "
        pdb=" CD  PRO H   9 "
        pdb=" CG  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     103.20   91.07   12.13 1.50e+00 4.44e-01 6.54e+01
  angle pdb=" N   ILE E 418 "
        pdb=" CA  ILE E 418 "
        pdb=" C   ILE E 418 "
      ideal   model   delta    sigma   weight residual
     113.53  108.95    4.58 9.80e-01 1.04e+00 2.19e+01
  angle pdb=" CA  PRO H   9 "
        pdb=" CB  PRO H   9 "
        pdb=" CG  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     104.50   96.01    8.49 1.90e+00 2.77e-01 2.00e+01
  angle pdb=" N   PRO H   9 "
        pdb=" CA  PRO H   9 "
        pdb=" CB  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     103.25   99.58    3.67 1.05e+00 9.07e-01 1.22e+01
  ... (remaining 4685 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.10: 1760
       14.10 -    28.20: 193
       28.20 -    42.29: 61
       42.29 -    56.39: 12
       56.39 -    70.49: 1
  Dihedral angle restraints: 2027
    sinusoidal: 782
      harmonic: 1245
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  91 "
           pdb=" CB  CYS L  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   22.51   70.49     1      1.00e+01 1.00e-02 6.39e+01
  dihedral pdb=" CB  CYS E 480 "
           pdb=" SG  CYS E 480 "
           pdb=" SG  CYS E 488 "
           pdb=" CB  CYS E 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.56  -37.56     1      1.00e+01 1.00e-02 1.99e+01
  dihedral pdb=" CA  LEU E 517 "
           pdb=" C   LEU E 517 "
           pdb=" N   LEU E 518 "
           pdb=" CA  LEU E 518 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 2024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 358
       0.039 -    0.079: 114
       0.079 -    0.118: 37
       0.118 -    0.157: 6
       0.157 -    0.197: 2
  Chirality restraints: 517
  Sorted by residual:
  chirality pdb=" CB  THR E 333 "
            pdb=" CA  THR E 333 "
            pdb=" OG1 THR E 333 "
            pdb=" CG2 THR E 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.68e-01
  chirality pdb=" CA  PRO H   9 "
            pdb=" N   PRO H   9 "
            pdb=" C   PRO H   9 "
            pdb=" CB  PRO H   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.89e-01
  chirality pdb=" CA  ASN H  86 "
            pdb=" N   ASN H  86 "
            pdb=" C   ASN H  86 "
            pdb=" CB  ASN H  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 514 not shown)

  Planarity restraints: 600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H   8 "    0.056 5.00e-02 4.00e+02   7.59e-02 9.21e+00
        pdb=" N   PRO H   9 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO H   9 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO H   9 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H  88 "   -0.034 5.00e-02 4.00e+02   5.09e-02 4.14e+00
        pdb=" N   PRO H  89 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO H  89 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H  89 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 490 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO E 491 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO E 491 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 491 "    0.019 5.00e-02 4.00e+02
  ... (remaining 597 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 50
        2.67 -     3.23: 3069
        3.23 -     3.79: 4699
        3.79 -     4.34: 6398
        4.34 -     4.90: 10716
  Nonbonded interactions: 24932
  Sorted by model distance:
  nonbonded pdb=" OG1 THR L  95 "
            pdb=" O   SER L  98 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" OG1 THR H 104 "
            pdb=" OD1 ASP H 107 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OG  SER E 349 "
            pdb=" O   LEU E 452 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER L  70 "
            pdb=" OG1 THR L  73 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG  SER H   7 "
            pdb=" OG1 THR H  21 "
     model   vdw
     2.285 3.040
  ... (remaining 24927 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.590
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.890
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
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      :  0.005   0.180   3447  Z= 0.161
  Angle     :  0.720  16.124   4702  Z= 0.408
  Chirality :  0.044   0.197    517
  Planarity :  0.005   0.076    600
  Dihedral  : 12.682  54.785   1217
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  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 : 0.00 %

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: -1.60 (0.40), residues: 423
  helix: -3.73 (0.83), residues: 21
  sheet: -0.23 (0.42), residues: 141
  loop : -1.33 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  45 
 TYR   0.011   0.001   TYR E 501 
 PHE   0.011   0.001   PHE L  65 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.005   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 3441)
  covalent geometry    : angle       0.71992 ( 4690)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       0.56352 (   12)
  hydrogen bonds       : bond        0.17692 (   93)
  hydrogen bonds       : angle       8.01526 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7649 (p0) cc_final: 0.6915 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0414
  time to fit residues: 3.6048
Evaluate side-chains
  52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.133732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 119)---------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.097234 restraints weight = 6895.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.097435 restraints weight = 5788.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.098119 restraints weight = 4645.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.098483 restraints weight = 3995.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.099079 restraints weight = 3648.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   3447  Z= 0.122
  Angle     :  0.587   6.412   4702  Z= 0.305
  Chirality :  0.044   0.144    517
  Planarity :  0.004   0.051    600
  Dihedral  :  4.650  23.600    470
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.63 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.41), residues: 423
  helix: -3.51 (0.91), residues: 20
  sheet:  0.09 (0.41), residues: 144
  loop : -1.24 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  45 
 TYR   0.009   0.001   TYR H  96 
 PHE   0.011   0.001   PHE H  24 
 TRP   0.004   0.001   TRP E 436 
 HIS   0.002   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3441)
  covalent geometry    : angle       0.58578 ( 4690)
  SS BOND              : bond        0.00223 (    6)
  SS BOND              : angle       0.82300 (   12)
  hydrogen bonds       : bond        0.03454 (   93)
  hydrogen bonds       : angle       6.40003 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7571 (p0) cc_final: 0.6928 (p0)
REVERT: H   45 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8221 (ptmm)
REVERT: H   84 MET cc_start: 0.7925 (tmm) cc_final: 0.7668 (tmm)
REVERT: L  108 LYS cc_start: 0.7873 (tppt) cc_final: 0.7539 (tptt)
  outliers start: 4
  outliers final: 4
  residues processed: 55
  average time/residue: 0.0396
  time to fit residues: 2.9799
Evaluate side-chains
  53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   63 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0770
   chunk 26 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0070
   overall best weight:    0.7558

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.132073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 98)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.096289 restraints weight = 6809.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.096981 restraints weight = 5452.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.097191 restraints weight = 4294.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.097232 restraints weight = 4102.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.097360 restraints weight = 4077.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3447  Z= 0.107
  Angle     :  0.543   5.202   4702  Z= 0.285
  Chirality :  0.043   0.145    517
  Planarity :  0.004   0.050    600
  Dihedral  :  4.569  22.987    470
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.59 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.41), residues: 423
  helix: -3.43 (0.95), residues: 20
  sheet:  0.21 (0.41), residues: 145
  loop : -1.19 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  45 
 TYR   0.009   0.001   TYR E 501 
 PHE   0.012   0.001   PHE L 103 
 TRP   0.005   0.001   TRP H  55 
 HIS   0.001   0.001   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 3441)
  covalent geometry    : angle       0.54211 ( 4690)
  SS BOND              : bond        0.00282 (    6)
  SS BOND              : angle       0.91413 (   12)
  hydrogen bonds       : bond        0.03259 (   93)
  hydrogen bonds       : angle       5.90034 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7611 (p0) cc_final: 0.6997 (p0)
REVERT: H   45 LYS cc_start: 0.8500 (ptmm) cc_final: 0.8177 (ptmm)
REVERT: H   84 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7525 (tmm)
REVERT: L   49 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7843 (tp)
REVERT: L   50 LEU cc_start: 0.8550 (mp) cc_final: 0.8336 (tt)
REVERT: L  108 LYS cc_start: 0.8128 (tppt) cc_final: 0.7913 (tptp)
  outliers start: 7
  outliers final: 5
  residues processed: 59
  average time/residue: 0.0436
  time to fit residues: 3.5093
Evaluate side-chains
  57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   84 MET
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   63 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.132658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.105721 restraints weight = 6730.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.104835 restraints weight = 12175.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.106237 restraints weight = 10194.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.106238 restraints weight = 6245.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.106469 restraints weight = 7182.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3447  Z= 0.099
  Angle     :  0.531   5.073   4702  Z= 0.278
  Chirality :  0.043   0.151    517
  Planarity :  0.004   0.050    600
  Dihedral  :  4.489  22.511    470
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.82 %
    Favored  : 82.75 %
  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 are not related in a simple way.
  whole: -1.19 (0.41), residues: 423
  helix: -3.39 (0.82), residues: 26
  sheet:  0.25 (0.41), residues: 146
  loop : -1.16 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  45 
 TYR   0.008   0.001   TYR E 501 
 PHE   0.011   0.001   PHE H  24 
 TRP   0.005   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3441)
  covalent geometry    : angle       0.52985 ( 4690)
  SS BOND              : bond        0.00332 (    6)
  SS BOND              : angle       0.89971 (   12)
  hydrogen bonds       : bond        0.03095 (   93)
  hydrogen bonds       : angle       5.64850 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7608 (p0) cc_final: 0.7021 (p0)
  outliers start: 9
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0433
  time to fit residues: 3.5006
Evaluate side-chains
  58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   63 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.126963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.095263 restraints weight = 6805.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.090087 restraints weight = 8461.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.090847 restraints weight = 6391.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.091601 restraints weight = 5338.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.091601 restraints weight = 4722.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3447  Z= 0.201
  Angle     :  0.639   7.904   4702  Z= 0.337
  Chirality :  0.046   0.166    517
  Planarity :  0.005   0.057    600
  Dihedral  :  5.295  22.717    470
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 15.63 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.41), residues: 423
  helix: -3.50 (0.82), residues: 26
  sheet:  0.08 (0.41), residues: 147
  loop : -1.25 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 454 
 TYR   0.015   0.002   TYR L  52 
 PHE   0.013   0.002   PHE E 429 
 TRP   0.006   0.001   TRP H  55 
 HIS   0.002   0.001   HIS L 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 3441)
  covalent geometry    : angle       0.63755 ( 4690)
  SS BOND              : bond        0.00412 (    6)
  SS BOND              : angle       1.16275 (   12)
  hydrogen bonds       : bond        0.03922 (   93)
  hydrogen bonds       : angle       6.05426 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7914 (p0) cc_final: 0.7361 (p0)
REVERT: E  474 GLN cc_start: 0.7177 (pp30) cc_final: 0.6754 (pp30)
  outliers start: 14
  outliers final: 12
  residues processed: 62
  average time/residue: 0.0474
  time to fit residues: 3.8628
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain H residue    3 THR
Chi-restraints excluded: chain H residue   16 GLN
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   63 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0060
   chunk 35 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0870
   chunk 22 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.2974

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.131347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.094326 restraints weight = 6834.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.095269 restraints weight = 5286.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.095728 restraints weight = 4437.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.095728 restraints weight = 3965.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.095728 restraints weight = 3965.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3447  Z= 0.101
  Angle     :  0.570   7.899   4702  Z= 0.295
  Chirality :  0.043   0.171    517
  Planarity :  0.004   0.056    600
  Dihedral  :  4.759  23.173    470
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.60 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.41), residues: 423
  helix: -3.45 (0.81), residues: 26
  sheet:  0.23 (0.40), residues: 152
  loop : -1.14 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 509 
 TYR   0.011   0.001   TYR E 380 
 PHE   0.013   0.001   PHE H  24 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.004   0.001   HIS L  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3441)
  covalent geometry    : angle       0.56909 ( 4690)
  SS BOND              : bond        0.00445 (    6)
  SS BOND              : angle       0.85914 (   12)
  hydrogen bonds       : bond        0.03061 (   93)
  hydrogen bonds       : angle       5.73868 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7751 (p0) cc_final: 0.7222 (p0)
REVERT: E  474 GLN cc_start: 0.7088 (pp30) cc_final: 0.6770 (pp30)
  outliers start: 8
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0479
  time to fit residues: 4.2094
Evaluate side-chains
  61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain H residue    3 THR
Chi-restraints excluded: chain H residue   16 GLN
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue   30 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0870
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 36 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** L  42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.131305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.094121 restraints weight = 7055.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.095069 restraints weight = 5309.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.095501 restraints weight = 4419.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.096008 restraints weight = 3946.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.096007 restraints weight = 3662.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3447  Z= 0.104
  Angle     :  0.553   6.556   4702  Z= 0.289
  Chirality :  0.043   0.171    517
  Planarity :  0.004   0.055    600
  Dihedral  :  4.642  21.223    470
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.79 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.41), residues: 423
  helix: -3.44 (0.81), residues: 26
  sheet:  0.34 (0.41), residues: 152
  loop : -1.13 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 498 
 TYR   0.008   0.001   TYR L  52 
 PHE   0.011   0.001   PHE H  24 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.002   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3441)
  covalent geometry    : angle       0.55227 ( 4690)
  SS BOND              : bond        0.00306 (    6)
  SS BOND              : angle       0.73338 (   12)
  hydrogen bonds       : bond        0.03011 (   93)
  hydrogen bonds       : angle       5.60685 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7728 (p0) cc_final: 0.7214 (p0)
REVERT: E  474 GLN cc_start: 0.6948 (pp30) cc_final: 0.6695 (pp30)
  outliers start: 11
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0416
  time to fit residues: 3.5352
Evaluate side-chains
  64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain H residue    3 THR
Chi-restraints excluded: chain H residue   16 GLN
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   63 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 24 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 28 optimal weight:   10.0000
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.131439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 103)---------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.094066 restraints weight = 6998.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.094997 restraints weight = 5356.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.095466 restraints weight = 4434.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.095466 restraints weight = 3917.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.095467 restraints weight = 3915.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3447  Z= 0.107
  Angle     :  0.556   6.477   4702  Z= 0.291
  Chirality :  0.044   0.173    517
  Planarity :  0.004   0.054    600
  Dihedral  :  4.626  21.700    470
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.14 %
    Favored  : 78.44 %
  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: -1.04 (0.41), residues: 423
  helix: -3.43 (0.80), residues: 26
  sheet:  0.40 (0.42), residues: 145
  loop : -1.06 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  60 
 TYR   0.008   0.001   TYR E 380 
 PHE   0.012   0.001   PHE H  24 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.001   0.000   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3441)
  covalent geometry    : angle       0.55530 ( 4690)
  SS BOND              : bond        0.00248 (    6)
  SS BOND              : angle       0.73244 (   12)
  hydrogen bonds       : bond        0.03002 (   93)
  hydrogen bonds       : angle       5.52672 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7756 (p0) cc_final: 0.7242 (p0)
REVERT: E  474 GLN cc_start: 0.6893 (pp30) cc_final: 0.6576 (pp30)
  outliers start: 9
  outliers final: 9
  residues processed: 60
  average time/residue: 0.0414
  time to fit residues: 3.4321
Evaluate side-chains
  64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain H residue    3 THR
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   63 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 11 optimal weight:    0.2980
   chunk 37 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0670
   chunk 24 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6120

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.132109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 112)---------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.098053 restraints weight = 6886.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.095261 restraints weight = 6383.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.095819 restraints weight = 5118.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.095822 restraints weight = 4425.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.095822 restraints weight = 4418.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3447  Z= 0.101
  Angle     :  0.543   5.905   4702  Z= 0.286
  Chirality :  0.043   0.168    517
  Planarity :  0.004   0.051    600
  Dihedral  :  4.515  20.774    470
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 18.87 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.41), residues: 423
  helix: -3.43 (0.80), residues: 26
  sheet:  0.73 (0.43), residues: 135
  loop : -1.17 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  60 
 TYR   0.008   0.001   TYR E 380 
 PHE   0.011   0.001   PHE H  24 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.002   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3441)
  covalent geometry    : angle       0.54223 ( 4690)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       0.72560 (   12)
  hydrogen bonds       : bond        0.02941 (   93)
  hydrogen bonds       : angle       5.39273 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7617 (p0) cc_final: 0.7101 (p0)
REVERT: E  474 GLN cc_start: 0.6800 (pp30) cc_final: 0.6561 (pp30)
REVERT: L  103 PHE cc_start: 0.3237 (OUTLIER) cc_final: 0.2413 (m-10)
  outliers start: 13
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0357
  time to fit residues: 2.9381
Evaluate side-chains
  61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  503 VAL
Chi-restraints excluded: chain H residue    3 THR
Chi-restraints excluded: chain H residue   16 GLN
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   63 ASN
Chi-restraints excluded: chain L residue  103 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.130855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.099493 restraints weight = 6787.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.097333 restraints weight = 10129.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.096219 restraints weight = 6922.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.096228 restraints weight = 7030.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096323 restraints weight = 5776.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3447  Z= 0.117
  Angle     :  0.558   5.732   4702  Z= 0.295
  Chirality :  0.044   0.176    517
  Planarity :  0.004   0.049    600
  Dihedral  :  4.653  21.613    470
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.60 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.41), residues: 423
  helix: -3.46 (0.79), residues: 26
  sheet:  0.46 (0.42), residues: 145
  loop : -1.03 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  60 
 TYR   0.009   0.001   TYR E 380 
 PHE   0.009   0.001   PHE H  24 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.002   0.000   HIS L  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3441)
  covalent geometry    : angle       0.55696 ( 4690)
  SS BOND              : bond        0.00291 (    6)
  SS BOND              : angle       0.74908 (   12)
  hydrogen bonds       : bond        0.03006 (   93)
  hydrogen bonds       : angle       5.44976 (  228)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7746 (p0) cc_final: 0.7228 (p0)
REVERT: E  474 GLN cc_start: 0.6835 (pp30) cc_final: 0.6602 (pp30)
REVERT: L  103 PHE cc_start: 0.3119 (OUTLIER) cc_final: 0.2085 (m-10)
  outliers start: 11
  outliers final: 10
  residues processed: 57
  average time/residue: 0.0430
  time to fit residues: 3.3521
Evaluate side-chains
  61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  503 VAL
Chi-restraints excluded: chain H residue    3 THR
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   63 ASN
Chi-restraints excluded: chain L residue  103 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 6 optimal weight:    0.1980
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.131742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.100378 restraints weight = 6996.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.098853 restraints weight = 8780.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.096393 restraints weight = 6121.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.096488 restraints weight = 6884.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.096593 restraints weight = 5814.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3447  Z= 0.105
  Angle     :  0.545   5.793   4702  Z= 0.287
  Chirality :  0.043   0.168    517
  Planarity :  0.004   0.048    600
  Dihedral  :  4.548  21.285    470
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.06 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.41), residues: 423
  helix: -3.41 (0.80), residues: 26
  sheet:  0.48 (0.42), residues: 145
  loop : -1.03 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  60 
 TYR   0.007   0.001   TYR H  96 
 PHE   0.010   0.001   PHE H  24 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.002   0.000   HIS L  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3441)
  covalent geometry    : angle       0.54464 ( 4690)
  SS BOND              : bond        0.00291 (    6)
  SS BOND              : angle       0.72557 (   12)
  hydrogen bonds       : bond        0.02894 (   93)
  hydrogen bonds       : angle       5.30714 (  228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 819.61 seconds
wall clock time: 14 minutes 43.44 seconds (883.44 seconds total)