Starting phenix.real_space_refine
on Wed Jun  4 15:23:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wee_32448/06_2025/7wee_32448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wee_32448/06_2025/7wee_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wee_32448/06_2025/7wee_32448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wee_32448/06_2025/7wee_32448.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wee_32448/06_2025/7wee_32448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wee_32448/06_2025/7wee_32448.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.26, per 1000 atoms: 0.97
  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: 0.81
  Conformation dependent library (CDL) restraints added in 424.2 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: 0.44
  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: 0.88

  Time building geometry restraints manager: 1.00 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:             1.890
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.690
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.840
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.006   0.001   TRP E 436 
 HIS   0.005   0.001   HIS L  41 
 PHE   0.011   0.001   PHE L  65 
 TYR   0.011   0.001   TYR E 501 
 ARG   0.005   0.000   ARG L  45 

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

*********************** 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  : 0.464 
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: 0.1229
  time to fit residues: 10.4303
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  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.126300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.097509 restraints weight = 7062.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.095101 restraints weight = 10645.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.091584 restraints weight = 7247.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   3447  Z= 0.261
  Angle     :  0.704   8.707   4702  Z= 0.372
  Chirality :  0.048   0.148    517
  Planarity :  0.005   0.051    600
  Dihedral  :  5.511  26.959    470
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.41), residues: 423
  helix: -3.44 (0.86), residues: 26
  sheet: -0.11 (0.40), residues: 149
  loop : -1.39 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 436 
 HIS   0.002   0.001   HIS L 100 
 PHE   0.016   0.002   PHE E 374 
 TYR   0.016   0.002   TYR L  52 
 ARG   0.002   0.000   ARG E 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04422 (   93)
  hydrogen bonds       : angle       6.73968 (  228)
  SS BOND              : bond        0.00484 (    6)
  SS BOND              : angle       1.17076 (   12)
  covalent geometry    : bond        0.00629 ( 3441)
  covalent geometry    : angle       0.70203 ( 4690)

*********************** 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
  60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.386 
Fit side-chains
REVERT: E  389 ASP cc_start: 0.7969 (p0) cc_final: 0.7397 (p0)
REVERT: E  474 GLN cc_start: 0.7244 (pp30) cc_final: 0.6874 (pp30)
REVERT: H   45 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8298 (ptmm)
REVERT: L   50 LEU cc_start: 0.8521 (mp) cc_final: 0.8305 (tp)
REVERT: L  108 LYS cc_start: 0.7982 (tppt) cc_final: 0.7592 (tptt)
  outliers start: 7
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1275
  time to fit residues: 9.2402
Evaluate side-chains
  55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   71 ILE
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 39 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0770
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.8740

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.129276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.097100 restraints weight = 6849.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 80)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.091547 restraints weight = 8702.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.092611 restraints weight = 6349.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3447  Z= 0.118
  Angle     :  0.590   7.015   4702  Z= 0.307
  Chirality :  0.044   0.144    517
  Planarity :  0.005   0.054    600
  Dihedral  :  5.046  26.231    470
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 17.25 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.41), residues: 423
  helix: -3.42 (0.84), residues: 26
  sheet: -0.10 (0.40), residues: 153
  loop : -1.22 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 505 
 PHE   0.013   0.001   PHE L 103 
 TYR   0.013   0.001   TYR E 380 
 ARG   0.001   0.000   ARG L  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (   93)
  hydrogen bonds       : angle       6.19216 (  228)
  SS BOND              : bond        0.00310 (    6)
  SS BOND              : angle       0.91633 (   12)
  covalent geometry    : bond        0.00281 ( 3441)
  covalent geometry    : angle       0.58908 ( 4690)

*********************** 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
  62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7809 (p0) cc_final: 0.7312 (p0)
REVERT: E  474 GLN cc_start: 0.7191 (pp30) cc_final: 0.6787 (pp30)
REVERT: H   45 LYS cc_start: 0.8564 (ptmm) cc_final: 0.8166 (ptmm)
REVERT: L   50 LEU cc_start: 0.8731 (mp) cc_final: 0.8423 (tt)
REVERT: L  108 LYS cc_start: 0.8011 (tppt) cc_final: 0.7758 (tptp)
  outliers start: 5
  outliers final: 5
  residues processed: 61
  average time/residue: 0.1218
  time to fit residues: 9.6693
Evaluate side-chains
  58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain H residue   47 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 35 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    2.2384

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

Flipped N/Q/H residues before XYZ refinement:
H 111 GLN
** L  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.125789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.094582 restraints weight = 7032.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.091564 restraints weight = 10374.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.089843 restraints weight = 7743.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3447  Z= 0.214
  Angle     :  0.651   6.824   4702  Z= 0.344
  Chirality :  0.046   0.147    517
  Planarity :  0.005   0.058    600
  Dihedral  :  5.493  27.096    470
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.33 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.40), residues: 423
  helix: -3.52 (0.84), residues: 26
  sheet: -0.07 (0.40), residues: 149
  loop : -1.47 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 436 
 HIS   0.002   0.001   HIS E 505 
 PHE   0.014   0.002   PHE E 429 
 TYR   0.015   0.002   TYR L  52 
 ARG   0.003   0.000   ARG E 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (   93)
  hydrogen bonds       : angle       6.21722 (  228)
  SS BOND              : bond        0.00494 (    6)
  SS BOND              : angle       1.20793 (   12)
  covalent geometry    : bond        0.00515 ( 3441)
  covalent geometry    : angle       0.64934 ( 4690)

*********************** 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
  65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7993 (p0) cc_final: 0.7444 (p0)
REVERT: E  474 GLN cc_start: 0.7271 (pp30) cc_final: 0.6968 (pp30)
REVERT: H   45 LYS cc_start: 0.8597 (ptmm) cc_final: 0.8306 (ptmm)
REVERT: L   50 LEU cc_start: 0.8673 (mp) cc_final: 0.8439 (tt)
REVERT: L  103 PHE cc_start: 0.4520 (OUTLIER) cc_final: 0.4002 (m-10)
REVERT: L  108 LYS cc_start: 0.8146 (tppt) cc_final: 0.7919 (tptp)
  outliers start: 14
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1027
  time to fit residues: 8.4702
Evaluate side-chains
  66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
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 L residue   30 VAL
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   63 ASN
Chi-restraints excluded: chain L residue  103 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3790 r_free = 0.3790 target = 0.128869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.096334 restraints weight = 7009.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 81)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.091326 restraints weight = 7932.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.092059 restraints weight = 6054.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3447  Z= 0.118
  Angle     :  0.589   7.849   4702  Z= 0.303
  Chirality :  0.044   0.146    517
  Planarity :  0.005   0.060    600
  Dihedral  :  5.045  25.360    470
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.29 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.40), residues: 423
  helix: -3.52 (0.79), residues: 26
  sheet: -0.09 (0.40), residues: 153
  loop : -1.28 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 436 
 HIS   0.001   0.000   HIS H 100 
 PHE   0.011   0.001   PHE H  24 
 TYR   0.010   0.001   TYR E 380 
 ARG   0.001   0.000   ARG E 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03359 (   93)
  hydrogen bonds       : angle       5.85775 (  228)
  SS BOND              : bond        0.00391 (    6)
  SS BOND              : angle       1.05593 (   12)
  covalent geometry    : bond        0.00276 ( 3441)
  covalent geometry    : angle       0.58700 ( 4690)

*********************** 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
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7886 (p0) cc_final: 0.7394 (p0)
REVERT: E  474 GLN cc_start: 0.7247 (pp30) cc_final: 0.6793 (pp30)
REVERT: H   45 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8290 (ptmm)
REVERT: L   49 LEU cc_start: 0.8079 (tt) cc_final: 0.7859 (tp)
REVERT: L   50 LEU cc_start: 0.8719 (mp) cc_final: 0.8427 (tt)
REVERT: L  103 PHE cc_start: 0.4123 (OUTLIER) cc_final: 0.3509 (m-10)
REVERT: L  108 LYS cc_start: 0.8093 (tppt) cc_final: 0.7888 (tptp)
  outliers start: 12
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1125
  time to fit residues: 10.4909
Evaluate side-chains
  66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
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 L residue   30 VAL
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   63 ASN
Chi-restraints excluded: chain L residue  103 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3769 r_free = 0.3769 target = 0.127467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.094613 restraints weight = 7033.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.089968 restraints weight = 7984.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.090921 restraints weight = 6047.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3447  Z= 0.154
  Angle     :  0.615   8.931   4702  Z= 0.314
  Chirality :  0.044   0.159    517
  Planarity :  0.005   0.057    600
  Dihedral  :  5.122  23.412    470
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.37 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.40), residues: 423
  helix: -3.50 (0.81), residues: 26
  sheet:  0.06 (0.42), residues: 143
  loop : -1.27 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 436 
 HIS   0.001   0.001   HIS E 505 
 PHE   0.010   0.001   PHE H  24 
 TYR   0.011   0.001   TYR L  52 
 ARG   0.002   0.000   ARG E 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (   93)
  hydrogen bonds       : angle       5.89244 (  228)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       1.00969 (   12)
  covalent geometry    : bond        0.00369 ( 3441)
  covalent geometry    : angle       0.61318 ( 4690)

*********************** 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
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7919 (p0) cc_final: 0.7439 (p0)
REVERT: E  474 GLN cc_start: 0.7167 (pp30) cc_final: 0.6726 (pp30)
REVERT: H   45 LYS cc_start: 0.8546 (ptmm) cc_final: 0.8325 (ptmm)
REVERT: L   50 LEU cc_start: 0.8741 (mp) cc_final: 0.8476 (tt)
REVERT: L  103 PHE cc_start: 0.4046 (OUTLIER) cc_final: 0.3453 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 73
  average time/residue: 0.1084
  time to fit residues: 10.4871
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  335 LEU
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    5 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
Chi-restraints excluded: chain L residue  103 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0040
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9396

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.128724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.096816 restraints weight = 6860.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.090946 restraints weight = 9008.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.092048 restraints weight = 6612.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3447  Z= 0.118
  Angle     :  0.601   8.196   4702  Z= 0.306
  Chirality :  0.044   0.154    517
  Planarity :  0.004   0.057    600
  Dihedral  :  4.980  23.199    470
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 23.18 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.40), residues: 423
  helix: -3.47 (0.81), residues: 26
  sheet:  0.07 (0.42), residues: 146
  loop : -1.26 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 505 
 PHE   0.010   0.001   PHE H  24 
 TYR   0.020   0.001   TYR E 501 
 ARG   0.001   0.000   ARG H  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03360 (   93)
  hydrogen bonds       : angle       5.75358 (  228)
  SS BOND              : bond        0.00382 (    6)
  SS BOND              : angle       0.91690 (   12)
  covalent geometry    : bond        0.00277 ( 3441)
  covalent geometry    : angle       0.59965 ( 4690)

*********************** 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
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7857 (p0) cc_final: 0.7383 (p0)
REVERT: E  474 GLN cc_start: 0.7135 (pp30) cc_final: 0.6678 (pp30)
REVERT: H   16 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6339 (pm20)
REVERT: H   45 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8242 (ptmm)
REVERT: L   49 LEU cc_start: 0.7973 (tt) cc_final: 0.7738 (tp)
REVERT: L   50 LEU cc_start: 0.8720 (mp) cc_final: 0.8435 (tt)
REVERT: L  103 PHE cc_start: 0.3988 (OUTLIER) cc_final: 0.3333 (m-10)
  outliers start: 14
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1067
  time to fit residues: 9.6913
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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   18 LEU
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    5 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
Chi-restraints excluded: chain L residue  103 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0170
   chunk 31 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.9224

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.129111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.097575 restraints weight = 6966.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 75)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.091896 restraints weight = 8606.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.092805 restraints weight = 6500.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3447  Z= 0.115
  Angle     :  0.588   7.114   4702  Z= 0.301
  Chirality :  0.044   0.170    517
  Planarity :  0.004   0.056    600
  Dihedral  :  4.832  21.645    470
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 23.45 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.40), residues: 423
  helix: -3.50 (0.79), residues: 26
  sheet:  0.14 (0.42), residues: 146
  loop : -1.24 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 505 
 PHE   0.011   0.001   PHE H  24 
 TYR   0.019   0.001   TYR E 501 
 ARG   0.002   0.000   ARG L  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (   93)
  hydrogen bonds       : angle       5.67221 (  228)
  SS BOND              : bond        0.00301 (    6)
  SS BOND              : angle       0.86106 (   12)
  covalent geometry    : bond        0.00271 ( 3441)
  covalent geometry    : angle       0.58723 ( 4690)

*********************** 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
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7855 (p0) cc_final: 0.7332 (p0)
REVERT: E  474 GLN cc_start: 0.7087 (pp30) cc_final: 0.6622 (pp30)
REVERT: H   16 GLN cc_start: 0.6497 (OUTLIER) cc_final: 0.6204 (pm20)
REVERT: H   45 LYS cc_start: 0.8504 (ptmm) cc_final: 0.8294 (ptmm)
REVERT: L   49 LEU cc_start: 0.7911 (tt) cc_final: 0.7675 (tp)
REVERT: L   50 LEU cc_start: 0.8758 (mp) cc_final: 0.8499 (tt)
REVERT: L  103 PHE cc_start: 0.3884 (OUTLIER) cc_final: 0.3060 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 68
  average time/residue: 0.1069
  time to fit residues: 9.6568
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
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 L residue    5 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
Chi-restraints excluded: chain L residue  103 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 30 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0470
   chunk 31 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.130728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 130)---------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.097567 restraints weight = 6806.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.094215 restraints weight = 7099.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.095022 restraints weight = 5530.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3447  Z= 0.099
  Angle     :  0.573   7.661   4702  Z= 0.293
  Chirality :  0.043   0.164    517
  Planarity :  0.004   0.055    600
  Dihedral  :  4.619  21.673    470
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 24.26 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.41), residues: 423
  helix: -3.83 (0.65), residues: 32
  sheet:  0.22 (0.42), residues: 148
  loop : -1.08 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 519 
 PHE   0.010   0.001   PHE H  24 
 TYR   0.017   0.001   TYR E 501 
 ARG   0.001   0.000   ARG L  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03029 (   93)
  hydrogen bonds       : angle       5.52874 (  228)
  SS BOND              : bond        0.00274 (    6)
  SS BOND              : angle       0.78354 (   12)
  covalent geometry    : bond        0.00226 ( 3441)
  covalent geometry    : angle       0.57273 ( 4690)

*********************** 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
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7758 (p0) cc_final: 0.7250 (p0)
REVERT: E  410 ILE cc_start: 0.8595 (mm) cc_final: 0.8316 (mm)
REVERT: E  474 GLN cc_start: 0.6869 (pp30) cc_final: 0.6456 (pp30)
REVERT: H   16 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.6004 (pm20)
REVERT: L   49 LEU cc_start: 0.7746 (tt) cc_final: 0.7523 (tp)
REVERT: L   50 LEU cc_start: 0.8734 (mp) cc_final: 0.8517 (tt)
REVERT: L  103 PHE cc_start: 0.3870 (OUTLIER) cc_final: 0.2981 (m-10)
  outliers start: 12
  outliers final: 10
  residues processed: 69
  average time/residue: 0.1280
  time to fit residues: 11.5660
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  335 LEU
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 L residue   30 VAL
Chi-restraints excluded: chain L residue   40 GLN
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 12 optimal weight:    0.0770
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0980
   chunk 21 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.3938

-------------------------------------------------------------------------------
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 = 0.3819 r_free = 0.3819 target = 0.131343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.099749 restraints weight = 6803.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.098305 restraints weight = 8842.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.098680 restraints weight = 7042.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3447  Z= 0.099
  Angle     :  0.573   6.813   4702  Z= 0.292
  Chirality :  0.043   0.172    517
  Planarity :  0.004   0.053    600
  Dihedral  :  4.503  20.114    470
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 24.80 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.40), residues: 423
  helix: -3.79 (0.66), residues: 32
  sheet:  0.63 (0.43), residues: 135
  loop : -1.22 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 519 
 PHE   0.010   0.001   PHE H  24 
 TYR   0.017   0.001   TYR E 501 
 ARG   0.001   0.000   ARG L  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03011 (   93)
  hydrogen bonds       : angle       5.38359 (  228)
  SS BOND              : bond        0.00229 (    6)
  SS BOND              : angle       0.71451 (   12)
  covalent geometry    : bond        0.00228 ( 3441)
  covalent geometry    : angle       0.57251 ( 4690)

********************** 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
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: E  389 ASP cc_start: 0.7592 (p0) cc_final: 0.7062 (p0)
REVERT: E  410 ILE cc_start: 0.8503 (mm) cc_final: 0.8232 (mm)
REVERT: E  474 GLN cc_start: 0.6729 (pp30) cc_final: 0.6492 (pp30)
REVERT: L   49 LEU cc_start: 0.7339 (tt) cc_final: 0.7115 (tp)
REVERT: L  103 PHE cc_start: 0.3574 (OUTLIER) cc_final: 0.2604 (m-10)
  outliers start: 13
  outliers final: 10
  residues processed: 68
  average time/residue: 0.1007
  time to fit residues: 9.3839
Evaluate side-chains
  68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  335 LEU
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 L residue   30 VAL
Chi-restraints excluded: chain L residue   40 GLN
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 2 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0670
   chunk 23 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    2.7524

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.124709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.093586 restraints weight = 6927.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.087865 restraints weight = 9455.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.088727 restraints weight = 6991.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   3447  Z= 0.256
  Angle     :  0.698   7.257   4702  Z= 0.368
  Chirality :  0.047   0.158    517
  Planarity :  0.005   0.046    600
  Dihedral  :  5.546  23.592    470
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 23.99 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.40), residues: 423
  helix: -3.68 (0.89), residues: 20
  sheet:  0.35 (0.43), residues: 140
  loop : -1.45 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.003   0.001   HIS E 505 
 PHE   0.016   0.002   PHE E 429 
 TYR   0.019   0.002   TYR E 501 
 ARG   0.003   0.000   ARG L  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04170 (   93)
  hydrogen bonds       : angle       6.06857 (  228)
  SS BOND              : bond        0.00409 (    6)
  SS BOND              : angle       1.05788 (   12)
  covalent geometry    : bond        0.00619 ( 3441)
  covalent geometry    : angle       0.69667 ( 4690)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1652.38 seconds
wall clock time: 29 minutes 32.57 seconds (1772.57 seconds total)