Starting phenix.real_space_refine
on Wed Jul 23 11:16:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xrq_38610/07_2025/8xrq_38610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xrq_38610/07_2025/8xrq_38610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xrq_38610/07_2025/8xrq_38610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xrq_38610/07_2025/8xrq_38610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xrq_38610/07_2025/8xrq_38610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xrq_38610/07_2025/8xrq_38610.cif"
  }
  resolution = 4.19
  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=   0.005
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      11      5.16       5
     C    2053      2.51       5
     N     537      2.21       5
     O     609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3210
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1462
          Classifications: {'peptide': 180}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170}
    Chain: "B"
      Number of atoms: 934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 934
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "C"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 814
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98}
  Time building chain proxies: 4.63, per 1000 atoms: 1.44
  Number of scatterers: 3210
  At special positions: 0
  Unit cell: (71.048, 84.744, 68.48, 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      11     16.00
     O     609      8.00
     N     537      7.00
     C    2053      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03

  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: 0.73
  Conformation dependent library (CDL) restraints added in 396.0 milliseconds
  

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  746

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 8 sheets defined
      4.9% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 365 through 371
      removed outlier: 3.566A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 5.067A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 421
      removed outlier: 3.524A  pdb=" N   TYR A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358
      removed outlier: 3.704A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 357 through 358
      removed outlier: 3.704A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59
      removed outlier: 3.877A  pdb=" N   ASN B  58 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR B  50 " --> pdb=" O   ASN B  58 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TRP B  34 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLN B  39 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL B  92 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   CYS B  95 " --> pdb=" O   TRP B 112 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   TRP B 112 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ARG B  97 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69
    Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 21
      removed outlier: 4.247A  pdb=" N   ILE C  75 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LEU C  21 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LEU C  73 " --> pdb=" O   LEU C  21 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54
      removed outlier: 3.687A  pdb=" N   ASN C  53 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   TYR C  49 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   LEU C  33 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN C  38 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   VAL C  85 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)

    48 hydrogen bonds defined for protein.
    105 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: 0.65

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 984
        1.34 -     1.46: 813
        1.46 -     1.58: 1490
        1.58 -     1.70: 2
        1.70 -     1.82: 12
  Bond restraints: 3301
  Sorted by residual:
  bond pdb=" C   PHE B  78 "
       pdb=" N   SER B  79 "
    ideal  model  delta    sigma   weight residual
    1.331  1.440 -0.110 1.41e-02 5.03e+03 6.06e+01
  bond pdb=" C   ILE B  29 "
       pdb=" N   SER B  30 "
    ideal  model  delta    sigma   weight residual
    1.332  1.419 -0.087 1.38e-02 5.25e+03 3.96e+01
  bond pdb=" C   MET B 117 "
       pdb=" N   VAL B 118 "
    ideal  model  delta    sigma   weight residual
    1.330  1.403 -0.073 1.21e-02 6.83e+03 3.67e+01
  bond pdb=" C   VAL B 118 "
       pdb=" N   THR B 119 "
    ideal  model  delta    sigma   weight residual
    1.331  1.260  0.071 1.23e-02 6.61e+03 3.32e+01
  bond pdb=" C   SER B  40 "
       pdb=" N   PRO B  41 "
    ideal  model  delta    sigma   weight residual
    1.331  1.388 -0.057 1.21e-02 6.83e+03 2.21e+01
  ... (remaining 3296 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 4337
        2.08 -     4.16: 119
        4.16 -     6.24: 27
        6.24 -     8.32: 7
        8.32 -    10.40: 2
  Bond angle restraints: 4492
  Sorted by residual:
  angle pdb=" C   SER B  40 "
        pdb=" N   PRO B  41 "
        pdb=" CA  PRO B  41 "
      ideal   model   delta    sigma   weight residual
     120.11  110.63    9.48 1.12e+00 7.97e-01 7.16e+01
  angle pdb=" N   SER B  62 "
        pdb=" CA  SER B  62 "
        pdb=" C   SER B  62 "
      ideal   model   delta    sigma   weight residual
     111.14  104.25    6.89 1.08e+00 8.57e-01 4.07e+01
  angle pdb=" CA  PRO C  40 "
        pdb=" N   PRO C  40 "
        pdb=" CD  PRO C  40 "
      ideal   model   delta    sigma   weight residual
     112.00  103.92    8.08 1.40e+00 5.10e-01 3.33e+01
  angle pdb=" O   PHE B  78 "
        pdb=" C   PHE B  78 "
        pdb=" N   SER B  79 "
      ideal   model   delta    sigma   weight residual
     123.06  129.73   -6.67 1.20e+00 6.94e-01 3.09e+01
  angle pdb=" CA  PHE B  78 "
        pdb=" C   PHE B  78 "
        pdb=" N   SER B  79 "
      ideal   model   delta    sigma   weight residual
     115.91  108.96    6.95 1.29e+00 6.01e-01 2.90e+01
  ... (remaining 4487 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 1674
       18.00 -    36.00: 197
       36.00 -    54.00: 43
       54.00 -    72.00: 6
       72.00 -    89.99: 4
  Dihedral angle restraints: 1924
    sinusoidal: 746
      harmonic: 1178
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.56  -64.56     1      1.00e+01 1.00e-02 5.48e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.81   49.81     1      1.00e+01 1.00e-02 3.40e+01
  dihedral pdb=" CA  ASP B  89 "
           pdb=" CB  ASP B  89 "
           pdb=" CG  ASP B  89 "
           pdb=" OD1 ASP B  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.16   59.16     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 1921 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 299
       0.038 -    0.075: 121
       0.075 -    0.113: 45
       0.113 -    0.151: 9
       0.151 -    0.188: 2
  Chirality restraints: 476
  Sorted by residual:
  chirality pdb=" CA  VAL B 118 "
            pdb=" N   VAL B 118 "
            pdb=" C   VAL B 118 "
            pdb=" CB  VAL B 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CA  VAL A 511 "
            pdb=" N   VAL A 511 "
            pdb=" C   VAL A 511 "
            pdb=" CB  VAL A 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.83e-01
  chirality pdb=" CA  VAL C 104 "
            pdb=" N   VAL C 104 "
            pdb=" C   VAL C 104 "
            pdb=" CB  VAL C 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 473 not shown)

  Planarity restraints: 578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  40 "    0.024 2.00e-02 2.50e+03   4.73e-02 2.24e+01
        pdb=" C   SER B  40 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   SER B  40 "    0.031 2.00e-02 2.50e+03
        pdb=" N   PRO B  41 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  39 "    0.068 5.00e-02 4.00e+02   9.81e-02 1.54e+01
        pdb=" N   PRO C  40 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO C  40 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C  40 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  29 "   -0.018 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   ILE B  29 "    0.065 2.00e-02 2.50e+03
        pdb=" O   ILE B  29 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   SER B  30 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 575 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1157
        2.84 -     3.35: 2737
        3.35 -     3.87: 4951
        3.87 -     4.38: 5461
        4.38 -     4.90: 9458
  Nonbonded interactions: 23764
  Sorted by model distance:
  nonbonded pdb=" O   THR A 430 "
            pdb=" OG1 THR A 430 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OE1 GLN C  42 "
            pdb=" O   ALA C  43 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" O   SER A 438 "
            pdb=" OG  SER A 438 "
     model   vdw
     2.442 3.040
  nonbonded pdb=" O   SER B 103 "
            pdb=" N   TRP B 105 "
     model   vdw
     2.463 3.120
  nonbonded pdb=" O   SER A 496 "
            pdb=" OG  SER A 496 "
     model   vdw
     2.463 3.040
  ... (remaining 23759 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:             6.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4714
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.110   3305  Z= 0.383
  Angle     :  0.868  10.399   4500  Z= 0.541
  Chirality :  0.047   0.188    476
  Planarity :  0.008   0.098    578
  Dihedral  : 15.749  89.994   1166
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.97 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 22.86 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.50 (0.38), residues: 401
  helix: -4.96 (0.50), residues: 6
  sheet: -1.66 (0.62), residues: 78
  loop : -2.69 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  35 
 HIS   0.001   0.001   HIS B  77 
 PHE   0.018   0.001   PHE C  83 
 TYR   0.008   0.001   TYR B  32 
 ARG   0.004   0.000   ARG B  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25843 (   45)
  hydrogen bonds       : angle      12.80089 (  105)
  SS BOND              : bond        0.00377 (    4)
  SS BOND              : angle       1.32614 (    8)
  covalent geometry    : bond        0.00611 ( 3301)
  covalent geometry    : angle       0.86693 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  489 TYR cc_start: 0.5626 (m-80) cc_final: 0.5294 (m-80)
REVERT: B    5 GLN cc_start: 0.6697 (mp10) cc_final: 0.6452 (mp10)
REVERT: B   36 TRP cc_start: 0.5921 (m100) cc_final: 0.5620 (m100)
  outliers start: 3
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1833
  time to fit residues: 13.8076
Evaluate side-chains
  58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 16 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0030
   chunk 12 optimal weight:    0.0010
   chunk 19 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0970
   chunk 36 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.0994

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 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 = 0.4442 r_free = 0.4442 target = 0.198942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.184805 restraints weight = 7082.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.188306 restraints weight = 4602.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.190850 restraints weight = 3159.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4707
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   3305  Z= 0.126
  Angle     :  0.674  11.275   4500  Z= 0.341
  Chirality :  0.047   0.256    476
  Planarity :  0.007   0.074    578
  Dihedral  :  4.764  21.253    452
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.72 %
    Favored  : 87.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.54 (0.38), residues: 401
  helix: -3.27 (0.91), residues: 21
  sheet: -1.84 (0.59), residues: 81
  loop : -2.64 (0.32), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 112 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.013   0.002   PHE B  78 
 TYR   0.029   0.002   TYR B  52 
 ARG   0.009   0.001   ARG C  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03085 (   45)
  hydrogen bonds       : angle       9.04593 (  105)
  SS BOND              : bond        0.00282 (    4)
  SS BOND              : angle       1.06728 (    8)
  covalent geometry    : bond        0.00304 ( 3301)
  covalent geometry    : angle       0.67260 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.1527 (ttmt) cc_final: 0.1186 (tppt)
REVERT: B   45 LEU cc_start: 0.7473 (mt) cc_final: 0.7272 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1973
  time to fit residues: 13.4748
Evaluate side-chains
  57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 GLN ** 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 = 0.4294 r_free = 0.4294 target = 0.186328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.170576 restraints weight = 6735.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.174106 restraints weight = 4515.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.176701 restraints weight = 3231.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5096
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   3305  Z= 0.301
  Angle     :  0.917   7.582   4500  Z= 0.492
  Chirality :  0.056   0.452    476
  Planarity :  0.008   0.094    578
  Dihedral  :  6.923  33.483    452
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.72 %
    Favored  : 86.03 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.00 %
    Favored  : 93.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -3.63 (0.36), residues: 401
  helix: -3.37 (0.69), residues: 27
  sheet: -1.24 (0.62), residues: 79
  loop : -2.89 (0.30), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP C  35 
 HIS   0.006   0.002   HIS A 505 
 PHE   0.049   0.004   PHE A 486 
 TYR   0.016   0.003   TYR B  50 
 ARG   0.007   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04753 (   45)
  hydrogen bonds       : angle       9.39716 (  105)
  SS BOND              : bond        0.01194 (    4)
  SS BOND              : angle       2.09005 (    8)
  covalent geometry    : bond        0.00642 ( 3301)
  covalent geometry    : angle       0.91395 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.6676 (p-90) cc_final: 0.6347 (p-90)
REVERT: B   45 LEU cc_start: 0.7716 (mt) cc_final: 0.7428 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 63
  average time/residue: 0.1665
  time to fit residues: 12.5753
Evaluate side-chains
  61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   chunk 0 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 GLN ** 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 = 0.4275 r_free = 0.4275 target = 0.184979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.170170 restraints weight = 6812.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.173455 restraints weight = 4720.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.175857 restraints weight = 3425.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5091
moved from start:          0.5827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   3305  Z= 0.212
  Angle     :  0.760   8.812   4500  Z= 0.400
  Chirality :  0.049   0.213    476
  Planarity :  0.007   0.089    578
  Dihedral  :  6.498  31.534    452
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 14.46 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -3.46 (0.37), residues: 401
  helix: -3.07 (0.84), residues: 27
  sheet: -1.45 (0.66), residues: 68
  loop : -2.65 (0.31), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  34 
 HIS   0.004   0.002   HIS C  91 
 PHE   0.026   0.002   PHE A 486 
 TYR   0.012   0.002   TYR A 369 
 ARG   0.004   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (   45)
  hydrogen bonds       : angle       8.87550 (  105)
  SS BOND              : bond        0.00666 (    4)
  SS BOND              : angle       1.95082 (    8)
  covalent geometry    : bond        0.00468 ( 3301)
  covalent geometry    : angle       0.75653 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.7621 (mt) cc_final: 0.7420 (mt)
REVERT: B   58 ASN cc_start: 0.6966 (t0) cc_final: 0.6733 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1735
  time to fit residues: 13.5699
Evaluate side-chains
  64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 36 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0980
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 GLN ** 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 = 0.4231 r_free = 0.4231 target = 0.181502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.165739 restraints weight = 6796.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.168989 restraints weight = 4644.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.171426 restraints weight = 3377.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5201
moved from start:          0.6774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   3305  Z= 0.284
  Angle     :  0.888  11.521   4500  Z= 0.476
  Chirality :  0.056   0.424    476
  Planarity :  0.007   0.084    578
  Dihedral  :  7.219  30.358    452
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 16.71 %
    Favored  : 83.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -3.93 (0.36), residues: 401
  helix: -3.90 (0.74), residues: 25
  sheet: -1.71 (0.60), residues: 75
  loop : -2.99 (0.30), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B 112 
 HIS   0.008   0.003   HIS C  91 
 PHE   0.040   0.003   PHE A 486 
 TYR   0.020   0.002   TYR A 508 
 ARG   0.007   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04567 (   45)
  hydrogen bonds       : angle       8.80482 (  105)
  SS BOND              : bond        0.00868 (    4)
  SS BOND              : angle       2.06033 (    8)
  covalent geometry    : bond        0.00613 ( 3301)
  covalent geometry    : angle       0.88488 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: B    5 GLN cc_start: 0.6893 (tp40) cc_final: 0.6678 (tp40)
REVERT: B   34 TRP cc_start: 0.7281 (m100) cc_final: 0.6920 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1896
  time to fit residues: 15.1915
Evaluate side-chains
  65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0870
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.182351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.167686 restraints weight = 6921.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.170931 restraints weight = 4741.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.173180 restraints weight = 3413.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5167
moved from start:          0.7037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   3305  Z= 0.232
  Angle     :  0.821  10.313   4500  Z= 0.433
  Chirality :  0.051   0.264    476
  Planarity :  0.007   0.085    578
  Dihedral  :  7.025  28.756    452
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 15.46 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.92 (0.35), residues: 401
  helix: -3.96 (0.66), residues: 27
  sheet: -1.61 (0.60), residues: 73
  loop : -2.99 (0.30), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 353 
 HIS   0.007   0.002   HIS C  91 
 PHE   0.023   0.003   PHE A 486 
 TYR   0.016   0.002   TYR A 423 
 ARG   0.006   0.001   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (   45)
  hydrogen bonds       : angle       8.73944 (  105)
  SS BOND              : bond        0.00644 (    4)
  SS BOND              : angle       2.20838 (    8)
  covalent geometry    : bond        0.00513 ( 3301)
  covalent geometry    : angle       0.81650 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    5 GLN cc_start: 0.6921 (tp40) cc_final: 0.6703 (tp40)
REVERT: C   56 THR cc_start: 0.8664 (t) cc_final: 0.8391 (p)
REVERT: C   61 ARG cc_start: 0.5388 (mtp-110) cc_final: 0.5100 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1790
  time to fit residues: 13.5518
Evaluate side-chains
  61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.0670
   chunk 22 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0670
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.1854

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 GLN ** 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 = 0.4260 r_free = 0.4260 target = 0.184213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.169285 restraints weight = 6774.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.172667 restraints weight = 4514.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.175138 restraints weight = 3196.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5121
moved from start:          0.7083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   3305  Z= 0.135
  Angle     :  0.706   7.141   4500  Z= 0.361
  Chirality :  0.046   0.189    476
  Planarity :  0.006   0.082    578
  Dihedral  :  5.860  22.456    452
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.47 %
    Favored  : 86.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.59 (0.37), residues: 401
  helix: -3.79 (0.71), residues: 27
  sheet: -1.28 (0.56), residues: 87
  loop : -2.81 (0.32), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 353 
 HIS   0.004   0.001   HIS C  91 
 PHE   0.019   0.002   PHE C  98 
 TYR   0.010   0.001   TYR A 369 
 ARG   0.004   0.001   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03050 (   45)
  hydrogen bonds       : angle       8.35519 (  105)
  SS BOND              : bond        0.00491 (    4)
  SS BOND              : angle       1.81313 (    8)
  covalent geometry    : bond        0.00310 ( 3301)
  covalent geometry    : angle       0.70290 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7185 (p-90) cc_final: 0.5757 (p-90)
REVERT: A  380 TYR cc_start: 0.6587 (m-80) cc_final: 0.6374 (m-80)
REVERT: B    5 GLN cc_start: 0.6948 (tp40) cc_final: 0.6713 (tp40)
REVERT: B   45 LEU cc_start: 0.7563 (mt) cc_final: 0.7303 (mt)
REVERT: B   58 ASN cc_start: 0.7025 (t0) cc_final: 0.6772 (t0)
REVERT: C   56 THR cc_start: 0.8648 (t) cc_final: 0.8399 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1648
  time to fit residues: 12.4801
Evaluate side-chains
  62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    0.0170
   chunk 25 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 37 optimal weight:    0.0060
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3234

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 GLN ** 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 = 0.4241 r_free = 0.4241 target = 0.182409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.167065 restraints weight = 6801.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.170510 restraints weight = 4567.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.172930 restraints weight = 3245.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5167
moved from start:          0.7348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   3305  Z= 0.182
  Angle     :  0.756   8.647   4500  Z= 0.391
  Chirality :  0.049   0.180    476
  Planarity :  0.007   0.082    578
  Dihedral  :  6.254  24.054    452
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 15.21 %
    Favored  : 84.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.65 (0.36), residues: 401
  helix: -3.81 (0.72), residues: 27
  sheet: -1.28 (0.59), residues: 81
  loop : -2.86 (0.31), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  34 
 HIS   0.008   0.002   HIS C  91 
 PHE   0.019   0.002   PHE A 486 
 TYR   0.020   0.002   TYR A 423 
 ARG   0.004   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03416 (   45)
  hydrogen bonds       : angle       8.38627 (  105)
  SS BOND              : bond        0.00565 (    4)
  SS BOND              : angle       1.85181 (    8)
  covalent geometry    : bond        0.00407 ( 3301)
  covalent geometry    : angle       0.75307 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7242 (p-90) cc_final: 0.6009 (p-90)
REVERT: B    5 GLN cc_start: 0.6984 (tp40) cc_final: 0.6748 (tp40)
REVERT: B   45 LEU cc_start: 0.7608 (mt) cc_final: 0.7365 (mt)
REVERT: C   56 THR cc_start: 0.8647 (t) cc_final: 0.8447 (p)
REVERT: C   61 ARG cc_start: 0.4585 (ttp-110) cc_final: 0.4101 (ptt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1890
  time to fit residues: 14.0646
Evaluate side-chains
  60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0070
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    0.2980
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0870
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
** C  42 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 = 0.4247 r_free = 0.4247 target = 0.183111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.167904 restraints weight = 6816.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.171303 restraints weight = 4595.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.173703 restraints weight = 3272.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5139
moved from start:          0.7397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   3305  Z= 0.151
  Angle     :  0.702   7.960   4500  Z= 0.361
  Chirality :  0.047   0.186    476
  Planarity :  0.006   0.081    578
  Dihedral  :  5.863  21.699    452
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.47 %
    Favored  : 86.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.64 (0.38), residues: 401
  helix: -3.83 (0.71), residues: 27
  sheet: -1.32 (0.54), residues: 94
  loop : -2.87 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  34 
 HIS   0.008   0.003   HIS C  91 
 PHE   0.016   0.002   PHE A 486 
 TYR   0.010   0.001   TYR A 369 
 ARG   0.009   0.001   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03004 (   45)
  hydrogen bonds       : angle       8.20499 (  105)
  SS BOND              : bond        0.00480 (    4)
  SS BOND              : angle       1.47524 (    8)
  covalent geometry    : bond        0.00345 ( 3301)
  covalent geometry    : angle       0.70016 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7215 (p-90) cc_final: 0.5978 (p-90)
REVERT: B    5 GLN cc_start: 0.7001 (tp40) cc_final: 0.6743 (tp40)
REVERT: B   45 LEU cc_start: 0.7578 (mt) cc_final: 0.7314 (mt)
REVERT: C   56 THR cc_start: 0.8656 (t) cc_final: 0.8431 (p)
REVERT: C   61 ARG cc_start: 0.4479 (ttp-110) cc_final: 0.4135 (ptt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2111
  time to fit residues: 15.2707
Evaluate side-chains
  58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 18 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0870
   chunk 27 optimal weight:    0.4980
   chunk 7 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 26 optimal weight:    0.4980
   chunk 6 optimal weight:    0.2980
   overall best weight:    0.2358

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
** C  42 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 = 0.4252 r_free = 0.4252 target = 0.183490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.169262 restraints weight = 6723.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.172453 restraints weight = 4593.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.174683 restraints weight = 3289.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5117
moved from start:          0.7481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   3305  Z= 0.146
  Angle     :  0.699   7.718   4500  Z= 0.358
  Chirality :  0.047   0.185    476
  Planarity :  0.006   0.082    578
  Dihedral  :  5.757  20.210    452
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.97 %
    Favored  : 86.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.58 (0.38), residues: 401
  helix: -3.78 (0.71), residues: 27
  sheet: -1.26 (0.57), residues: 87
  loop : -2.82 (0.32), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  34 
 HIS   0.007   0.002   HIS C  91 
 PHE   0.025   0.002   PHE A 456 
 TYR   0.019   0.001   TYR A 423 
 ARG   0.006   0.001   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02928 (   45)
  hydrogen bonds       : angle       8.13646 (  105)
  SS BOND              : bond        0.00476 (    4)
  SS BOND              : angle       1.42197 (    8)
  covalent geometry    : bond        0.00337 ( 3301)
  covalent geometry    : angle       0.69712 ( 4492)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7210 (p-90) cc_final: 0.6063 (p-90)
REVERT: B    5 GLN cc_start: 0.6912 (tp40) cc_final: 0.6662 (tp40)
REVERT: B   45 LEU cc_start: 0.7606 (mt) cc_final: 0.7339 (mt)
REVERT: C   56 THR cc_start: 0.8594 (t) cc_final: 0.8368 (p)
REVERT: C   61 ARG cc_start: 0.4366 (ttp-110) cc_final: 0.3929 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1771
  time to fit residues: 12.6390
Evaluate side-chains
  59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0020
   chunk 8 optimal weight:    0.4980
   chunk 20 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0000
   chunk 19 optimal weight:    0.0980
   chunk 37 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0030
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.0802

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
** C  42 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 = 0.4288 r_free = 0.4288 target = 0.186890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.172032 restraints weight = 6722.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.175338 restraints weight = 4556.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.177814 restraints weight = 3271.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5055
moved from start:          0.7405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   3305  Z= 0.103
  Angle     :  0.620   6.090   4500  Z= 0.314
  Chirality :  0.044   0.195    476
  Planarity :  0.006   0.080    578
  Dihedral  :  4.898  19.237    452
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.22 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -3.42 (0.38), residues: 401
  helix: -3.55 (0.74), residues: 27
  sheet: -1.17 (0.54), residues: 95
  loop : -2.74 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.005   0.002   HIS C  91 
 PHE   0.012   0.001   PHE A 490 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.003   0.000   ARG C  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02408 (   45)
  hydrogen bonds       : angle       7.61975 (  105)
  SS BOND              : bond        0.00351 (    4)
  SS BOND              : angle       1.17353 (    8)
  covalent geometry    : bond        0.00244 ( 3301)
  covalent geometry    : angle       0.61875 ( 4492)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3599.86 seconds
wall clock time: 65 minutes 27.82 seconds (3927.82 seconds total)