Starting phenix.real_space_refine
on Fri May  9 16:53:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xrq_38610/05_2025/8xrq_38610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xrq_38610/05_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_38610/05_2025/8xrq_38610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xrq_38610/05_2025/8xrq_38610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xrq_38610/05_2025/8xrq_38610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xrq_38610/05_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-5687/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: 4.73, per 1000 atoms: 1.47
  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: 0.72
  Conformation dependent library (CDL) restraints added in 369.1 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: 0.69

  Time building geometry restraints manager: 0.87 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:             5.460
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.180
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.750
-------------------------------------------------------------------------------
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  : 0.355 
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: 0.2081
  time to fit residues: 15.6850
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  : 0.501 
-------------------------------------------------------------------------------
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 = 24)----------------|
| 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 = 0.190851 restraints weight = 3159.580|
|-----------------------------------------------------------------------------|
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  : 0.341 
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: 0.1976
  time to fit residues: 13.5339
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  : 0.338 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.185425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.169731 restraints weight = 6713.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.173196 restraints weight = 4529.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.175745 restraints weight = 3243.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5117
moved from start:          0.5327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   3305  Z= 0.316
  Angle     :  0.950   7.627   4500  Z= 0.511
  Chirality :  0.058   0.442    476
  Planarity :  0.008   0.094    578
  Dihedral  :  7.218  34.796    452
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.97 %
    Favored  : 85.79 %
  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: -3.73 (0.36), residues: 401
  helix: -3.47 (0.67), residues: 27
  sheet: -1.32 (0.61), residues: 79
  loop : -2.95 (0.30), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP C  35 
 HIS   0.007   0.003   HIS A 505 
 PHE   0.053   0.004   PHE A 486 
 TYR   0.017   0.003   TYR B  50 
 ARG   0.008   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04902 (   45)
  hydrogen bonds       : angle       9.55102 (  105)
  SS BOND              : bond        0.01294 (    4)
  SS BOND              : angle       2.19044 (    8)
  covalent geometry    : bond        0.00679 ( 3301)
  covalent geometry    : angle       0.94671 ( 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
  68 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 ASP cc_start: 0.4658 (p0) cc_final: 0.4281 (p0)
REVERT: A  353 TRP cc_start: 0.6695 (p-90) cc_final: 0.6452 (p-90)
REVERT: A  491 PRO cc_start: 0.7491 (Cg_endo) cc_final: 0.7234 (Cg_exo)
REVERT: B   45 LEU cc_start: 0.7709 (mt) cc_final: 0.7421 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 68
  average time/residue: 0.1645
  time to fit residues: 13.5424
Evaluate side-chains
  66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0050
   chunk 35 optimal weight:    0.0170
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 0 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.3232

-------------------------------------------------------------------------------
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 = 0.4284 r_free = 0.4284 target = 0.186020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.169921 restraints weight = 6749.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.173618 restraints weight = 4589.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.176239 restraints weight = 3292.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5081
moved from start:          0.5807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3305  Z= 0.183
  Angle     :  0.726   8.128   4500  Z= 0.379
  Chirality :  0.048   0.205    476
  Planarity :  0.007   0.088    578
  Dihedral  :  6.220  26.587    452
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.22 %
    Favored  : 86.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  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: -3.40 (0.38), residues: 401
  helix: -3.09 (0.86), residues: 27
  sheet: -1.31 (0.60), residues: 79
  loop : -2.66 (0.32), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 112 
 HIS   0.004   0.002   HIS C  91 
 PHE   0.020   0.002   PHE A 486 
 TYR   0.013   0.001   TYR A 369 
 ARG   0.004   0.001   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03350 (   45)
  hydrogen bonds       : angle       8.83000 (  105)
  SS BOND              : bond        0.00528 (    4)
  SS BOND              : angle       1.87736 (    8)
  covalent geometry    : bond        0.00404 ( 3301)
  covalent geometry    : angle       0.72218 ( 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
  64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  448 ASN cc_start: 0.7882 (t0) cc_final: 0.7643 (t0)
REVERT: B   45 LEU cc_start: 0.7583 (mt) cc_final: 0.7371 (mt)
REVERT: B   58 ASN cc_start: 0.6929 (t0) cc_final: 0.6670 (t0)
REVERT: C   56 THR cc_start: 0.8642 (t) cc_final: 0.8360 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1732
  time to fit residues: 13.3255
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  : 0.351 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 36 optimal weight:    0.3980
   chunk 31 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.3958

-------------------------------------------------------------------------------
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 = 0.4255 r_free = 0.4255 target = 0.183669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.167591 restraints weight = 6824.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.171068 restraints weight = 4685.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.173582 restraints weight = 3392.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5145
moved from start:          0.6396

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= 0.210
  Angle     :  0.776   8.800   4500  Z= 0.409
  Chirality :  0.051   0.383    476
  Planarity :  0.007   0.084    578
  Dihedral  :  6.525  26.014    452
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.97 %
    Favored  : 85.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  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: -3.52 (0.37), residues: 401
  helix: -3.34 (0.89), residues: 27
  sheet: -1.26 (0.60), residues: 79
  loop : -2.77 (0.31), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  34 
 HIS   0.007   0.003   HIS C  91 
 PHE   0.030   0.003   PHE A 486 
 TYR   0.016   0.002   TYR A 508 
 ARG   0.004   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03887 (   45)
  hydrogen bonds       : angle       8.38598 (  105)
  SS BOND              : bond        0.00576 (    4)
  SS BOND              : angle       1.65210 (    8)
  covalent geometry    : bond        0.00459 ( 3301)
  covalent geometry    : angle       0.77331 ( 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
  65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  491 PRO cc_start: 0.7410 (Cg_endo) cc_final: 0.7122 (Cg_exo)
REVERT: B   34 TRP cc_start: 0.7329 (m100) cc_final: 0.7004 (m100)
REVERT: B   45 LEU cc_start: 0.7648 (mt) cc_final: 0.7436 (mt)
REVERT: B   58 ASN cc_start: 0.6963 (t0) cc_final: 0.6752 (t0)
REVERT: C    2 ILE cc_start: 0.7140 (pt) cc_final: 0.6735 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1843
  time to fit residues: 14.2297
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  : 0.359 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0170
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.181621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.165361 restraints weight = 6856.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.168856 restraints weight = 4620.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.171382 restraints weight = 3324.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5185
moved from start:          0.6967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   3305  Z= 0.245
  Angle     :  0.828  10.256   4500  Z= 0.438
  Chirality :  0.050   0.240    476
  Planarity :  0.007   0.086    578
  Dihedral  :  6.940  28.435    452
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 15.96 %
    Favored  : 83.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  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: -3.81 (0.36), residues: 401
  helix: -3.76 (0.73), residues: 27
  sheet: -1.42 (0.59), residues: 79
  loop : -2.97 (0.30), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP B 112 
 HIS   0.007   0.002   HIS C  91 
 PHE   0.042   0.003   PHE A 486 
 TYR   0.016   0.002   TYR A 423 
 ARG   0.008   0.001   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (   45)
  hydrogen bonds       : angle       8.62066 (  105)
  SS BOND              : bond        0.00820 (    4)
  SS BOND              : angle       2.48623 (    8)
  covalent geometry    : bond        0.00537 ( 3301)
  covalent geometry    : angle       0.82172 ( 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
  67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 ARG cc_start: 0.6708 (ttt90) cc_final: 0.6159 (ttt180)
REVERT: B    5 GLN cc_start: 0.6966 (tp40) cc_final: 0.6747 (tp40)
REVERT: C    3 VAL cc_start: 0.6544 (p) cc_final: 0.6230 (p)
REVERT: C   56 THR cc_start: 0.8697 (t) cc_final: 0.8421 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1793
  time to fit residues: 14.3279
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  : 0.341 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 31 optimal weight:    0.2980
   chunk 34 optimal weight:    0.0000
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.2542

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.183338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.168199 restraints weight = 6770.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.171562 restraints weight = 4543.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.173999 restraints weight = 3248.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5144
moved from start:          0.7107

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= 0.157
  Angle     :  0.724   7.718   4500  Z= 0.375
  Chirality :  0.047   0.185    476
  Planarity :  0.007   0.082    578
  Dihedral  :  6.098  24.766    452
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.51
  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: -3.62 (0.37), residues: 401
  helix: -3.68 (0.77), residues: 27
  sheet: -1.33 (0.53), residues: 94
  loop : -2.87 (0.32), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 353 
 HIS   0.008   0.002   HIS C  91 
 PHE   0.019   0.002   PHE A 486 
 TYR   0.011   0.001   TYR A 369 
 ARG   0.003   0.001   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03098 (   45)
  hydrogen bonds       : angle       8.10116 (  105)
  SS BOND              : bond        0.00495 (    4)
  SS BOND              : angle       1.81375 (    8)
  covalent geometry    : bond        0.00350 ( 3301)
  covalent geometry    : angle       0.72085 ( 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  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 TYR cc_start: 0.6635 (m-80) cc_final: 0.6423 (m-80)
REVERT: B    5 GLN cc_start: 0.6951 (tp40) cc_final: 0.6732 (tp40)
REVERT: B   45 LEU cc_start: 0.7687 (mt) cc_final: 0.7363 (mm)
REVERT: C   56 THR cc_start: 0.8678 (t) cc_final: 0.8434 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1770
  time to fit residues: 13.3234
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  : 0.366 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 25 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 37 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0970
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.2936

-------------------------------------------------------------------------------
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 = 0.4238 r_free = 0.4238 target = 0.182138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.166592 restraints weight = 6661.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.170063 restraints weight = 4441.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.172435 restraints weight = 3156.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5169
moved from start:          0.7391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3305  Z= 0.168
  Angle     :  0.734   8.435   4500  Z= 0.379
  Chirality :  0.047   0.175    476
  Planarity :  0.007   0.083    578
  Dihedral  :  6.118  24.442    452
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 15.46 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  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: -3.61 (0.37), residues: 401
  helix: -3.73 (0.76), residues: 27
  sheet: -1.35 (0.55), residues: 87
  loop : -2.82 (0.32), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 353 
 HIS   0.009   0.002   HIS C  91 
 PHE   0.021   0.002   PHE A 486 
 TYR   0.022   0.002   TYR A 423 
 ARG   0.003   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (   45)
  hydrogen bonds       : angle       8.03436 (  105)
  SS BOND              : bond        0.00468 (    4)
  SS BOND              : angle       1.78673 (    8)
  covalent geometry    : bond        0.00378 ( 3301)
  covalent geometry    : angle       0.73074 ( 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
  64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7239 (p-90) cc_final: 0.5989 (p-90)
REVERT: B    5 GLN cc_start: 0.6967 (tp40) cc_final: 0.6728 (tp40)
REVERT: B   45 LEU cc_start: 0.7689 (mt) cc_final: 0.7342 (mm)
REVERT: C   56 THR cc_start: 0.8639 (t) cc_final: 0.8417 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1752
  time to fit residues: 13.4551
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  : 0.431 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0070
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 5 optimal weight:    0.0770
   chunk 1 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.4243 r_free = 0.4243 target = 0.182524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.167536 restraints weight = 6747.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.170875 restraints weight = 4515.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.173323 restraints weight = 3204.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5156
moved from start:          0.7502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3305  Z= 0.167
  Angle     :  0.733   8.535   4500  Z= 0.379
  Chirality :  0.047   0.182    476
  Planarity :  0.007   0.082    578
  Dihedral  :  6.015  21.236    452
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 14.46 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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: -3.66 (0.37), residues: 401
  helix: -3.84 (0.71), residues: 27
  sheet: -1.42 (0.52), residues: 94
  loop : -2.85 (0.32), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 353 
 HIS   0.009   0.002   HIS C  91 
 PHE   0.021   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        0.03201 (   45)
  hydrogen bonds       : angle       8.29938 (  105)
  SS BOND              : bond        0.00592 (    4)
  SS BOND              : angle       1.64253 (    8)
  covalent geometry    : bond        0.00373 ( 3301)
  covalent geometry    : angle       0.73025 ( 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
  62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7218 (p-90) cc_final: 0.6086 (p-90)
REVERT: B    5 GLN cc_start: 0.6973 (tp40) cc_final: 0.6728 (tp40)
REVERT: B   45 LEU cc_start: 0.7520 (mt) cc_final: 0.7241 (mt)
REVERT: C    3 VAL cc_start: 0.6542 (p) cc_final: 0.6086 (p)
REVERT: C   56 THR cc_start: 0.8681 (t) cc_final: 0.8444 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1803
  time to fit residues: 13.3871
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  : 0.351 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 26 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4215 r_free = 0.4215 target = 0.179900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.164363 restraints weight = 6670.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.167681 restraints weight = 4559.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.170072 restraints weight = 3256.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5233
moved from start:          0.7919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   3305  Z= 0.251
  Angle     :  0.857  10.483   4500  Z= 0.451
  Chirality :  0.053   0.218    476
  Planarity :  0.008   0.083    578
  Dihedral  :  6.974  24.596    452
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 18.45 %
    Favored  : 81.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  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: -3.98 (0.36), residues: 401
  helix: -4.22 (0.62), residues: 25
  sheet: -1.68 (0.53), residues: 87
  loop : -3.05 (0.31), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  34 
 HIS   0.012   0.003   HIS C  91 
 PHE   0.030   0.003   PHE A 486 
 TYR   0.026   0.002   TYR A 423 
 ARG   0.007   0.001   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04059 (   45)
  hydrogen bonds       : angle       8.76612 (  105)
  SS BOND              : bond        0.00739 (    4)
  SS BOND              : angle       1.90832 (    8)
  covalent geometry    : bond        0.00557 ( 3301)
  covalent geometry    : angle       0.85444 ( 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
  63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7195 (p-90) cc_final: 0.6453 (p-90)
REVERT: B    5 GLN cc_start: 0.7057 (tp40) cc_final: 0.6786 (tp40)
REVERT: B   45 LEU cc_start: 0.7601 (mt) cc_final: 0.7342 (mt)
REVERT: C   56 THR cc_start: 0.8638 (t) cc_final: 0.8405 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1908
  time to fit residues: 14.2131
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  : 0.323 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0980
   chunk 37 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0770
   chunk 35 optimal weight:    0.0770
   overall best weight:    0.1094

-------------------------------------------------------------------------------
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 = 0.4269 r_free = 0.4269 target = 0.184912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.170777 restraints weight = 6675.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.173938 restraints weight = 4553.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.176221 restraints weight = 3269.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5095
moved from start:          0.7725

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= 0.120
  Angle     :  0.685   6.213   4500  Z= 0.351
  Chirality :  0.046   0.191    476
  Planarity :  0.007   0.081    578
  Dihedral  :  5.589  20.280    452
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.97 %
    Favored  : 87.78 %
  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: -3.63 (0.37), residues: 401
  helix: -3.90 (0.70), residues: 27
  sheet: -1.38 (0.53), residues: 94
  loop : -2.83 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 353 
 HIS   0.006   0.002   HIS C  91 
 PHE   0.027   0.002   PHE A 456 
 TYR   0.012   0.001   TYR A 501 
 ARG   0.003   0.000   ARG C  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02689 (   45)
  hydrogen bonds       : angle       8.12040 (  105)
  SS BOND              : bond        0.00420 (    4)
  SS BOND              : angle       1.24901 (    8)
  covalent geometry    : bond        0.00280 ( 3301)
  covalent geometry    : angle       0.68330 ( 4492)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1817.99 seconds
wall clock time: 32 minutes 31.93 seconds (1951.93 seconds total)