Starting phenix.real_space_refine
on Fri May  9 23:53:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c02_16353/05_2025/8c02_16353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c02_16353/05_2025/8c02_16353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c02_16353/05_2025/8c02_16353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c02_16353/05_2025/8c02_16353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c02_16353/05_2025/8c02_16353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c02_16353/05_2025/8c02_16353.cif"
  }
  resolution = 4.09
  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=   0.001 sd=   0.027
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      31      5.16       5
     C    2767      2.51       5
     N     695      2.21       5
     O     749      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 4242
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3300
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 9, 'TRANS': 419}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 942
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
  Time building chain proxies: 2.81, per 1000 atoms: 0.66
  Number of scatterers: 4242
  At special positions: 0
  Unit cell: (76.818, 100.254, 72.912, 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      31     16.00
     O     749      8.00
     N     695      7.00
     C    2767      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  98 " 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: 1.06
  Conformation dependent library (CDL) restraints added in 501.2 milliseconds
  

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1004

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      72.5% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 22
    Processing helix  chain 'A' and resid 23 through 54
    Processing helix  chain 'A' and resid 57 through 86
      removed outlier: 3.897A  pdb=" N   THR A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   ALA A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
    Processing helix  chain 'A' and resid 116 through 122
    Processing helix  chain 'A' and resid 127 through 164
    Processing helix  chain 'A' and resid 166 through 199
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 230
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.077A  pdb=" N   VAL A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LYS A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 231 through 236'
    Processing helix  chain 'A' and resid 288 through 305
      removed outlier: 3.856A  pdb=" N   PHE A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'A' and resid 331 through 336
    Processing helix  chain 'A' and resid 338 through 367
      removed outlier: 3.695A  pdb=" N   ARG A 365 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS A 366 " --> pdb=" O   TRP A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 393
    Processing helix  chain 'A' and resid 451 through 483
      removed outlier: 3.642A  pdb=" N   VAL A 455 " --> pdb=" O   PRO A 451 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 467 " --> pdb=" O   ILE A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 514
    Processing helix  chain 'A' and resid 519 through 546
    Processing helix  chain 'B' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9
    Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15
      removed outlier: 6.523A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG B  37 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   MET B  36 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ALA B  52 " --> pdb=" O   MET B  36 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TRP B  38 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 15
      removed outlier: 6.523A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   LYS B 101 " --> pdb=" O   TYR B 112 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   TYR B 112 " --> pdb=" O   LYS B 101 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR B 103 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1014 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: 1.21

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1312
        1.34 -     1.46: 1032
        1.46 -     1.58: 1939
        1.58 -     1.70: 0
        1.70 -     1.81: 52
  Bond restraints: 4335
  Sorted by residual:
  bond pdb=" N   MET A 288 "
       pdb=" CA  MET A 288 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.037 1.25e-02 6.40e+03 8.87e+00
  bond pdb=" N   TYR A 318 "
       pdb=" CA  TYR A 318 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.031 1.32e-02 5.74e+03 5.40e+00
  bond pdb=" CG  GLN A  93 "
       pdb=" CD  GLN A  93 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.31e+00
  bond pdb=" CG1 ILE A 136 "
       pdb=" CD1 ILE A 136 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.14e+00
  bond pdb=" CG  LEU A 222 "
       pdb=" CD1 LEU A 222 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  ... (remaining 4330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 5701
        1.98 -     3.97: 149
        3.97 -     5.95: 33
        5.95 -     7.94: 12
        7.94 -     9.92: 3
  Bond angle restraints: 5898
  Sorted by residual:
  angle pdb=" CA  LYS B  78 "
        pdb=" CB  LYS B  78 "
        pdb=" CG  LYS B  78 "
      ideal   model   delta    sigma   weight residual
     114.10  121.78   -7.68 2.00e+00 2.50e-01 1.48e+01
  angle pdb=" CA  GLU A 486 "
        pdb=" CB  GLU A 486 "
        pdb=" CG  GLU A 486 "
      ideal   model   delta    sigma   weight residual
     114.10  121.55   -7.45 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" N   GLN A  93 "
        pdb=" CA  GLN A  93 "
        pdb=" CB  GLN A  93 "
      ideal   model   delta    sigma   weight residual
     110.28  115.21   -4.93 1.55e+00 4.16e-01 1.01e+01
  angle pdb=" CB  LYS A 549 "
        pdb=" CG  LYS A 549 "
        pdb=" CD  LYS A 549 "
      ideal   model   delta    sigma   weight residual
     111.30  118.34   -7.04 2.30e+00 1.89e-01 9.36e+00
  angle pdb=" CA  GLU A 290 "
        pdb=" CB  GLU A 290 "
        pdb=" CG  GLU A 290 "
      ideal   model   delta    sigma   weight residual
     114.10  120.04   -5.94 2.00e+00 2.50e-01 8.81e+00
  ... (remaining 5893 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 2262
       16.19 -    32.38: 187
       32.38 -    48.57: 43
       48.57 -    64.76: 7
       64.76 -    80.95: 5
  Dihedral angle restraints: 2504
    sinusoidal: 930
      harmonic: 1574
  Sorted by residual:
  dihedral pdb=" CA  THR A 122 "
           pdb=" C   THR A 122 "
           pdb=" N   MET A 123 "
           pdb=" CA  MET A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.55  -17.45     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  GLU B  46 "
           pdb=" C   GLU B  46 "
           pdb=" N   ARG B  47 "
           pdb=" CA  ARG B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.72  -17.28     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  MET B 105 "
           pdb=" C   MET B 105 "
           pdb=" N   ALA B 106 "
           pdb=" CA  ALA B 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.97   17.03     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 2501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 473
       0.039 -    0.077: 164
       0.077 -    0.116: 48
       0.116 -    0.155: 7
       0.155 -    0.193: 4
  Chirality restraints: 696
  Sorted by residual:
  chirality pdb=" CA  GLU A 290 "
            pdb=" N   GLU A 290 "
            pdb=" C   GLU A 290 "
            pdb=" CB  GLU A 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.36e-01
  chirality pdb=" CA  GLN A  93 "
            pdb=" N   GLN A  93 "
            pdb=" C   GLN A  93 "
            pdb=" CB  GLN A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" CB  ILE B  56 "
            pdb=" CA  ILE B  56 "
            pdb=" CG1 ILE B  56 "
            pdb=" CG2 ILE B  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.81e-01
  ... (remaining 693 not shown)

  Planarity restraints: 719
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 514 "   -0.054 5.00e-02 4.00e+02   8.30e-02 1.10e+01
        pdb=" N   PRO A 515 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 515 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 515 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  29 "   -0.044 5.00e-02 4.00e+02   6.61e-02 6.99e+00
        pdb=" N   PRO B  30 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B  30 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  30 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 317 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.62e+00
        pdb=" C   LEU A 317 "    0.044 2.00e-02 2.50e+03
        pdb=" O   LEU A 317 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TYR A 318 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 716 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 718
        2.76 -     3.29: 4563
        3.29 -     3.83: 7381
        3.83 -     4.36: 7786
        4.36 -     4.90: 13676
  Nonbonded interactions: 34124
  Sorted by model distance:
  nonbonded pdb=" O   CYS B  24 "
            pdb=" OG1 THR B  80 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   VAL A 358 "
            pdb=" OG1 THR A 361 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   ALA B  54 "
            pdb=" NH2 ARG B  74 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" N   MET B 105 "
            pdb=" O   TRP B 108 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" O   THR A 230 "
            pdb=" OG1 THR A 230 "
     model   vdw
     2.339 3.040
  ... (remaining 34119 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:             0.240
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.590
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
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      :  0.004   0.057   4336  Z= 0.188
  Angle     :  0.833   9.920   5900  Z= 0.419
  Chirality :  0.045   0.193    696
  Planarity :  0.007   0.083    719
  Dihedral  : 13.159  80.949   1497
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  0.00 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.35), residues: 541
  helix:  2.10 (0.26), residues: 367
  sheet: -1.31 (0.64), residues: 39
  loop : -1.40 (0.53), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  38 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.016   0.002   PHE A 530 
 TYR   0.030   0.002   TYR A  29 
 ARG   0.007   0.001   ARG A  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12218 (  344)
  hydrogen bonds       : angle       5.58573 ( 1014)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       2.16103 (    2)
  covalent geometry    : bond        0.00409 ( 4335)
  covalent geometry    : angle       0.83181 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 192
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8755 (t80) cc_final: 0.8459 (t80)
REVERT: A   36 THR cc_start: 0.9349 (m) cc_final: 0.9145 (t)
REVERT: A  111 MET cc_start: 0.8545 (tpt) cc_final: 0.8277 (mmm)
REVERT: A  184 THR cc_start: 0.9334 (m) cc_final: 0.8956 (t)
REVERT: A  290 GLU cc_start: 0.8139 (pm20) cc_final: 0.7931 (pm20)
REVERT: A  312 MET cc_start: 0.8837 (tpt) cc_final: 0.8058 (tpp)
REVERT: A  473 ASP cc_start: 0.9390 (t70) cc_final: 0.9177 (t0)
REVERT: A  536 ILE cc_start: 0.8342 (mm) cc_final: 0.8104 (mm)
REVERT: B   20 LEU cc_start: 0.8822 (tt) cc_final: 0.8434 (mt)
REVERT: B   70 PHE cc_start: 0.7802 (m-10) cc_final: 0.7413 (m-80)
REVERT: B   92 ASP cc_start: 0.7493 (m-30) cc_final: 0.6904 (m-30)
REVERT: B  119 VAL cc_start: 0.9269 (t) cc_final: 0.9062 (t)
  outliers start: 2
  outliers final: 1
  residues processed: 192
  average time/residue: 0.1306
  time to fit residues: 32.1675
Evaluate side-chains
  159 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0040
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 GLN
A 335 GLN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.134577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.106428 restraints weight = 8659.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.109723 restraints weight = 5051.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.112052 restraints weight = 3512.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4336  Z= 0.167
  Angle     :  0.672   8.160   5900  Z= 0.343
  Chirality :  0.041   0.163    696
  Planarity :  0.005   0.066    719
  Dihedral  :  4.131  16.134    590
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.00 (0.36), residues: 541
  helix:  2.36 (0.26), residues: 371
  sheet: -0.11 (0.74), residues: 43
  loop : -1.39 (0.54), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  38 
 HIS   0.003   0.001   HIS A  32 
 PHE   0.006   0.001   PHE B 107 
 TYR   0.024   0.002   TYR A  29 
 ARG   0.006   0.001   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  344)
  hydrogen bonds       : angle       4.58185 ( 1014)
  SS BOND              : bond        0.00717 (    1)
  SS BOND              : angle       1.98604 (    2)
  covalent geometry    : bond        0.00369 ( 4335)
  covalent geometry    : angle       0.67074 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8762 (t80) cc_final: 0.8556 (t80)
REVERT: A  111 MET cc_start: 0.8668 (tpt) cc_final: 0.8291 (mmm)
REVERT: A  179 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8101 (mtm-85)
REVERT: A  180 ILE cc_start: 0.8367 (mm) cc_final: 0.8163 (mm)
REVERT: A  488 GLU cc_start: 0.7366 (tp30) cc_final: 0.7119 (tp30)
REVERT: A  536 ILE cc_start: 0.8261 (mm) cc_final: 0.8045 (mm)
REVERT: B    6 LEU cc_start: 0.8637 (pp) cc_final: 0.8346 (pp)
REVERT: B    8 GLU cc_start: 0.7534 (mp0) cc_final: 0.5922 (mp0)
REVERT: B   34 ASN cc_start: 0.8164 (m-40) cc_final: 0.7559 (m110)
REVERT: B   38 TRP cc_start: 0.8373 (m100) cc_final: 0.8014 (m100)
REVERT: B   92 ASP cc_start: 0.7334 (m-30) cc_final: 0.6929 (m-30)
REVERT: B  117 THR cc_start: 0.8763 (p) cc_final: 0.8445 (t)
REVERT: B  119 VAL cc_start: 0.9295 (t) cc_final: 0.9065 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1477
  time to fit residues: 36.1315
Evaluate side-chains
  158 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0020
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0770
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4346

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** 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 = 0.3764 r_free = 0.3764 target = 0.137017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.109040 restraints weight = 8655.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112507 restraints weight = 4984.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.114905 restraints weight = 3393.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4336  Z= 0.143
  Angle     :  0.638   9.164   5900  Z= 0.329
  Chirality :  0.040   0.162    696
  Planarity :  0.004   0.046    719
  Dihedral  :  3.930  16.866    590
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.30 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.36), residues: 541
  helix:  2.39 (0.26), residues: 370
  sheet: -0.05 (0.81), residues: 38
  loop : -1.31 (0.52), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  42 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.009   0.001   PHE A 292 
 TYR   0.016   0.001   TYR B  62 
 ARG   0.005   0.001   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04259 (  344)
  hydrogen bonds       : angle       4.37679 ( 1014)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       1.74358 (    2)
  covalent geometry    : bond        0.00314 ( 4335)
  covalent geometry    : angle       0.63759 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8770 (t80) cc_final: 0.8506 (t80)
REVERT: A   29 TYR cc_start: 0.9291 (m-10) cc_final: 0.9064 (m-10)
REVERT: A   52 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8557 (mm-30)
REVERT: A   79 ILE cc_start: 0.8984 (mm) cc_final: 0.8770 (tp)
REVERT: A  179 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7985 (mtm-85)
REVERT: A  180 ILE cc_start: 0.8238 (mm) cc_final: 0.7981 (mm)
REVERT: A  312 MET cc_start: 0.8566 (tpp) cc_final: 0.7427 (tpp)
REVERT: A  495 VAL cc_start: 0.9562 (m) cc_final: 0.9356 (m)
REVERT: A  536 ILE cc_start: 0.8225 (mm) cc_final: 0.8020 (mm)
REVERT: B   34 ASN cc_start: 0.8053 (m-40) cc_final: 0.7621 (m110)
REVERT: B   38 TRP cc_start: 0.8170 (m100) cc_final: 0.7919 (m100)
REVERT: B   70 PHE cc_start: 0.7654 (m-10) cc_final: 0.7269 (m-80)
REVERT: B   92 ASP cc_start: 0.7608 (m-30) cc_final: 0.6987 (m-30)
REVERT: B   97 TYR cc_start: 0.7798 (m-80) cc_final: 0.7212 (m-10)
REVERT: B  108 TRP cc_start: 0.8450 (t-100) cc_final: 0.7843 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1465
  time to fit residues: 35.0767
Evaluate side-chains
  163 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 GLN
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.135910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.108695 restraints weight = 8642.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.112206 restraints weight = 4845.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114705 restraints weight = 3226.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4336  Z= 0.148
  Angle     :  0.644   8.844   5900  Z= 0.329
  Chirality :  0.039   0.147    696
  Planarity :  0.004   0.036    719
  Dihedral  :  3.869  15.513    590
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.85 %
    Favored  : 94.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.37), residues: 541
  helix:  2.43 (0.26), residues: 372
  sheet:  0.25 (0.84), residues: 38
  loop : -1.19 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 470 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.009   0.001   PHE A 292 
 TYR   0.014   0.001   TYR A 302 
 ARG   0.004   0.000   ARG A  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04206 (  344)
  hydrogen bonds       : angle       4.34905 ( 1014)
  SS BOND              : bond        0.00519 (    1)
  SS BOND              : angle       1.14712 (    2)
  covalent geometry    : bond        0.00323 ( 4335)
  covalent geometry    : angle       0.64368 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8700 (t80) cc_final: 0.8391 (t80)
REVERT: A  111 MET cc_start: 0.8239 (mmm) cc_final: 0.7944 (mmm)
REVERT: A  119 GLU cc_start: 0.8042 (pm20) cc_final: 0.7758 (pm20)
REVERT: A  180 ILE cc_start: 0.8173 (mm) cc_final: 0.7951 (mm)
REVERT: A  302 TYR cc_start: 0.8587 (t80) cc_final: 0.7948 (t80)
REVERT: A  309 LEU cc_start: 0.8774 (mt) cc_final: 0.8310 (mt)
REVERT: A  335 GLN cc_start: 0.7525 (tp40) cc_final: 0.6659 (tt0)
REVERT: A  485 ILE cc_start: 0.8896 (mp) cc_final: 0.8403 (mt)
REVERT: B   34 ASN cc_start: 0.8348 (m-40) cc_final: 0.7981 (m110)
REVERT: B   46 GLU cc_start: 0.7463 (pp20) cc_final: 0.7232 (pp20)
REVERT: B   70 PHE cc_start: 0.7530 (m-10) cc_final: 0.7290 (m-80)
REVERT: B   92 ASP cc_start: 0.7383 (m-30) cc_final: 0.6934 (m-30)
REVERT: B   97 TYR cc_start: 0.7848 (m-80) cc_final: 0.7322 (m-10)
REVERT: B  119 VAL cc_start: 0.8863 (m) cc_final: 0.8477 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1369
  time to fit residues: 33.6187
Evaluate side-chains
  165 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** 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 = 0.3773 r_free = 0.3773 target = 0.137072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.110077 restraints weight = 8761.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.113606 restraints weight = 4977.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.116086 restraints weight = 3350.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4336  Z= 0.146
  Angle     :  0.675   8.837   5900  Z= 0.340
  Chirality :  0.039   0.146    696
  Planarity :  0.004   0.035    719
  Dihedral  :  3.869  15.567    590
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.30 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.36), residues: 541
  helix:  2.43 (0.26), residues: 370
  sheet:  0.42 (0.81), residues: 38
  loop : -1.11 (0.54), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 108 
 HIS   0.003   0.001   HIS A  32 
 PHE   0.009   0.001   PHE A 292 
 TYR   0.013   0.001   TYR B  62 
 ARG   0.008   0.001   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  344)
  hydrogen bonds       : angle       4.31715 ( 1014)
  SS BOND              : bond        0.00336 (    1)
  SS BOND              : angle       0.63809 (    2)
  covalent geometry    : bond        0.00326 ( 4335)
  covalent geometry    : angle       0.67532 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8681 (t80) cc_final: 0.8345 (t80)
REVERT: A   29 TYR cc_start: 0.9189 (m-10) cc_final: 0.8890 (m-80)
REVERT: A   30 LEU cc_start: 0.9412 (tp) cc_final: 0.9145 (tt)
REVERT: A   52 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8819 (mm-30)
REVERT: A  111 MET cc_start: 0.8161 (mmm) cc_final: 0.7860 (mmm)
REVERT: A  119 GLU cc_start: 0.8068 (pm20) cc_final: 0.7846 (pm20)
REVERT: A  179 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8178 (ttm110)
REVERT: A  180 ILE cc_start: 0.8177 (mm) cc_final: 0.7927 (mm)
REVERT: A  229 LYS cc_start: 0.8423 (tttt) cc_final: 0.8048 (ttpt)
REVERT: A  335 GLN cc_start: 0.7521 (tp40) cc_final: 0.6446 (tt0)
REVERT: B   30 PRO cc_start: 0.9497 (Cg_exo) cc_final: 0.8929 (Cg_endo)
REVERT: B   31 VAL cc_start: 0.8408 (m) cc_final: 0.8082 (m)
REVERT: B   34 ASN cc_start: 0.8385 (m-40) cc_final: 0.8012 (m-40)
REVERT: B   92 ASP cc_start: 0.7434 (m-30) cc_final: 0.7023 (m-30)
REVERT: B   97 TYR cc_start: 0.7785 (m-80) cc_final: 0.7288 (m-10)
REVERT: B  119 VAL cc_start: 0.8754 (m) cc_final: 0.8371 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1383
  time to fit residues: 33.1293
Evaluate side-chains
  165 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0370
   chunk 8 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 ASN ** 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 = 0.3783 r_free = 0.3783 target = 0.137486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.110296 restraints weight = 8690.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.113741 restraints weight = 5023.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116006 restraints weight = 3419.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4336  Z= 0.148
  Angle     :  0.686   8.771   5900  Z= 0.346
  Chirality :  0.040   0.152    696
  Planarity :  0.004   0.045    719
  Dihedral  :  3.861  15.090    590
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.18 (0.36), residues: 541
  helix:  2.38 (0.26), residues: 370
  sheet:  0.51 (0.73), residues: 43
  loop : -1.12 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  33 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.021   0.001   PHE B  70 
 TYR   0.015   0.001   TYR B 110 
 ARG   0.005   0.001   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04106 (  344)
  hydrogen bonds       : angle       4.29153 ( 1014)
  SS BOND              : bond        0.00355 (    1)
  SS BOND              : angle       0.60252 (    2)
  covalent geometry    : bond        0.00333 ( 4335)
  covalent geometry    : angle       0.68644 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8652 (t80) cc_final: 0.8332 (t80)
REVERT: A   29 TYR cc_start: 0.9223 (m-10) cc_final: 0.8999 (m-10)
REVERT: A   30 LEU cc_start: 0.9403 (tp) cc_final: 0.9141 (tt)
REVERT: A   52 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8363 (mm-30)
REVERT: A  111 MET cc_start: 0.8266 (mmm) cc_final: 0.7866 (mmm)
REVERT: A  119 GLU cc_start: 0.8226 (pm20) cc_final: 0.7915 (pm20)
REVERT: A  180 ILE cc_start: 0.8473 (mm) cc_final: 0.8244 (mm)
REVERT: A  229 LYS cc_start: 0.8470 (tttt) cc_final: 0.8164 (ttpt)
REVERT: A  293 ARG cc_start: 0.8751 (ttp-110) cc_final: 0.8490 (ptp-110)
REVERT: A  335 GLN cc_start: 0.7682 (tp40) cc_final: 0.6758 (tt0)
REVERT: A  533 MET cc_start: 0.7521 (mmm) cc_final: 0.7213 (ttt)
REVERT: B   30 PRO cc_start: 0.9446 (Cg_exo) cc_final: 0.8769 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8396 (m-40) cc_final: 0.7898 (m110)
REVERT: B   92 ASP cc_start: 0.7278 (m-30) cc_final: 0.6901 (m-30)
REVERT: B   97 TYR cc_start: 0.7796 (m-80) cc_final: 0.7401 (m-10)
REVERT: B  119 VAL cc_start: 0.8762 (m) cc_final: 0.8454 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1474
  time to fit residues: 34.8073
Evaluate side-chains
  167 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.0470
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0470
   chunk 12 optimal weight:    0.6980
   chunk 43 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.2976

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** 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 = 0.3807 r_free = 0.3807 target = 0.139682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.113077 restraints weight = 8962.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116809 restraints weight = 5043.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.119427 restraints weight = 3346.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4336  Z= 0.135
  Angle     :  0.680   8.788   5900  Z= 0.342
  Chirality :  0.040   0.157    696
  Planarity :  0.004   0.041    719
  Dihedral  :  3.867  14.653    590
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.36), residues: 541
  helix:  2.35 (0.26), residues: 369
  sheet:  0.73 (0.69), residues: 43
  loop : -1.14 (0.56), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  42 
 HIS   0.003   0.001   HIS A  32 
 PHE   0.012   0.001   PHE A 292 
 TYR   0.013   0.001   TYR B 110 
 ARG   0.005   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  344)
  hydrogen bonds       : angle       4.24094 ( 1014)
  SS BOND              : bond        0.00479 (    1)
  SS BOND              : angle       0.76130 (    2)
  covalent geometry    : bond        0.00297 ( 4335)
  covalent geometry    : angle       0.67962 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8568 (t80) cc_final: 0.8337 (t80)
REVERT: A   51 VAL cc_start: 0.8279 (t) cc_final: 0.7990 (t)
REVERT: A   52 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8305 (mm-30)
REVERT: A  111 MET cc_start: 0.8223 (mmm) cc_final: 0.7797 (mmm)
REVERT: A  119 GLU cc_start: 0.8351 (pm20) cc_final: 0.8076 (pm20)
REVERT: A  190 MET cc_start: 0.8748 (tmm) cc_final: 0.8426 (tmm)
REVERT: A  229 LYS cc_start: 0.8573 (tttt) cc_final: 0.8300 (ttpt)
REVERT: A  335 GLN cc_start: 0.7760 (tp40) cc_final: 0.6908 (tt0)
REVERT: A  533 MET cc_start: 0.7206 (mmm) cc_final: 0.6896 (ttt)
REVERT: B   30 PRO cc_start: 0.9339 (Cg_exo) cc_final: 0.8754 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8480 (m-40) cc_final: 0.7923 (m110)
REVERT: B   39 TYR cc_start: 0.8095 (m-10) cc_final: 0.7539 (m-10)
REVERT: B   97 TYR cc_start: 0.7729 (m-80) cc_final: 0.7260 (m-10)
REVERT: B  105 MET cc_start: 0.7929 (mmp) cc_final: 0.7654 (mmm)
REVERT: B  119 VAL cc_start: 0.8644 (m) cc_final: 0.8328 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1316
  time to fit residues: 31.4143
Evaluate side-chains
  160 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0980
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 50 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.141206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114316 restraints weight = 8351.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.117726 restraints weight = 4855.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.120198 restraints weight = 3322.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4336  Z= 0.143
  Angle     :  0.693   8.909   5900  Z= 0.352
  Chirality :  0.040   0.166    696
  Planarity :  0.004   0.042    719
  Dihedral  :  3.885  14.414    590
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.36), residues: 541
  helix:  2.33 (0.26), residues: 370
  sheet:  0.95 (0.72), residues: 43
  loop : -1.05 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 113 
 HIS   0.003   0.001   HIS A  32 
 PHE   0.010   0.001   PHE A 530 
 TYR   0.017   0.002   TYR B  97 
 ARG   0.005   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  344)
  hydrogen bonds       : angle       4.23654 ( 1014)
  SS BOND              : bond        0.00395 (    1)
  SS BOND              : angle       0.71999 (    2)
  covalent geometry    : bond        0.00323 ( 4335)
  covalent geometry    : angle       0.69288 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8275 (mm-30)
REVERT: A  111 MET cc_start: 0.8126 (mmm) cc_final: 0.7761 (mmm)
REVERT: A  119 GLU cc_start: 0.8348 (pm20) cc_final: 0.8054 (pm20)
REVERT: A  190 MET cc_start: 0.8733 (tmm) cc_final: 0.8425 (tmm)
REVERT: A  196 MET cc_start: 0.8001 (tpt) cc_final: 0.7712 (tpt)
REVERT: A  229 LYS cc_start: 0.8475 (tttt) cc_final: 0.8148 (ttpt)
REVERT: A  293 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8351 (ptp-170)
REVERT: A  335 GLN cc_start: 0.7662 (tp40) cc_final: 0.6788 (tt0)
REVERT: A  533 MET cc_start: 0.7384 (mmm) cc_final: 0.6895 (ttt)
REVERT: B   30 PRO cc_start: 0.9308 (Cg_exo) cc_final: 0.8766 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8358 (m-40) cc_final: 0.7838 (m110)
REVERT: B   45 LYS cc_start: 0.6493 (pttm) cc_final: 0.5328 (pptt)
REVERT: B   97 TYR cc_start: 0.7662 (m-80) cc_final: 0.7291 (m-10)
REVERT: B  119 VAL cc_start: 0.8668 (m) cc_final: 0.8332 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1354
  time to fit residues: 30.6056
Evaluate side-chains
  162 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** 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 = 0.3812 r_free = 0.3812 target = 0.140330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.112732 restraints weight = 8665.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116285 restraints weight = 4967.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.118908 restraints weight = 3375.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.4495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4336  Z= 0.167
  Angle     :  0.763   9.361   5900  Z= 0.386
  Chirality :  0.042   0.193    696
  Planarity :  0.005   0.080    719
  Dihedral  :  4.136  16.617    590
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.36), residues: 541
  helix:  2.25 (0.26), residues: 370
  sheet:  1.13 (0.73), residues: 43
  loop : -1.08 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 113 
 HIS   0.007   0.001   HIS A 535 
 PHE   0.018   0.002   PHE A 292 
 TYR   0.015   0.001   TYR A  29 
 ARG   0.005   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  344)
  hydrogen bonds       : angle       4.34847 ( 1014)
  SS BOND              : bond        0.00482 (    1)
  SS BOND              : angle       0.74103 (    2)
  covalent geometry    : bond        0.00385 ( 4335)
  covalent geometry    : angle       0.76334 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.9277 (tp) cc_final: 0.8996 (tt)
REVERT: A  111 MET cc_start: 0.8268 (mmm) cc_final: 0.7824 (mmm)
REVERT: A  119 GLU cc_start: 0.8413 (pm20) cc_final: 0.8121 (pm20)
REVERT: A  190 MET cc_start: 0.8609 (tmm) cc_final: 0.8283 (tmm)
REVERT: A  229 LYS cc_start: 0.8469 (tttt) cc_final: 0.8132 (ttpt)
REVERT: A  335 GLN cc_start: 0.7667 (tp40) cc_final: 0.6726 (tt0)
REVERT: A  533 MET cc_start: 0.7319 (mmm) cc_final: 0.6714 (ttt)
REVERT: B   30 PRO cc_start: 0.9349 (Cg_exo) cc_final: 0.8781 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8396 (m-40) cc_final: 0.7771 (m110)
REVERT: B   39 TYR cc_start: 0.7595 (m-10) cc_final: 0.7331 (m-10)
REVERT: B   45 LYS cc_start: 0.6749 (pttm) cc_final: 0.5572 (pptt)
REVERT: B   97 TYR cc_start: 0.7766 (m-80) cc_final: 0.7399 (m-10)
REVERT: B  119 VAL cc_start: 0.8693 (m) cc_final: 0.8346 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1389
  time to fit residues: 31.3725
Evaluate side-chains
  159 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.136323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.108364 restraints weight = 8513.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.111816 restraints weight = 4958.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.114199 restraints weight = 3398.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   4336  Z= 0.197
  Angle     :  0.793   9.587   5900  Z= 0.404
  Chirality :  0.043   0.201    696
  Planarity :  0.004   0.039    719
  Dihedral  :  4.049  14.462    590
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.36), residues: 541
  helix:  2.04 (0.26), residues: 371
  sheet:  1.01 (0.76), residues: 43
  loop : -1.17 (0.57), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  38 
 HIS   0.007   0.001   HIS A 535 
 PHE   0.012   0.001   PHE A 541 
 TYR   0.015   0.002   TYR B 110 
 ARG   0.011   0.001   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04431 (  344)
  hydrogen bonds       : angle       4.57178 ( 1014)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       0.22712 (    2)
  covalent geometry    : bond        0.00466 ( 4335)
  covalent geometry    : angle       0.79295 ( 5898)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8716 (mm-30)
REVERT: A  111 MET cc_start: 0.8390 (mmm) cc_final: 0.7931 (mmm)
REVERT: A  119 GLU cc_start: 0.8421 (pm20) cc_final: 0.8149 (pm20)
REVERT: A  190 MET cc_start: 0.8583 (tmm) cc_final: 0.8278 (tmm)
REVERT: A  196 MET cc_start: 0.7735 (tpt) cc_final: 0.7518 (tpt)
REVERT: A  229 LYS cc_start: 0.8505 (tttt) cc_final: 0.8159 (ttpt)
REVERT: A  335 GLN cc_start: 0.7518 (tp40) cc_final: 0.6605 (tt0)
REVERT: A  393 MET cc_start: 0.7456 (mmm) cc_final: 0.7075 (mmt)
REVERT: A  473 ASP cc_start: 0.9323 (t0) cc_final: 0.9083 (t0)
REVERT: A  488 GLU cc_start: 0.7603 (tp30) cc_final: 0.7364 (tp30)
REVERT: A  533 MET cc_start: 0.7329 (mmm) cc_final: 0.6176 (ttt)
REVERT: B   30 PRO cc_start: 0.9365 (Cg_exo) cc_final: 0.8805 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8377 (m-40) cc_final: 0.7747 (m110)
REVERT: B  119 VAL cc_start: 0.8787 (m) cc_final: 0.8476 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1384
  time to fit residues: 31.1136
Evaluate side-chains
  160 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 18 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.140064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.111938 restraints weight = 8488.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.115503 restraints weight = 4883.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.118012 restraints weight = 3333.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4336  Z= 0.167
  Angle     :  0.789  14.121   5900  Z= 0.394
  Chirality :  0.042   0.171    696
  Planarity :  0.004   0.036    719
  Dihedral  :  4.213  14.376    590
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.36), residues: 541
  helix:  1.98 (0.26), residues: 370
  sheet:  1.45 (0.79), residues: 38
  loop : -1.07 (0.57), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  38 
 HIS   0.007   0.001   HIS A 535 
 PHE   0.033   0.002   PHE A 292 
 TYR   0.016   0.001   TYR A  29 
 ARG   0.010   0.001   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  344)
  hydrogen bonds       : angle       4.46435 ( 1014)
  SS BOND              : bond        0.00733 (    1)
  SS BOND              : angle       1.47379 (    2)
  covalent geometry    : bond        0.00394 ( 4335)
  covalent geometry    : angle       0.78833 ( 5898)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1674.93 seconds
wall clock time: 29 minutes 52.85 seconds (1792.85 seconds total)