Starting phenix.real_space_refine
on Sat May 10 01:37:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u5n_41929/05_2025/8u5n_41929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u5n_41929/05_2025/8u5n_41929.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u5n_41929/05_2025/8u5n_41929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u5n_41929/05_2025/8u5n_41929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u5n_41929/05_2025/8u5n_41929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u5n_41929/05_2025/8u5n_41929.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.017
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      28      5.16       5
     C    3032      2.51       5
     N     703      2.21       5
     O     772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4535
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 577, 4522
          Classifications: {'peptide': 577}
          Link IDs: {'PTRANS': 21, 'TRANS': 555}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'IAC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.41, per 1000 atoms: 0.75
  Number of scatterers: 4535
  At special positions: 0
  Unit cell: (72.0265, 63.1617, 95.2966, 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      28     16.00
     O     772      8.00
     N     703      7.00
     C    3032      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.30
  Conformation dependent library (CDL) restraints added in 573.2 milliseconds
  

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      89.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 62
    Processing helix  chain 'A' and resid 66 through 80
    Processing helix  chain 'A' and resid 80 through 93
    Processing helix  chain 'A' and resid 94 through 98
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.631A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 143
      removed outlier: 3.687A  pdb=" N   LYS A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 164 through 196
      removed outlier: 3.794A  pdb=" N   TYR A 168 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ILE A 169 " --> pdb=" O   TYR A 165 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 202 through 217
    Processing helix  chain 'A' and resid 217 through 234
      removed outlier: 3.664A  pdb=" N   PHE A 231 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 251
      removed outlier: 3.927A  pdb=" N   SER A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 264
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 322
    Processing helix  chain 'A' and resid 326 through 336
      removed outlier: 4.042A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.777A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 368 through 370
      No H-bonds generated for 'chain 'A' and resid 368 through 370'
    Processing helix  chain 'A' and resid 371 through 404
    Processing helix  chain 'A' and resid 405 through 408
    Processing helix  chain 'A' and resid 409 through 436
      removed outlier: 4.298A  pdb=" N   LEU A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 473
      removed outlier: 3.581A  pdb=" N   GLY A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 503
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
    Processing helix  chain 'A' and resid 516 through 547
      removed outlier: 3.563A  pdb=" N   MET A 521 " --> pdb=" O   GLY A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 682
    Processing helix  chain 'A' and resid 687 through 712
      removed outlier: 3.602A  pdb=" N   GLU A 691 " --> pdb=" O   ARG A 687 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)

    377 hydrogen bonds defined for protein.
    1116 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: 1.41

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 858
        1.33 -     1.45: 1109
        1.45 -     1.57: 2632
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 4644
  Sorted by residual:
  bond pdb=" C1  IAC A 901 "
       pdb=" C7  IAC A 901 "
    ideal  model  delta    sigma   weight residual
    1.433  1.357  0.076 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" C   IAC A 901 "
       pdb=" C1  IAC A 901 "
    ideal  model  delta    sigma   weight residual
    1.414  1.363  0.051 2.00e-02 2.50e+03 6.58e+00
  bond pdb=" C   PHE A 115 "
       pdb=" O   PHE A 115 "
    ideal  model  delta    sigma   weight residual
    1.236  1.210  0.026 1.15e-02 7.56e+03 5.28e+00
  bond pdb=" C17 IAC A 901 "
       pdb=" C7  IAC A 901 "
    ideal  model  delta    sigma   weight residual
    1.487  1.521 -0.034 2.00e-02 2.50e+03 2.96e+00
  bond pdb=" CG  LEU A 414 "
       pdb=" CD1 LEU A 414 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.31e+00
  ... (remaining 4639 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 6147
        2.29 -     4.57: 143
        4.57 -     6.86: 20
        6.86 -     9.14: 1
        9.14 -    11.43: 2
  Bond angle restraints: 6313
  Sorted by residual:
  angle pdb=" C   PHE A 115 "
        pdb=" CA  PHE A 115 "
        pdb=" CB  PHE A 115 "
      ideal   model   delta    sigma   weight residual
     110.88  103.53    7.35 1.57e+00 4.06e-01 2.19e+01
  angle pdb=" CA  PHE A 115 "
        pdb=" C   PHE A 115 "
        pdb=" O   PHE A 115 "
      ideal   model   delta    sigma   weight residual
     120.82  116.58    4.24 1.05e+00 9.07e-01 1.63e+01
  angle pdb=" C17 IAC A 901 "
        pdb=" C7  IAC A 901 "
        pdb=" C8  IAC A 901 "
      ideal   model   delta    sigma   weight residual
     127.34  115.91   11.43 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" O   PHE A 115 "
        pdb=" C   PHE A 115 "
        pdb=" N   ILE A 116 "
      ideal   model   delta    sigma   weight residual
     122.07  125.34   -3.27 1.03e+00 9.43e-01 1.01e+01
  angle pdb=" C1  IAC A 901 "
        pdb=" C7  IAC A 901 "
        pdb=" C17 IAC A 901 "
      ideal   model   delta    sigma   weight residual
     126.92  136.15   -9.23 3.00e+00 1.11e-01 9.46e+00
  ... (remaining 6308 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 2434
       15.42 -    30.84: 223
       30.84 -    46.26: 32
       46.26 -    61.68: 18
       61.68 -    77.10: 4
  Dihedral angle restraints: 2711
    sinusoidal: 1036
      harmonic: 1675
  Sorted by residual:
  dihedral pdb=" CA  GLY A 686 "
           pdb=" C   GLY A 686 "
           pdb=" N   ARG A 687 "
           pdb=" CA  ARG A 687 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.02  -26.98     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  ASP A 508 "
           pdb=" C   ASP A 508 "
           pdb=" N   SER A 509 "
           pdb=" CA  SER A 509 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.54  -25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  LYS A 504 "
           pdb=" C   LYS A 504 "
           pdb=" N   HIS A 505 "
           pdb=" CA  HIS A 505 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.88  -24.12     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 2708 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 422
       0.033 -    0.067: 221
       0.067 -    0.100: 73
       0.100 -    0.134: 29
       0.134 -    0.167: 11
  Chirality restraints: 756
  Sorted by residual:
  chirality pdb=" CA  VAL A  98 "
            pdb=" N   VAL A  98 "
            pdb=" C   VAL A  98 "
            pdb=" CB  VAL A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CA  TYR A 451 "
            pdb=" N   TYR A 451 "
            pdb=" C   TYR A 451 "
            pdb=" CB  TYR A 451 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CB  VAL A 389 "
            pdb=" CA  VAL A 389 "
            pdb=" CG1 VAL A 389 "
            pdb=" CG2 VAL A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.16 2.00e-01 2.50e+01 6.80e-01
  ... (remaining 753 not shown)

  Planarity restraints: 764
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 285 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   ALA A 285 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 285 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS A 286 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 447 "    0.026 2.00e-02 2.50e+03   1.70e-02 5.03e+00
        pdb=" CG  PHE A 447 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 447 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 447 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 447 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 447 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 447 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 689 "    0.028 2.00e-02 2.50e+03   1.50e-02 4.48e+00
        pdb=" CG  TYR A 689 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 689 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 689 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 689 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 689 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 689 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 689 "    0.011 2.00e-02 2.50e+03
  ... (remaining 761 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1183
        2.80 -     3.33: 4820
        3.33 -     3.85: 7890
        3.85 -     4.38: 9503
        4.38 -     4.90: 15518
  Nonbonded interactions: 38914
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 144 "
            pdb=" OD1 ASP A 146 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OH  TYR A 359 "
            pdb=" OD2 ASP A 385 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   VAL A 340 "
            pdb=" OG1 THR A 344 "
     model   vdw
     2.438 3.040
  nonbonded pdb=" N   ASP A 508 "
            pdb=" OD1 ASP A 508 "
     model   vdw
     2.468 3.120
  nonbonded pdb=" O   ILE A 357 "
            pdb=" OG  SER A 361 "
     model   vdw
     2.550 3.040
  ... (remaining 38909 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             2.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     14.800
  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:10.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
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   0.076   4644  Z= 0.295
  Angle     :  0.855  11.427   6313  Z= 0.478
  Chirality :  0.048   0.167    756
  Planarity :  0.007   0.048    764
  Dihedral  : 12.971  77.103   1631
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  4.59 %
    Favored  : 94.61 %
  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: -0.95 (0.32), residues: 573
  helix: -0.38 (0.22), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.01 (0.55), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP A 193 
 HIS   0.004   0.002   HIS A 658 
 PHE   0.033   0.004   PHE A 447 
 TYR   0.028   0.005   TYR A 689 
 ARG   0.003   0.001   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11734 (  377)
  hydrogen bonds       : angle       6.05596 ( 1116)
  covalent geometry    : bond        0.00631 ( 4644)
  covalent geometry    : angle       0.85502 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 181
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ILE cc_start: 0.8523 (mt) cc_final: 0.8161 (mt)
REVERT: A  178 MET cc_start: 0.6546 (ptt) cc_final: 0.6333 (tmt)
  outliers start: 4
  outliers final: 3
  residues processed: 184
  average time/residue: 0.6566
  time to fit residues: 128.4839
Evaluate side-chains
  100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  695 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0980
   chunk 14 optimal weight:    0.1980
   chunk 29 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
A 380 GLN
A 409 GLN
** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 693 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.102858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.091622 restraints weight = 12379.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 3.68
r_work: 0.3507 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4644  Z= 0.183
  Angle     :  0.788  13.780   6313  Z= 0.389
  Chirality :  0.045   0.178    756
  Planarity :  0.005   0.038    764
  Dihedral  :  6.556  53.614    615
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 18.36 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.34), residues: 573
  helix:  0.80 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -0.61 (0.61), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 363 
 HIS   0.001   0.001   HIS A 505 
 PHE   0.018   0.002   PHE A 681 
 TYR   0.037   0.003   TYR A 104 
 ARG   0.009   0.001   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05052 (  377)
  hydrogen bonds       : angle       5.13614 ( 1116)
  covalent geometry    : bond        0.00390 ( 4644)
  covalent geometry    : angle       0.78787 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8550 (mm) cc_final: 0.8290 (tp)
REVERT: A  178 MET cc_start: 0.7679 (ptt) cc_final: 0.6771 (tpt)
REVERT: A  179 MET cc_start: 0.7892 (mtm) cc_final: 0.7380 (mmt)
REVERT: A  361 SER cc_start: 0.9438 (m) cc_final: 0.9237 (p)
REVERT: A  409 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8427 (tt0)
REVERT: A  476 ARG cc_start: 0.8370 (mmp80) cc_final: 0.8000 (tmt170)
REVERT: A  499 LEU cc_start: 0.9163 (mt) cc_final: 0.8783 (mt)
REVERT: A  532 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9098 (tt)
  outliers start: 28
  outliers final: 8
  residues processed: 135
  average time/residue: 0.5375
  time to fit residues: 78.3708
Evaluate side-chains
  103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  532 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 16 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0870
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 672 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.103459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.092121 restraints weight = 12525.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.78
r_work: 0.3520 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
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      :  0.003   0.034   4644  Z= 0.162
  Angle     :  0.712   8.364   6313  Z= 0.349
  Chirality :  0.043   0.143    756
  Planarity :  0.004   0.036    764
  Dihedral  :  5.261  50.862    609
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 19.96 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.54 (0.35), residues: 573
  helix:  1.32 (0.23), residues: 464
  sheet:  None (None), residues: 0
  loop :  0.01 (0.68), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 412 
 PHE   0.026   0.002   PHE A 384 
 TYR   0.030   0.002   TYR A 104 
 ARG   0.003   0.001   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04795 (  377)
  hydrogen bonds       : angle       4.79242 ( 1116)
  covalent geometry    : bond        0.00348 ( 4644)
  covalent geometry    : angle       0.71181 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.7912 (t0) cc_final: 0.7701 (t0)
REVERT: A  144 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7573 (t)
REVERT: A  178 MET cc_start: 0.7523 (ptt) cc_final: 0.6753 (tpt)
REVERT: A  179 MET cc_start: 0.8078 (mtm) cc_final: 0.7491 (mmt)
REVERT: A  186 ILE cc_start: 0.8534 (mt) cc_final: 0.8246 (mt)
REVERT: A  220 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7762 (t)
REVERT: A  284 THR cc_start: 0.9491 (m) cc_final: 0.9231 (p)
REVERT: A  338 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7871 (tmm)
REVERT: A  347 MET cc_start: 0.8571 (tmm) cc_final: 0.8324 (tmm)
REVERT: A  351 THR cc_start: 0.8865 (m) cc_final: 0.8541 (m)
REVERT: A  409 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8234 (tt0)
REVERT: A  445 LEU cc_start: 0.9138 (mm) cc_final: 0.8601 (tm)
REVERT: A  499 LEU cc_start: 0.9280 (mt) cc_final: 0.8976 (mt)
REVERT: A  670 PHE cc_start: 0.8537 (t80) cc_final: 0.8216 (m-80)
REVERT: A  691 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8256 (mp0)
  outliers start: 34
  outliers final: 8
  residues processed: 134
  average time/residue: 0.5289
  time to fit residues: 76.4709
Evaluate side-chains
  108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.1980
   chunk 26 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
** A 672 ASN ** 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 = 0.3935 r_free = 0.3935 target = 0.105589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.094383 restraints weight = 12838.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 3.85
r_work: 0.3529 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.7427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4644  Z= 0.156
  Angle     :  0.697   8.018   6313  Z= 0.349
  Chirality :  0.042   0.167    756
  Planarity :  0.004   0.033    764
  Dihedral  :  5.050  46.774    609
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 23.15 %
    Favored  : 72.26 %
  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:  1.72 (0.36), residues: 573
  helix:  1.47 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop :  0.01 (0.68), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 678 
 HIS   0.005   0.001   HIS A 412 
 PHE   0.026   0.002   PHE A 695 
 TYR   0.029   0.002   TYR A 104 
 ARG   0.004   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04500 (  377)
  hydrogen bonds       : angle       4.66948 ( 1116)
  covalent geometry    : bond        0.00343 ( 4644)
  covalent geometry    : angle       0.69742 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8047 (t0) cc_final: 0.7815 (t0)
REVERT: A  103 LEU cc_start: 0.8756 (mm) cc_final: 0.8419 (tp)
REVERT: A  178 MET cc_start: 0.7190 (ptt) cc_final: 0.6623 (tpt)
REVERT: A  179 MET cc_start: 0.8040 (mtm) cc_final: 0.7496 (mmt)
REVERT: A  186 ILE cc_start: 0.8688 (mt) cc_final: 0.8478 (mt)
REVERT: A  221 PHE cc_start: 0.7373 (t80) cc_final: 0.7166 (t80)
REVERT: A  284 THR cc_start: 0.9574 (m) cc_final: 0.9318 (p)
REVERT: A  293 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8881 (tp)
REVERT: A  296 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8859 (mm-30)
REVERT: A  351 THR cc_start: 0.8874 (m) cc_final: 0.8620 (m)
REVERT: A  381 ASN cc_start: 0.8767 (m-40) cc_final: 0.8396 (m110)
REVERT: A  409 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8441 (tt0)
REVERT: A  412 HIS cc_start: 0.8902 (m90) cc_final: 0.8191 (m90)
REVERT: A  413 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8140 (mpt)
REVERT: A  415 THR cc_start: 0.8748 (m) cc_final: 0.8475 (p)
REVERT: A  429 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.6838 (tmm)
REVERT: A  445 LEU cc_start: 0.9285 (mm) cc_final: 0.8808 (tm)
REVERT: A  451 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7490 (m-80)
REVERT: A  499 LEU cc_start: 0.9306 (mt) cc_final: 0.9015 (mt)
REVERT: A  670 PHE cc_start: 0.8664 (t80) cc_final: 0.8315 (m-80)
REVERT: A  691 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8415 (mp0)
  outliers start: 23
  outliers final: 9
  residues processed: 126
  average time/residue: 0.5882
  time to fit residues: 80.2963
Evaluate side-chains
  112 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  691 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0070
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
A 380 GLN
A 672 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.104119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.092106 restraints weight = 13072.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 4.01
r_work: 0.3472 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.8210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4644  Z= 0.154
  Angle     :  0.702   8.170   6313  Z= 0.349
  Chirality :  0.042   0.170    756
  Planarity :  0.004   0.030    764
  Dihedral  :  4.829  44.117    609
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 25.95 %
    Favored  : 69.26 %
  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:  1.80 (0.36), residues: 573
  helix:  1.52 (0.24), residues: 467
  sheet:  None (None), residues: 0
  loop : -0.06 (0.68), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 678 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.022   0.001   PHE A  87 
 TYR   0.025   0.002   TYR A 104 
 ARG   0.001   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04463 (  377)
  hydrogen bonds       : angle       4.66441 ( 1116)
  covalent geometry    : bond        0.00338 ( 4644)
  covalent geometry    : angle       0.70234 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9689 (tp) cc_final: 0.9349 (pp)
REVERT: A  103 LEU cc_start: 0.8836 (mm) cc_final: 0.8597 (tp)
REVERT: A  177 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8137 (mt)
REVERT: A  178 MET cc_start: 0.7142 (ptt) cc_final: 0.6623 (tpt)
REVERT: A  221 PHE cc_start: 0.7369 (t80) cc_final: 0.7071 (t80)
REVERT: A  284 THR cc_start: 0.9592 (m) cc_final: 0.9357 (p)
REVERT: A  296 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8912 (mt-10)
REVERT: A  300 LEU cc_start: 0.9170 (tm) cc_final: 0.8795 (pp)
REVERT: A  301 LEU cc_start: 0.8993 (mt) cc_final: 0.8562 (mt)
REVERT: A  392 ILE cc_start: 0.9228 (mm) cc_final: 0.9017 (tp)
REVERT: A  409 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8418 (tt0)
REVERT: A  412 HIS cc_start: 0.8908 (m90) cc_final: 0.8231 (m90)
REVERT: A  413 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8019 (mpt)
REVERT: A  429 MET cc_start: 0.8418 (tmm) cc_final: 0.7150 (tmm)
REVERT: A  445 LEU cc_start: 0.9393 (mm) cc_final: 0.9016 (tm)
REVERT: A  451 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7718 (m-80)
REVERT: A  495 LEU cc_start: 0.9541 (mm) cc_final: 0.9336 (mp)
REVERT: A  499 LEU cc_start: 0.9310 (mt) cc_final: 0.9092 (mt)
REVERT: A  521 MET cc_start: 0.9074 (mmm) cc_final: 0.8819 (mmm)
REVERT: A  691 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8538 (pm20)
  outliers start: 24
  outliers final: 6
  residues processed: 129
  average time/residue: 0.4620
  time to fit residues: 65.0439
Evaluate side-chains
  109 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  201 GLN
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  691 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
A 433 ASN
A 443 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.102283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.090234 restraints weight = 12922.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 3.93
r_work: 0.3441 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.8901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4644  Z= 0.190
  Angle     :  0.735  13.957   6313  Z= 0.369
  Chirality :  0.045   0.168    756
  Planarity :  0.004   0.033    764
  Dihedral  :  4.773  43.282    609
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.34 %
    Favored  : 66.67 %
  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:  1.78 (0.36), residues: 573
  helix:  1.53 (0.24), residues: 467
  sheet:  None (None), residues: 0
  loop : -0.19 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 678 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.019   0.002   PHE A 695 
 TYR   0.027   0.003   TYR A 170 
 ARG   0.002   0.000   ARG A 474 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04614 (  377)
  hydrogen bonds       : angle       4.75492 ( 1116)
  covalent geometry    : bond        0.00426 ( 4644)
  covalent geometry    : angle       0.73527 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8984 (mt)
REVERT: A   58 ILE cc_start: 0.9539 (tp) cc_final: 0.9223 (pp)
REVERT: A   99 ASP cc_start: 0.7939 (t0) cc_final: 0.7738 (t0)
REVERT: A  103 LEU cc_start: 0.8940 (mm) cc_final: 0.8644 (tp)
REVERT: A  178 MET cc_start: 0.7323 (ptt) cc_final: 0.6927 (tpt)
REVERT: A  296 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8883 (mt-10)
REVERT: A  340 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9194 (m)
REVERT: A  413 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8103 (mpt)
REVERT: A  445 LEU cc_start: 0.9402 (mm) cc_final: 0.9099 (tm)
REVERT: A  453 SER cc_start: 0.8931 (m) cc_final: 0.8607 (p)
REVERT: A  487 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.9018 (p)
REVERT: A  691 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8473 (mp0)
  outliers start: 20
  outliers final: 8
  residues processed: 127
  average time/residue: 0.4402
  time to fit residues: 61.2536
Evaluate side-chains
  106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  691 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0070
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 143 GLN
A 230 ASN
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.104696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.092674 restraints weight = 13010.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 4.01
r_work: 0.3524 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.9370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4644  Z= 0.162
  Angle     :  0.762  12.704   6313  Z= 0.374
  Chirality :  0.047   0.230    756
  Planarity :  0.004   0.033    764
  Dihedral  :  4.749  42.237    609
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 33.33 %
    Favored  : 62.87 %
  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:  1.73 (0.36), residues: 573
  helix:  1.51 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop : -0.30 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 363 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.041   0.001   PHE A 221 
 TYR   0.030   0.002   TYR A 458 
 ARG   0.001   0.000   ARG A 474 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04505 (  377)
  hydrogen bonds       : angle       4.84790 ( 1116)
  covalent geometry    : bond        0.00367 ( 4644)
  covalent geometry    : angle       0.76175 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9503 (tp) cc_final: 0.9205 (pp)
REVERT: A  100 TRP cc_start: 0.5453 (m-10) cc_final: 0.5019 (m100)
REVERT: A  178 MET cc_start: 0.7682 (ptt) cc_final: 0.7279 (tpt)
REVERT: A  263 THR cc_start: 0.8697 (p) cc_final: 0.8484 (t)
REVERT: A  267 LYS cc_start: 0.8888 (tptt) cc_final: 0.8186 (ptmt)
REVERT: A  296 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8885 (mt-10)
REVERT: A  318 PHE cc_start: 0.9230 (t80) cc_final: 0.9002 (t80)
REVERT: A  340 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9177 (m)
REVERT: A  406 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8730 (tttm)
REVERT: A  413 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7991 (mpt)
REVERT: A  445 LEU cc_start: 0.9399 (mm) cc_final: 0.9099 (tm)
  outliers start: 19
  outliers final: 7
  residues processed: 116
  average time/residue: 0.5338
  time to fit residues: 66.9433
Evaluate side-chains
  102 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  481 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 20 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 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 = 0.3922 r_free = 0.3922 target = 0.105424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.093324 restraints weight = 13096.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 3.95
r_work: 0.3521 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.9771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4644  Z= 0.170
  Angle     :  0.787  13.243   6313  Z= 0.391
  Chirality :  0.048   0.242    756
  Planarity :  0.004   0.030    764
  Dihedral  :  4.677  40.114    609
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 33.53 %
    Favored  : 62.48 %
  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:  1.56 (0.35), residues: 573
  helix:  1.37 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop : -0.28 (0.64), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 363 
 HIS   0.001   0.001   HIS A 505 
 PHE   0.039   0.002   PHE A 221 
 TYR   0.041   0.002   TYR A 458 
 ARG   0.002   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04582 (  377)
  hydrogen bonds       : angle       4.88811 ( 1116)
  covalent geometry    : bond        0.00387 ( 4644)
  covalent geometry    : angle       0.78689 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9479 (tp) cc_final: 0.9169 (pp)
REVERT: A  100 TRP cc_start: 0.5576 (m-10) cc_final: 0.5205 (m100)
REVERT: A  178 MET cc_start: 0.7783 (ptt) cc_final: 0.7358 (tpt)
REVERT: A  296 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8955 (mt-10)
REVERT: A  318 PHE cc_start: 0.9244 (t80) cc_final: 0.8989 (t80)
REVERT: A  335 GLN cc_start: 0.9416 (mt0) cc_final: 0.8996 (mt0)
REVERT: A  340 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9160 (m)
REVERT: A  406 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8777 (tttm)
REVERT: A  413 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7880 (mpt)
REVERT: A  445 LEU cc_start: 0.9409 (mm) cc_final: 0.9121 (tm)
REVERT: A  451 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8313 (m-80)
REVERT: A  675 SER cc_start: 0.9437 (OUTLIER) cc_final: 0.9175 (p)
REVERT: A  691 GLU cc_start: 0.8739 (mp0) cc_final: 0.8453 (pm20)
  outliers start: 20
  outliers final: 8
  residues processed: 117
  average time/residue: 0.5096
  time to fit residues: 64.6333
Evaluate side-chains
  103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  675 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 52 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 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 = 0.3919 r_free = 0.3919 target = 0.105914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.093707 restraints weight = 12995.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 4.00
r_work: 0.3527 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          1.0045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4644  Z= 0.175
  Angle     :  0.839  12.559   6313  Z= 0.413
  Chirality :  0.049   0.224    756
  Planarity :  0.005   0.031    764
  Dihedral  :  4.703  37.929    609
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 35.13 %
    Favored  : 61.88 %
  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:  1.37 (0.35), residues: 573
  helix:  1.24 (0.24), residues: 467
  sheet:  None (None), residues: 0
  loop : -0.31 (0.62), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 396 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.040   0.002   PHE A 221 
 TYR   0.045   0.003   TYR A 458 
 ARG   0.002   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04620 (  377)
  hydrogen bonds       : angle       4.93959 ( 1116)
  covalent geometry    : bond        0.00403 ( 4644)
  covalent geometry    : angle       0.83888 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9409 (tp) cc_final: 0.9111 (pp)
REVERT: A  100 TRP cc_start: 0.5567 (m-10) cc_final: 0.5222 (m100)
REVERT: A  178 MET cc_start: 0.7824 (ptt) cc_final: 0.7340 (tmt)
REVERT: A  268 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8527 (tp)
REVERT: A  296 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8930 (mt-10)
REVERT: A  335 GLN cc_start: 0.9394 (mt0) cc_final: 0.8978 (mt0)
REVERT: A  340 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9187 (m)
REVERT: A  409 GLN cc_start: 0.8985 (tp40) cc_final: 0.8559 (tm-30)
REVERT: A  413 MET cc_start: 0.8180 (mpt) cc_final: 0.7660 (mpt)
REVERT: A  445 LEU cc_start: 0.9413 (mm) cc_final: 0.9158 (tm)
REVERT: A  451 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8281 (m-10)
REVERT: A  675 SER cc_start: 0.9443 (OUTLIER) cc_final: 0.9180 (p)
REVERT: A  691 GLU cc_start: 0.8806 (mp0) cc_final: 0.8497 (pm20)
  outliers start: 15
  outliers final: 6
  residues processed: 106
  average time/residue: 0.5327
  time to fit residues: 61.5356
Evaluate side-chains
  101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  675 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   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  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 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 = 0.3921 r_free = 0.3921 target = 0.106043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.094210 restraints weight = 13067.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 3.95
r_work: 0.3495 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          1.0287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4644  Z= 0.181
  Angle     :  0.862  12.920   6313  Z= 0.423
  Chirality :  0.050   0.226    756
  Planarity :  0.005   0.031    764
  Dihedral  :  4.709  35.796    609
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 35.13 %
    Favored  : 61.68 %
  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:  1.34 (0.35), residues: 573
  helix:  1.21 (0.24), residues: 467
  sheet:  None (None), residues: 0
  loop : -0.23 (0.62), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 193 
 HIS   0.001   0.000   HIS A 310 
 PHE   0.040   0.002   PHE A 221 
 TYR   0.054   0.003   TYR A 458 
 ARG   0.001   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04669 (  377)
  hydrogen bonds       : angle       4.93409 ( 1116)
  covalent geometry    : bond        0.00424 ( 4644)
  covalent geometry    : angle       0.86168 ( 6313)

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9414 (tp) cc_final: 0.9131 (pp)
REVERT: A  100 TRP cc_start: 0.5708 (m-10) cc_final: 0.5364 (m100)
REVERT: A  178 MET cc_start: 0.7938 (ptt) cc_final: 0.7413 (tmt)
REVERT: A  296 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8926 (mt-10)
REVERT: A  335 GLN cc_start: 0.9385 (mt0) cc_final: 0.8972 (mt0)
REVERT: A  340 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9211 (m)
REVERT: A  413 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7823 (mpt)
REVERT: A  445 LEU cc_start: 0.9414 (mm) cc_final: 0.9171 (tm)
REVERT: A  451 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8397 (m-10)
REVERT: A  675 SER cc_start: 0.9455 (OUTLIER) cc_final: 0.9195 (p)
REVERT: A  691 GLU cc_start: 0.8761 (mp0) cc_final: 0.8447 (pm20)
  outliers start: 16
  outliers final: 8
  residues processed: 107
  average time/residue: 0.5129
  time to fit residues: 59.5119
Evaluate side-chains
  96 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  658 HIS
Chi-restraints excluded: chain A residue  675 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0670
   chunk 35 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 143 GLN
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.106005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.094255 restraints weight = 13038.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 3.87
r_work: 0.3559 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          1.0479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4644  Z= 0.179
  Angle     :  0.911  12.362   6313  Z= 0.437
  Chirality :  0.051   0.249    756
  Planarity :  0.005   0.031    764
  Dihedral  :  4.683  33.437    609
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 36.53 %
    Favored  : 60.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.35), residues: 573
  helix:  1.19 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop : -0.19 (0.63), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 396 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.050   0.002   PHE A 137 
 TYR   0.058   0.003   TYR A 458 
 ARG   0.001   0.000   ARG A 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04651 (  377)
  hydrogen bonds       : angle       4.93737 ( 1116)
  covalent geometry    : bond        0.00416 ( 4644)
  covalent geometry    : angle       0.91079 ( 6313)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2891.49 seconds
wall clock time: 50 minutes 46.68 seconds (3046.68 seconds total)