Starting phenix.real_space_refine
on Fri Aug 22 14:59:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u5n_41929/08_2025/8u5n_41929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u5n_41929/08_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_41929/08_2025/8u5n_41929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u5n_41929/08_2025/8u5n_41929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u5n_41929/08_2025/8u5n_41929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u5n_41929/08_2025/8u5n_41929.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.37, per 1000 atoms: 0.30
  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: 0.40
  Conformation dependent library (CDL) restraints added in 181.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.11
  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: 0.68

  Time building geometry restraints manager: 0.53 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:             2.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.090
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:8.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.720
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.001   ARG A 270 
 TYR   0.028   0.005   TYR A 689 
 PHE   0.033   0.004   PHE A 447 
 TRP   0.020   0.004   TRP A 193 
 HIS   0.004   0.002   HIS A 658 

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

*********************** 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  : 0.193 
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: 0.2879
  time to fit residues: 56.2724
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  : 0.177 
-------------------------------------------------------------------------------
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 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 230 ASN
A 409 GLN
A 672 ASN
A 693 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.101732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.090189 restraints weight = 12625.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 3.77
r_work: 0.3512 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4644  Z= 0.238
  Angle     :  0.839  13.194   6313  Z= 0.419
  Chirality :  0.047   0.183    756
  Planarity :  0.006   0.040    764
  Dihedral  :  6.715  54.822    615
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  6.59 %
    Allowed  : 17.96 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.33), residues: 573
  helix:  0.68 (0.23), residues: 463
  sheet:  None (None), residues: 0
  loop : -0.82 (0.59), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 476 
 TYR   0.028   0.003   TYR A 104 
 PHE   0.020   0.002   PHE A 681 
 TRP   0.019   0.003   TRP A 363 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 4644)
  covalent geometry    : angle       0.83878 ( 6313)
  hydrogen bonds       : bond        0.05209 (  377)
  hydrogen bonds       : angle       5.20252 ( 1116)

*********************** 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
  150 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8287 (tmtt)
REVERT: A  103 LEU cc_start: 0.8724 (mm) cc_final: 0.8407 (tp)
REVERT: A  178 MET cc_start: 0.7715 (ptt) cc_final: 0.7019 (tpt)
REVERT: A  179 MET cc_start: 0.8071 (mtm) cc_final: 0.7654 (mmp)
REVERT: A  213 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8157 (tpp80)
REVERT: A  296 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8981 (mm-30)
REVERT: A  347 MET cc_start: 0.8580 (tmm) cc_final: 0.8272 (tmm)
REVERT: A  351 THR cc_start: 0.8865 (m) cc_final: 0.8548 (m)
REVERT: A  384 PHE cc_start: 0.8351 (t80) cc_final: 0.8010 (t80)
REVERT: A  388 ILE cc_start: 0.9215 (mt) cc_final: 0.8901 (mp)
REVERT: A  409 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8513 (tm-30)
REVERT: A  445 LEU cc_start: 0.9138 (mm) cc_final: 0.8570 (tm)
REVERT: A  476 ARG cc_start: 0.8427 (mmp80) cc_final: 0.8086 (tmt170)
REVERT: A  499 LEU cc_start: 0.9258 (mt) cc_final: 0.8910 (mt)
REVERT: A  542 MET cc_start: 0.8832 (ppp) cc_final: 0.8621 (ppp)
  outliers start: 33
  outliers final: 7
  residues processed: 136
  average time/residue: 0.2526
  time to fit residues: 37.0380
Evaluate side-chains
  96 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
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  213 ARG
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  481 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   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 143 GLN
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3881 r_free = 0.3881 target = 0.102165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.090617 restraints weight = 12670.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 3.86
r_work: 0.3503 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.7070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4644  Z= 0.168
  Angle     :  0.701   7.117   6313  Z= 0.350
  Chirality :  0.044   0.170    756
  Planarity :  0.005   0.036    764
  Dihedral  :  5.392  53.778    609
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 21.76 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.35), residues: 573
  helix:  1.24 (0.23), residues: 468
  sheet:  None (None), residues: 0
  loop : -0.20 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 476 
 TYR   0.031   0.002   TYR A 104 
 PHE   0.034   0.002   PHE A 221 
 TRP   0.008   0.001   TRP A 678 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4644)
  covalent geometry    : angle       0.70066 ( 6313)
  hydrogen bonds       : bond        0.04795 (  377)
  hydrogen bonds       : angle       4.80935 ( 1116)

*********************** 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
  144 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.7482 (ptt) cc_final: 0.6998 (tpt)
REVERT: A  179 MET cc_start: 0.8267 (mtm) cc_final: 0.7671 (mmt)
REVERT: A  284 THR cc_start: 0.9570 (m) cc_final: 0.9313 (p)
REVERT: A  296 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8805 (mm-30)
REVERT: A  388 ILE cc_start: 0.9384 (mt) cc_final: 0.9096 (mp)
REVERT: A  409 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8419 (tt0)
REVERT: A  415 THR cc_start: 0.8846 (m) cc_final: 0.8554 (p)
REVERT: A  445 LEU cc_start: 0.9280 (mm) cc_final: 0.8766 (tm)
REVERT: A  451 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7598 (m-80)
REVERT: A  495 LEU cc_start: 0.9533 (mm) cc_final: 0.9324 (mp)
REVERT: A  499 LEU cc_start: 0.9344 (mt) cc_final: 0.9033 (mt)
REVERT: A  540 MET cc_start: 0.9034 (ppp) cc_final: 0.8805 (ppp)
REVERT: A  542 MET cc_start: 0.8933 (ppp) cc_final: 0.8716 (ppp)
  outliers start: 29
  outliers final: 7
  residues processed: 131
  average time/residue: 0.2395
  time to fit residues: 33.9269
Evaluate side-chains
  102 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
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  248 LEU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  451 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 412 HIS
A 672 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.101624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.089749 restraints weight = 12989.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 3.97
r_work: 0.3487 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.8149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4644  Z= 0.170
  Angle     :  0.713   9.793   6313  Z= 0.350
  Chirality :  0.044   0.184    756
  Planarity :  0.005   0.034    764
  Dihedral  :  5.219  53.777    609
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 23.95 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.36), residues: 573
  helix:  1.45 (0.24), residues: 464
  sheet:  None (None), residues: 0
  loop : -0.11 (0.68), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 295 
 TYR   0.026   0.002   TYR A 104 
 PHE   0.029   0.002   PHE A 221 
 TRP   0.010   0.001   TRP A 193 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4644)
  covalent geometry    : angle       0.71275 ( 6313)
  hydrogen bonds       : bond        0.04524 (  377)
  hydrogen bonds       : angle       4.71222 ( 1116)

*********************** 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
  135 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 CYS cc_start: 0.8592 (m) cc_final: 0.8356 (m)
REVERT: A   58 ILE cc_start: 0.9690 (OUTLIER) cc_final: 0.9327 (pp)
REVERT: A  178 MET cc_start: 0.7304 (ptt) cc_final: 0.7004 (tpt)
REVERT: A  179 MET cc_start: 0.8318 (mtm) cc_final: 0.7764 (mmt)
REVERT: A  268 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8665 (tp)
REVERT: A  278 VAL cc_start: 0.8158 (t) cc_final: 0.7926 (p)
REVERT: A  284 THR cc_start: 0.9612 (m) cc_final: 0.9330 (p)
REVERT: A  388 ILE cc_start: 0.9327 (mt) cc_final: 0.9080 (mp)
REVERT: A  396 TRP cc_start: 0.6475 (t60) cc_final: 0.6244 (t60)
REVERT: A  409 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8205 (tt0)
REVERT: A  412 HIS cc_start: 0.8790 (m90) cc_final: 0.8050 (m-70)
REVERT: A  415 THR cc_start: 0.8936 (m) cc_final: 0.8669 (p)
REVERT: A  445 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8934 (tm)
REVERT: A  451 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7642 (m-80)
REVERT: A  499 LEU cc_start: 0.9417 (mt) cc_final: 0.9145 (mt)
REVERT: A  672 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8123 (t0)
REVERT: A  692 LEU cc_start: 0.9289 (tm) cc_final: 0.8915 (pp)
  outliers start: 22
  outliers final: 10
  residues processed: 123
  average time/residue: 0.2258
  time to fit residues: 30.3639
Evaluate side-chains
  114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  672 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   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 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 672 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.110472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.098860 restraints weight = 13245.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 4.03
r_work: 0.3486 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.8699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4644  Z= 0.166
  Angle     :  0.741  13.341   6313  Z= 0.361
  Chirality :  0.044   0.170    756
  Planarity :  0.005   0.032    764
  Dihedral  :  5.157  54.103    609
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 27.54 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.36), residues: 573
  helix:  1.42 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -0.20 (0.67), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 474 
 TYR   0.028   0.003   TYR A 458 
 PHE   0.035   0.002   PHE A 221 
 TRP   0.008   0.001   TRP A 193 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4644)
  covalent geometry    : angle       0.74116 ( 6313)
  hydrogen bonds       : bond        0.04433 (  377)
  hydrogen bonds       : angle       4.70959 ( 1116)

*********************** 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
  129 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9298 (pp)
REVERT: A  178 MET cc_start: 0.7345 (ptt) cc_final: 0.7084 (tpt)
REVERT: A  268 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8608 (tp)
REVERT: A  278 VAL cc_start: 0.8197 (t) cc_final: 0.7992 (p)
REVERT: A  284 THR cc_start: 0.9632 (m) cc_final: 0.9386 (p)
REVERT: A  301 LEU cc_start: 0.8939 (mm) cc_final: 0.8649 (mp)
REVERT: A  351 THR cc_start: 0.8982 (m) cc_final: 0.8759 (p)
REVERT: A  388 ILE cc_start: 0.9374 (mt) cc_final: 0.9129 (mp)
REVERT: A  392 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8916 (tp)
REVERT: A  394 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (tt)
REVERT: A  396 TRP cc_start: 0.6421 (t60) cc_final: 0.6195 (t60)
REVERT: A  409 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8308 (tt0)
REVERT: A  412 HIS cc_start: 0.8961 (m90) cc_final: 0.8438 (m-70)
REVERT: A  445 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8945 (tm)
REVERT: A  521 MET cc_start: 0.9145 (mmm) cc_final: 0.8924 (mmm)
REVERT: A  670 PHE cc_start: 0.8797 (t80) cc_final: 0.8531 (m-80)
REVERT: A  692 LEU cc_start: 0.9413 (tm) cc_final: 0.8732 (pp)
  outliers start: 21
  outliers final: 5
  residues processed: 117
  average time/residue: 0.2102
  time to fit residues: 26.9769
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  481 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0030
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.5590

-------------------------------------------------------------------------------
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 672 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.104290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.092657 restraints weight = 13323.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 3.91
r_work: 0.3477 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.9063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4644  Z= 0.158
  Angle     :  0.720   8.696   6313  Z= 0.359
  Chirality :  0.045   0.164    756
  Planarity :  0.004   0.032    764
  Dihedral  :  5.093  53.845    609
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.74 %
    Favored  : 66.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.35), residues: 573
  helix:  1.47 (0.24), residues: 471
  sheet:  None (None), residues: 0
  loop : -0.48 (0.67), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 474 
 TYR   0.029   0.003   TYR A 170 
 PHE   0.037   0.001   PHE A 221 
 TRP   0.008   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 4644)
  covalent geometry    : angle       0.72036 ( 6313)
  hydrogen bonds       : bond        0.04459 (  377)
  hydrogen bonds       : angle       4.79447 ( 1116)

*********************** 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
  130 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8116 (ptmt)
REVERT: A  301 LEU cc_start: 0.9015 (mm) cc_final: 0.8708 (mp)
REVERT: A  318 PHE cc_start: 0.9287 (t80) cc_final: 0.9074 (t80)
REVERT: A  340 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9203 (m)
REVERT: A  351 THR cc_start: 0.8990 (m) cc_final: 0.8765 (p)
REVERT: A  388 ILE cc_start: 0.9324 (mt) cc_final: 0.9101 (mp)
REVERT: A  392 ILE cc_start: 0.9163 (tp) cc_final: 0.8903 (tp)
REVERT: A  396 TRP cc_start: 0.6424 (t60) cc_final: 0.6213 (t60)
REVERT: A  409 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8215 (tt0)
REVERT: A  412 HIS cc_start: 0.8886 (m90) cc_final: 0.8352 (m-70)
REVERT: A  415 THR cc_start: 0.8765 (m) cc_final: 0.8490 (p)
REVERT: A  438 LYS cc_start: 0.7218 (mttt) cc_final: 0.7015 (tttm)
REVERT: A  445 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9004 (tm)
REVERT: A  451 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8320 (m-80)
REVERT: A  453 SER cc_start: 0.8848 (m) cc_final: 0.8532 (p)
REVERT: A  670 PHE cc_start: 0.8902 (t80) cc_final: 0.8608 (m-80)
  outliers start: 20
  outliers final: 9
  residues processed: 120
  average time/residue: 0.2311
  time to fit residues: 30.0276
Evaluate side-chains
  108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
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  186 ILE
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  322 VAL
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  445 LEU
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.102128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.090508 restraints weight = 13203.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 3.90
r_work: 0.3452 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.9731

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= 0.196
  Angle     :  0.795  10.362   6313  Z= 0.396
  Chirality :  0.049   0.255    756
  Planarity :  0.005   0.033    764
  Dihedral  :  5.189  56.242    609
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 30.14 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.35), residues: 573
  helix:  1.29 (0.24), residues: 472
  sheet:  None (None), residues: 0
  loop : -0.53 (0.68), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 476 
 TYR   0.038   0.003   TYR A 170 
 PHE   0.034   0.002   PHE A 221 
 TRP   0.008   0.001   TRP A 193 
 HIS   0.004   0.002   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 4644)
  covalent geometry    : angle       0.79501 ( 6313)
  hydrogen bonds       : bond        0.04637 (  377)
  hydrogen bonds       : angle       4.72467 ( 1116)

*********************** 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  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9597 (tp) cc_final: 0.9316 (pp)
REVERT: A  100 TRP cc_start: 0.5712 (m-10) cc_final: 0.5271 (m100)
REVERT: A  128 ASP cc_start: 0.8545 (m-30) cc_final: 0.8342 (p0)
REVERT: A  179 MET cc_start: 0.8358 (mtm) cc_final: 0.7793 (mmt)
REVERT: A  318 PHE cc_start: 0.9400 (t80) cc_final: 0.9150 (t80)
REVERT: A  320 TYR cc_start: 0.8561 (t80) cc_final: 0.8152 (t80)
REVERT: A  335 GLN cc_start: 0.9429 (mt0) cc_final: 0.9064 (mt0)
REVERT: A  340 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9226 (m)
REVERT: A  388 ILE cc_start: 0.9302 (mt) cc_final: 0.9042 (mp)
REVERT: A  392 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9017 (tp)
REVERT: A  396 TRP cc_start: 0.6619 (t60) cc_final: 0.6403 (t60)
REVERT: A  445 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9079 (tm)
REVERT: A  451 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8434 (m-80)
REVERT: A  453 SER cc_start: 0.8893 (m) cc_final: 0.8579 (t)
REVERT: A  540 MET cc_start: 0.9094 (ppp) cc_final: 0.8849 (ppp)
  outliers start: 19
  outliers final: 8
  residues processed: 114
  average time/residue: 0.2214
  time to fit residues: 27.4862
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  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  186 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  390 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  451 TYR
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 30 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0970
   chunk 48 optimal weight:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 412 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.105452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.093253 restraints weight = 13555.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 4.17
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          1.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   4644  Z= 0.167
  Angle     :  0.779  10.375   6313  Z= 0.389
  Chirality :  0.048   0.246    756
  Planarity :  0.005   0.030    764
  Dihedral  :  5.203  56.863    609
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 32.53 %
    Favored  : 64.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.35), residues: 573
  helix:  1.23 (0.24), residues: 470
  sheet:  None (None), residues: 0
  loop : -0.61 (0.65), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 476 
 TYR   0.038   0.003   TYR A 170 
 PHE   0.032   0.001   PHE A 221 
 TRP   0.007   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4644)
  covalent geometry    : angle       0.77876 ( 6313)
  hydrogen bonds       : bond        0.04530 (  377)
  hydrogen bonds       : angle       4.82806 ( 1116)

*********************** 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
  115 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A   58 ILE cc_start: 0.9530 (tp) cc_final: 0.9258 (pp)
REVERT: A  179 MET cc_start: 0.7637 (mtm) cc_final: 0.7269 (mmp)
REVERT: A  318 PHE cc_start: 0.9304 (t80) cc_final: 0.9093 (t80)
REVERT: A  320 TYR cc_start: 0.8345 (t80) cc_final: 0.7924 (t80)
REVERT: A  335 GLN cc_start: 0.9371 (mt0) cc_final: 0.8973 (mt0)
REVERT: A  388 ILE cc_start: 0.9276 (mt) cc_final: 0.9056 (mp)
REVERT: A  392 ILE cc_start: 0.9224 (tp) cc_final: 0.8991 (tp)
REVERT: A  396 TRP cc_start: 0.6528 (t60) cc_final: 0.6327 (t60)
REVERT: A  445 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9040 (tm)
REVERT: A  451 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.8169 (m-80)
  outliers start: 15
  outliers final: 8
  residues processed: 108
  average time/residue: 0.1991
  time to fit residues: 23.5899
Evaluate side-chains
  99 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  481 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 13 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   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  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 143 GLN ** 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 = 0.3947 r_free = 0.3947 target = 0.105483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.093294 restraints weight = 13620.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 4.10
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          1.0302

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= 0.189
  Angle     :  0.817   9.613   6313  Z= 0.410
  Chirality :  0.049   0.217    756
  Planarity :  0.005   0.031    764
  Dihedral  :  5.266  57.835    609
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 32.93 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.35), residues: 573
  helix:  1.12 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -0.52 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 476 
 TYR   0.035   0.003   TYR A 458 
 PHE   0.032   0.002   PHE A 221 
 TRP   0.019   0.001   TRP A 100 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 4644)
  covalent geometry    : angle       0.81706 ( 6313)
  hydrogen bonds       : bond        0.04649 (  377)
  hydrogen bonds       : angle       4.93674 ( 1116)

*********************** 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
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   58 ILE cc_start: 0.9515 (tp) cc_final: 0.9210 (pp)
REVERT: A  179 MET cc_start: 0.7681 (mtm) cc_final: 0.7265 (mmt)
REVERT: A  335 GLN cc_start: 0.9382 (mt0) cc_final: 0.8997 (mt0)
REVERT: A  388 ILE cc_start: 0.9234 (mt) cc_final: 0.8968 (mp)
REVERT: A  392 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9025 (tp)
REVERT: A  396 TRP cc_start: 0.6741 (t60) cc_final: 0.6492 (t60)
REVERT: A  409 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8531 (tm-30)
REVERT: A  445 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9054 (tm)
REVERT: A  483 ILE cc_start: 0.9104 (mp) cc_final: 0.8768 (tp)
  outliers start: 15
  outliers final: 7
  residues processed: 104
  average time/residue: 0.2463
  time to fit residues: 27.9382
Evaluate side-chains
  99 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  481 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0970
   chunk 41 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 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 = 0.3960 r_free = 0.3960 target = 0.107089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.094690 restraints weight = 13546.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 4.13
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          1.0516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4644  Z= 0.173
  Angle     :  0.851  11.015   6313  Z= 0.418
  Chirality :  0.049   0.212    756
  Planarity :  0.005   0.031    764
  Dihedral  :  5.249  58.181    609
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 33.53 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.35), residues: 573
  helix:  1.10 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -0.64 (0.59), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 476 
 TYR   0.031   0.002   TYR A 458 
 PHE   0.033   0.001   PHE A 221 
 TRP   0.022   0.001   TRP A 100 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4644)
  covalent geometry    : angle       0.85089 ( 6313)
  hydrogen bonds       : bond        0.04555 (  377)
  hydrogen bonds       : angle       4.96272 ( 1116)

********************** 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
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9485 (tp) cc_final: 0.9178 (pp)
REVERT: A  100 TRP cc_start: 0.8362 (m100) cc_final: 0.7500 (m-10)
REVERT: A  179 MET cc_start: 0.7672 (mtm) cc_final: 0.7290 (mmt)
REVERT: A  335 GLN cc_start: 0.9381 (mt0) cc_final: 0.8980 (mt0)
REVERT: A  388 ILE cc_start: 0.9253 (mt) cc_final: 0.8978 (mp)
REVERT: A  392 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9020 (tp)
REVERT: A  396 TRP cc_start: 0.6806 (t60) cc_final: 0.6544 (t60)
REVERT: A  409 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8398 (tm-30)
REVERT: A  445 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9056 (tm)
REVERT: A  483 ILE cc_start: 0.9110 (mp) cc_final: 0.8767 (tp)
  outliers start: 11
  outliers final: 7
  residues processed: 105
  average time/residue: 0.2493
  time to fit residues: 28.4318
Evaluate side-chains
  100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  481 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    0.0870
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0870
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 ** 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 = 0.3987 r_free = 0.3987 target = 0.108353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.096461 restraints weight = 13345.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 4.02
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          1.0742

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= 0.165
  Angle     :  0.887  14.021   6313  Z= 0.421
  Chirality :  0.049   0.210    756
  Planarity :  0.005   0.034    764
  Dihedral  :  5.219  57.844    609
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 34.53 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.35), residues: 573
  helix:  1.14 (0.24), residues: 464
  sheet:  None (None), residues: 0
  loop : -0.68 (0.59), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 474 
 TYR   0.027   0.002   TYR A 458 
 PHE   0.034   0.002   PHE A 221 
 TRP   0.011   0.001   TRP A 100 
 HIS   0.001   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4644)
  covalent geometry    : angle       0.88747 ( 6313)
  hydrogen bonds       : bond        0.04488 (  377)
  hydrogen bonds       : angle       4.91909 ( 1116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1315.38 seconds
wall clock time: 23 minutes 17.30 seconds (1397.30 seconds total)