Starting phenix.real_space_refine
on Thu Jun  5 00:02:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u5n_41929/06_2025/8u5n_41929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u5n_41929/06_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_41929/06_2025/8u5n_41929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u5n_41929/06_2025/8u5n_41929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u5n_41929/06_2025/8u5n_41929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u5n_41929/06_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 3.31, per 1000 atoms: 0.73
  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: 1.05
  Conformation dependent library (CDL) restraints added in 492.1 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: 0.42
  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: 1.35

  Time building geometry restraints manager: 1.26 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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.580
  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:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.830
-------------------------------------------------------------------------------
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  : 0.532 
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: 0.6881
  time to fit residues: 134.5895
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  : 0.508 
-------------------------------------------------------------------------------
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: 0.3506 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3506
-------------------------------------------------------------------------------
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  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8549 (mm) cc_final: 0.8291 (tp)
REVERT: A  178 MET cc_start: 0.7678 (ptt) cc_final: 0.6769 (tpt)
REVERT: A  179 MET cc_start: 0.7889 (mtm) cc_final: 0.7378 (mmt)
REVERT: A  409 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8430 (tt0)
REVERT: A  476 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8008 (tmt170)
REVERT: A  499 LEU cc_start: 0.9163 (mt) cc_final: 0.8784 (mt)
REVERT: A  532 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9097 (tt)
  outliers start: 28
  outliers final: 8
  residues processed: 135
  average time/residue: 0.5373
  time to fit residues: 78.3185
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  : 0.465 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 16 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 52 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0980
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.2980

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.103278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.091838 restraints weight = 12455.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 3.79
r_work: 0.3528 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.6067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4644  Z= 0.162
  Angle     :  0.710   8.499   6313  Z= 0.349
  Chirality :  0.043   0.143    756
  Planarity :  0.004   0.036    764
  Dihedral  :  5.275  50.806    609
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 20.56 %
    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 (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:  1.53 (0.35), residues: 573
  helix:  1.32 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop : -0.05 (0.67), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 363 
 HIS   0.002   0.001   HIS A 412 
 PHE   0.023   0.002   PHE A 384 
 TYR   0.029   0.002   TYR A 104 
 ARG   0.004   0.001   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04730 (  377)
  hydrogen bonds       : angle       4.82029 ( 1116)
  covalent geometry    : bond        0.00335 ( 4644)
  covalent geometry    : angle       0.70989 ( 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
  143 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 108
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.7496 (ptt) cc_final: 0.6709 (tpt)
REVERT: A  179 MET cc_start: 0.8038 (mtm) cc_final: 0.7416 (mmt)
REVERT: A  220 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7764 (t)
REVERT: A  338 MET cc_start: 0.8353 (ttp) cc_final: 0.7829 (tmm)
REVERT: A  409 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8339 (tt0)
REVERT: A  412 HIS cc_start: 0.8479 (m-70) cc_final: 0.8123 (m90)
REVERT: A  429 MET cc_start: 0.8142 (tpp) cc_final: 0.7918 (tmm)
REVERT: A  445 LEU cc_start: 0.9145 (mm) cc_final: 0.8574 (tm)
REVERT: A  451 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7422 (m-80)
REVERT: A  499 LEU cc_start: 0.9234 (mt) cc_final: 0.8907 (mt)
REVERT: A  670 PHE cc_start: 0.8439 (t80) cc_final: 0.8212 (m-80)
REVERT: A  691 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (pm20)
  outliers start: 35
  outliers final: 11
  residues processed: 127
  average time/residue: 0.5170
  time to fit residues: 70.9714
Evaluate side-chains
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
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  220 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  262 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  669 LEU
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:    0.0670
   chunk 14 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.102135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.090857 restraints weight = 12779.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 3.85
r_work: 0.3526 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.7104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4644  Z= 0.164
  Angle     :  0.707   8.974   6313  Z= 0.351
  Chirality :  0.043   0.167    756
  Planarity :  0.004   0.033    764
  Dihedral  :  5.132  47.120    609
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 23.75 %
    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 (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:  1.74 (0.36), residues: 573
  helix:  1.46 (0.24), residues: 466
  sheet:  None (None), residues: 0
  loop :  0.05 (0.67), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 363 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.024   0.002   PHE A 695 
 TYR   0.028   0.002   TYR A 104 
 ARG   0.004   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04524 (  377)
  hydrogen bonds       : angle       4.77104 ( 1116)
  covalent geometry    : bond        0.00359 ( 4644)
  covalent geometry    : angle       0.70733 ( 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
  145 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9738 (tp) cc_final: 0.9358 (pp)
REVERT: A  103 LEU cc_start: 0.8748 (mm) cc_final: 0.8362 (tp)
REVERT: A  178 MET cc_start: 0.7463 (ptt) cc_final: 0.6730 (tpt)
REVERT: A  179 MET cc_start: 0.8022 (mtm) cc_final: 0.7455 (mmt)
REVERT: A  186 ILE cc_start: 0.8636 (mt) cc_final: 0.8435 (mt)
REVERT: A  284 THR cc_start: 0.9558 (m) cc_final: 0.9294 (p)
REVERT: A  296 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8848 (mm-30)
REVERT: A  351 THR cc_start: 0.8904 (m) cc_final: 0.8625 (m)
REVERT: A  381 ASN cc_start: 0.8856 (m-40) cc_final: 0.8640 (m110)
REVERT: A  409 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8035 (tt0)
REVERT: A  412 HIS cc_start: 0.8745 (m-70) cc_final: 0.7895 (m-70)
REVERT: A  415 THR cc_start: 0.8858 (m) cc_final: 0.8618 (p)
REVERT: A  445 LEU cc_start: 0.9303 (mm) cc_final: 0.8824 (tm)
REVERT: A  499 LEU cc_start: 0.9323 (mt) cc_final: 0.9046 (mt)
REVERT: A  670 PHE cc_start: 0.8558 (t80) cc_final: 0.8243 (m-80)
REVERT: A  691 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8399 (mp0)
REVERT: A  692 LEU cc_start: 0.9361 (tm) cc_final: 0.9066 (pp)
  outliers start: 23
  outliers final: 11
  residues processed: 133
  average time/residue: 0.4865
  time to fit residues: 70.4319
Evaluate side-chains
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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  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  481 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 412 HIS
A 433 ASN
A 443 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.103070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.091488 restraints weight = 13070.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 3.92
r_work: 0.3525 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.7886

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= 0.163
  Angle     :  0.733   8.271   6313  Z= 0.361
  Chirality :  0.043   0.210    756
  Planarity :  0.004   0.031    764
  Dihedral  :  4.941  44.073    609
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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:  1.75 (0.36), residues: 573
  helix:  1.54 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop : -0.40 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 363 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.015   0.002   PHE A 384 
 TYR   0.024   0.002   TYR A 104 
 ARG   0.004   0.000   ARG A 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04466 (  377)
  hydrogen bonds       : angle       4.71489 ( 1116)
  covalent geometry    : bond        0.00366 ( 4644)
  covalent geometry    : angle       0.73322 ( 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
  136 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9661 (tp) cc_final: 0.9256 (pp)
REVERT: A  103 LEU cc_start: 0.8794 (mm) cc_final: 0.8450 (tp)
REVERT: A  170 TYR cc_start: 0.8902 (m-80) cc_final: 0.8690 (m-10)
REVERT: A  177 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7931 (mt)
REVERT: A  178 MET cc_start: 0.7073 (ptt) cc_final: 0.6614 (tpt)
REVERT: A  179 MET cc_start: 0.8210 (mtm) cc_final: 0.7606 (mmt)
REVERT: A  221 PHE cc_start: 0.7384 (t80) cc_final: 0.7123 (t80)
REVERT: A  284 THR cc_start: 0.9576 (m) cc_final: 0.9312 (p)
REVERT: A  296 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8928 (mm-30)
REVERT: A  381 ASN cc_start: 0.8763 (m-40) cc_final: 0.8397 (m110)
REVERT: A  385 ASP cc_start: 0.8128 (m-30) cc_final: 0.7911 (m-30)
REVERT: A  392 ILE cc_start: 0.9126 (mm) cc_final: 0.8913 (tp)
REVERT: A  396 TRP cc_start: 0.6401 (t60) cc_final: 0.6177 (t60)
REVERT: A  409 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8220 (tt0)
REVERT: A  412 HIS cc_start: 0.8932 (m90) cc_final: 0.8352 (m-70)
REVERT: A  429 MET cc_start: 0.8238 (tmm) cc_final: 0.7242 (tmm)
REVERT: A  445 LEU cc_start: 0.9305 (mm) cc_final: 0.8892 (tm)
REVERT: A  499 LEU cc_start: 0.9348 (mt) cc_final: 0.9109 (mt)
REVERT: A  670 PHE cc_start: 0.8646 (t80) cc_final: 0.8253 (m-80)
REVERT: A  691 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8432 (mp0)
  outliers start: 24
  outliers final: 10
  residues processed: 124
  average time/residue: 0.4668
  time to fit residues: 63.4005
Evaluate side-chains
  118 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 2.137 
-------------------------------------------------------------------------------
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  177 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  390 SER
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  481 VAL
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:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.5782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.103427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.091748 restraints weight = 12852.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 3.92
r_work: 0.3499 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.8578

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= 0.166
  Angle     :  0.765  14.044   6313  Z= 0.368
  Chirality :  0.044   0.162    756
  Planarity :  0.004   0.035    764
  Dihedral  :  4.842  41.102    609
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 28.54 %
    Favored  : 67.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.74 (0.36), residues: 573
  helix:  1.56 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop : -0.50 (0.64), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 678 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.022   0.002   PHE A 695 
 TYR   0.022   0.002   TYR A 104 
 ARG   0.002   0.000   ARG A 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  377)
  hydrogen bonds       : angle       4.74166 ( 1116)
  covalent geometry    : bond        0.00379 ( 4644)
  covalent geometry    : angle       0.76495 ( 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
  139 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9647 (tp) cc_final: 0.9327 (pp)
REVERT: A  103 LEU cc_start: 0.8907 (mm) cc_final: 0.8652 (tp)
REVERT: A  178 MET cc_start: 0.7218 (ptt) cc_final: 0.6807 (tpt)
REVERT: A  179 MET cc_start: 0.8319 (mtm) cc_final: 0.7746 (mmt)
REVERT: A  268 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8579 (tp)
REVERT: A  278 VAL cc_start: 0.8182 (t) cc_final: 0.7976 (p)
REVERT: A  284 THR cc_start: 0.9626 (m) cc_final: 0.9401 (p)
REVERT: A  296 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8834 (mm-30)
REVERT: A  300 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9123 (pt)
REVERT: A  301 LEU cc_start: 0.9035 (mt) cc_final: 0.8770 (mp)
REVERT: A  381 ASN cc_start: 0.8779 (m-40) cc_final: 0.8422 (m110)
REVERT: A  394 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8385 (tt)
REVERT: A  396 TRP cc_start: 0.6360 (t60) cc_final: 0.6149 (t60)
REVERT: A  409 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8137 (tt0)
REVERT: A  412 HIS cc_start: 0.8934 (m90) cc_final: 0.8527 (m-70)
REVERT: A  419 LEU cc_start: 0.8624 (mt) cc_final: 0.8368 (mm)
REVERT: A  445 LEU cc_start: 0.9386 (mm) cc_final: 0.9054 (tm)
REVERT: A  453 SER cc_start: 0.8916 (m) cc_final: 0.8484 (p)
REVERT: A  495 LEU cc_start: 0.9546 (mm) cc_final: 0.9274 (mp)
REVERT: A  691 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8419 (mp0)
  outliers start: 20
  outliers final: 8
  residues processed: 127
  average time/residue: 0.4450
  time to fit residues: 62.0179
Evaluate side-chains
  116 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
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  248 LEU
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  481 VAL
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:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0050
   chunk 29 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0870
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.3572

-------------------------------------------------------------------------------
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 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.105127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.093198 restraints weight = 12964.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 4.03
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.9008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4644  Z= 0.156
  Angle     :  0.776  10.478   6313  Z= 0.383
  Chirality :  0.048   0.241    756
  Planarity :  0.004   0.033    764
  Dihedral  :  4.689  37.454    609
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 31.94 %
    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 (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:  1.58 (0.35), residues: 573
  helix:  1.46 (0.24), residues: 467
  sheet:  None (None), residues: 0
  loop : -0.64 (0.64), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 363 
 HIS   0.002   0.001   HIS A 412 
 PHE   0.041   0.002   PHE A 221 
 TYR   0.027   0.002   TYR A 170 
 ARG   0.001   0.000   ARG A 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04532 (  377)
  hydrogen bonds       : angle       4.84027 ( 1116)
  covalent geometry    : bond        0.00352 ( 4644)
  covalent geometry    : angle       0.77599 ( 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
  138 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9055 (mm)
REVERT: A   58 ILE cc_start: 0.9544 (tp) cc_final: 0.9209 (pp)
REVERT: A  103 LEU cc_start: 0.8850 (mm) cc_final: 0.8635 (tp)
REVERT: A  178 MET cc_start: 0.7133 (ptt) cc_final: 0.6891 (tpt)
REVERT: A  278 VAL cc_start: 0.8252 (t) cc_final: 0.8035 (p)
REVERT: A  287 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8636 (mm)
REVERT: A  301 LEU cc_start: 0.9001 (mt) cc_final: 0.8666 (mp)
REVERT: A  318 PHE cc_start: 0.9175 (t80) cc_final: 0.8949 (t80)
REVERT: A  394 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8255 (tt)
REVERT: A  396 TRP cc_start: 0.6255 (t60) cc_final: 0.6026 (t60)
REVERT: A  412 HIS cc_start: 0.8682 (m90) cc_final: 0.8350 (m-70)
REVERT: A  413 MET cc_start: 0.7932 (mmt) cc_final: 0.7664 (mmt)
REVERT: A  415 THR cc_start: 0.8629 (m) cc_final: 0.8360 (p)
REVERT: A  445 LEU cc_start: 0.9360 (mm) cc_final: 0.9069 (tm)
REVERT: A  453 SER cc_start: 0.8817 (m) cc_final: 0.8391 (p)
REVERT: A  670 PHE cc_start: 0.8738 (t80) cc_final: 0.8360 (m-80)
REVERT: A  675 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8928 (p)
REVERT: A  691 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8255 (mp0)
  outliers start: 19
  outliers final: 6
  residues processed: 129
  average time/residue: 0.4751
  time to fit residues: 66.8214
Evaluate side-chains
  113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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  223 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  675 SER
Chi-restraints excluded: chain A residue  691 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.104167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.091959 restraints weight = 13108.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 3.98
r_work: 0.3538 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.9510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4644  Z= 0.188
  Angle     :  0.821  11.891   6313  Z= 0.409
  Chirality :  0.049   0.208    756
  Planarity :  0.004   0.034    764
  Dihedral  :  4.683  35.047    609
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 33.73 %
    Favored  : 63.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.29 (0.35), residues: 573
  helix:  1.21 (0.23), residues: 470
  sheet:  None (None), residues: 0
  loop : -0.53 (0.66), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.038   0.002   PHE A 221 
 TYR   0.030   0.002   TYR A 170 
 ARG   0.002   0.000   ARG A 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04749 (  377)
  hydrogen bonds       : angle       4.96370 ( 1116)
  covalent geometry    : bond        0.00443 ( 4644)
  covalent geometry    : angle       0.82130 ( 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
  130 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9553 (tp) cc_final: 0.9245 (pp)
REVERT: A  100 TRP cc_start: 0.5515 (m-10) cc_final: 0.5099 (m100)
REVERT: A  128 ASP cc_start: 0.9065 (p0) cc_final: 0.8763 (p0)
REVERT: A  178 MET cc_start: 0.7581 (ptt) cc_final: 0.7157 (tmt)
REVERT: A  268 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8668 (tp)
REVERT: A  301 LEU cc_start: 0.8975 (mt) cc_final: 0.8589 (mp)
REVERT: A  320 TYR cc_start: 0.8569 (t80) cc_final: 0.7994 (t80)
REVERT: A  396 TRP cc_start: 0.6319 (t60) cc_final: 0.6110 (t60)
REVERT: A  413 MET cc_start: 0.8284 (mmt) cc_final: 0.7991 (mmt)
REVERT: A  445 LEU cc_start: 0.9360 (mm) cc_final: 0.9088 (tm)
REVERT: A  453 SER cc_start: 0.8824 (m) cc_final: 0.8615 (p)
REVERT: A  675 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.9010 (p)
REVERT: A  691 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8519 (mp0)
  outliers start: 16
  outliers final: 7
  residues processed: 124
  average time/residue: 0.4782
  time to fit residues: 64.8187
Evaluate side-chains
  113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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  223 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  675 SER
Chi-restraints excluded: chain A residue  691 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0970
   chunk 51 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0570
   chunk 41 optimal weight:    0.0970
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.2894

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.111313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.099350 restraints weight = 13065.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 4.05
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.9844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4644  Z= 0.160
  Angle     :  0.843  13.104   6313  Z= 0.411
  Chirality :  0.048   0.209    756
  Planarity :  0.005   0.035    764
  Dihedral  :  4.599  30.335    609
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 35.33 %
    Favored  : 61.28 %
  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:  1.28 (0.35), residues: 573
  helix:  1.21 (0.23), residues: 467
  sheet:  None (None), residues: 0
  loop : -0.52 (0.62), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 363 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.043   0.002   PHE A 221 
 TYR   0.038   0.002   TYR A 170 
 ARG   0.001   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  377)
  hydrogen bonds       : angle       5.00732 ( 1116)
  covalent geometry    : bond        0.00364 ( 4644)
  covalent geometry    : angle       0.84295 ( 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
  133 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9488 (tp) cc_final: 0.9156 (pp)
REVERT: A  221 PHE cc_start: 0.6723 (t80) cc_final: 0.6502 (t80)
REVERT: A  301 LEU cc_start: 0.8915 (mt) cc_final: 0.8615 (mt)
REVERT: A  320 TYR cc_start: 0.8376 (t80) cc_final: 0.7703 (t80)
REVERT: A  335 GLN cc_start: 0.9311 (mt0) cc_final: 0.8867 (mt0)
REVERT: A  340 VAL cc_start: 0.9354 (p) cc_final: 0.9148 (m)
REVERT: A  396 TRP cc_start: 0.6453 (t60) cc_final: 0.6201 (t60)
REVERT: A  445 LEU cc_start: 0.9363 (mm) cc_final: 0.9126 (tm)
REVERT: A  483 ILE cc_start: 0.9156 (mp) cc_final: 0.8808 (tp)
REVERT: A  670 PHE cc_start: 0.8766 (t80) cc_final: 0.8408 (m-80)
REVERT: A  675 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.9020 (p)
  outliers start: 17
  outliers final: 6
  residues processed: 125
  average time/residue: 0.5479
  time to fit residues: 74.6230
Evaluate side-chains
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
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  322 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  414 LEU
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:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   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  89 ASN
** 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 = 0.3888 r_free = 0.3888 target = 0.103635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.091829 restraints weight = 13114.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 3.92
r_work: 0.3488 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          1.0167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   4644  Z= 0.210
  Angle     :  0.887  13.162   6313  Z= 0.436
  Chirality :  0.050   0.212    756
  Planarity :  0.005   0.038    764
  Dihedral  :  4.659  28.654    609
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 38.32 %
    Favored  : 60.08 %
  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:  1.10 (0.34), residues: 573
  helix:  1.10 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -0.62 (0.60), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 193 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.040   0.002   PHE A 221 
 TYR   0.045   0.002   TYR A 170 
 ARG   0.002   0.000   ARG A 474 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04729 (  377)
  hydrogen bonds       : angle       5.02774 ( 1116)
  covalent geometry    : bond        0.00502 ( 4644)
  covalent geometry    : angle       0.88663 ( 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
  114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9443 (tp) cc_final: 0.9129 (pp)
REVERT: A  137 PHE cc_start: 0.8867 (m-80) cc_final: 0.8633 (m-80)
REVERT: A  296 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8203 (mp0)
REVERT: A  301 LEU cc_start: 0.9039 (mt) cc_final: 0.8741 (mt)
REVERT: A  320 TYR cc_start: 0.8601 (t80) cc_final: 0.8088 (t80)
REVERT: A  335 GLN cc_start: 0.9384 (mt0) cc_final: 0.8981 (mt0)
REVERT: A  340 VAL cc_start: 0.9362 (p) cc_final: 0.9162 (m)
REVERT: A  396 TRP cc_start: 0.6563 (t60) cc_final: 0.6354 (t60)
REVERT: A  445 LEU cc_start: 0.9390 (mm) cc_final: 0.9163 (tm)
REVERT: A  453 SER cc_start: 0.8845 (m) cc_final: 0.8581 (t)
REVERT: A  675 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.9092 (p)
REVERT: A  691 GLU cc_start: 0.8775 (mp0) cc_final: 0.8460 (pm20)
  outliers start: 8
  outliers final: 5
  residues processed: 112
  average time/residue: 0.5385
  time to fit residues: 65.1338
Evaluate side-chains
  106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
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  325 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  438 LYS
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:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0270
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3904 r_free = 0.3904 target = 0.104465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.092503 restraints weight = 13037.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 4.01
r_work: 0.3518 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          1.0467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   4644  Z= 0.199
  Angle     :  0.909  13.011   6313  Z= 0.446
  Chirality :  0.050   0.210    756
  Planarity :  0.005   0.042    764
  Dihedral  :  4.764  26.333    609
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 37.92 %
    Favored  : 59.68 %
  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:  0.93 (0.34), residues: 573
  helix:  0.99 (0.23), residues: 463
  sheet:  None (None), residues: 0
  loop : -0.66 (0.58), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 193 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.040   0.002   PHE A 221 
 TYR   0.044   0.002   TYR A 170 
 ARG   0.001   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04694 (  377)
  hydrogen bonds       : angle       5.13141 ( 1116)
  covalent geometry    : bond        0.00477 ( 4644)
  covalent geometry    : angle       0.90866 ( 6313)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2953.00 seconds
wall clock time: 51 minutes 30.69 seconds (3090.69 seconds total)