Starting phenix.real_space_refine
on Fri Aug 22 14:38:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u5v_41934/08_2025/8u5v_41934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u5v_41934/08_2025/8u5v_41934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u5v_41934/08_2025/8u5v_41934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u5v_41934/08_2025/8u5v_41934.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u5v_41934/08_2025/8u5v_41934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u5v_41934/08_2025/8u5v_41934.cif"
  }
  resolution = 2.77
  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=  -0.001 sd=   0.075
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    2957      2.51       5
     N     674      2.21       5
     O     738      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 4397
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 556, 4359
          Classifications: {'peptide': 556}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 535}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'IAC': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 0.97, per 1000 atoms: 0.22
  Number of scatterers: 4397
  At special positions: 0
  Unit cell: (90.8642, 69.8103, 76.4589, 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     738      8.00
     N     674      7.00
     C    2957      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: 0.38
  Conformation dependent library (CDL) restraints added in 202.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1042

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      90.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  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
      removed outlier: 3.719A  pdb=" N   LYS A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   GLY A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 129 through 143
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.539A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 196
      removed outlier: 3.800A  pdb=" N   TYR A 168 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE A 169 " --> pdb=" O   TYR A 165 " (cutoff:3.500A)
      removed outlier: 4.175A  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 216
    Processing helix  chain 'A' and resid 217 through 234
    Processing helix  chain 'A' and resid 238 through 265
      removed outlier: 4.252A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   SER A 253 " --> pdb=" O   GLY A 249 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   GLY A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 265 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
    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 337
      removed outlier: 4.280A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 367
      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 409
    Processing helix  chain 'A' and resid 411 through 436
      removed outlier: 3.671A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 474
    Processing helix  chain 'A' and resid 480 through 500
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
    Processing helix  chain 'A' and resid 516 through 544
      removed outlier: 3.564A  pdb=" N   GLN A 544 " --> pdb=" O   MET A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 679
    Processing helix  chain 'A' and resid 688 through 711
      removed outlier: 5.763A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1086 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: 0.47

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 649
        1.30 -     1.43: 1202
        1.43 -     1.55: 2607
        1.55 -     1.68: 1
        1.68 -     1.81: 45
  Bond restraints: 4504
  Sorted by residual:
  bond pdb=" C   PHE A 447 "
       pdb=" O   PHE A 447 "
    ideal  model  delta    sigma   weight residual
    1.237  1.168  0.069 1.19e-02 7.06e+03 3.35e+01
  bond pdb=" C   TYR A 689 "
       pdb=" O   TYR A 689 "
    ideal  model  delta    sigma   weight residual
    1.237  1.191  0.045 1.17e-02 7.31e+03 1.49e+01
  bond pdb=" C1  IAC A 901 "
       pdb=" C7  IAC A 901 "
    ideal  model  delta    sigma   weight residual
    1.433  1.366  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C   LEU A 692 "
       pdb=" O   LEU A 692 "
    ideal  model  delta    sigma   weight residual
    1.236  1.196  0.040 1.31e-02 5.83e+03 9.41e+00
  bond pdb=" N   VAL A 448 "
       pdb=" CA  VAL A 448 "
    ideal  model  delta    sigma   weight residual
    1.462  1.496 -0.034 1.18e-02 7.18e+03 8.32e+00
  ... (remaining 4499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 5860
        2.35 -     4.70: 232
        4.70 -     7.05: 25
        7.05 -     9.40: 6
        9.40 -    11.75: 2
  Bond angle restraints: 6125
  Sorted by residual:
  angle pdb=" N   THR A 457 "
        pdb=" CA  THR A 457 "
        pdb=" C   THR A 457 "
      ideal   model   delta    sigma   weight residual
     111.36  103.41    7.95 1.09e+00 8.42e-01 5.32e+01
  angle pdb=" N   GLN A 693 "
        pdb=" CA  GLN A 693 "
        pdb=" C   GLN A 693 "
      ideal   model   delta    sigma   weight residual
     111.36  103.46    7.90 1.09e+00 8.42e-01 5.26e+01
  angle pdb=" CA  TYR A 689 "
        pdb=" C   TYR A 689 "
        pdb=" O   TYR A 689 "
      ideal   model   delta    sigma   weight residual
     120.55  114.61    5.94 1.06e+00 8.90e-01 3.14e+01
  angle pdb=" C   TYR A 451 "
        pdb=" CA  TYR A 451 "
        pdb=" CB  TYR A 451 "
      ideal   model   delta    sigma   weight residual
     110.85  119.85   -9.00 1.70e+00 3.46e-01 2.80e+01
  angle pdb=" C   TRP A 460 "
        pdb=" N   THR A 461 "
        pdb=" CA  THR A 461 "
      ideal   model   delta    sigma   weight residual
     120.28  114.12    6.16 1.34e+00 5.57e-01 2.12e+01
  ... (remaining 6120 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    14.79: 2423
       14.79 -    29.57: 200
       29.57 -    44.35: 30
       44.35 -    59.13: 13
       59.13 -    73.91: 3
  Dihedral angle restraints: 2669
    sinusoidal: 1056
      harmonic: 1613
  Sorted by residual:
  dihedral pdb=" C   TYR A 451 "
           pdb=" N   TYR A 451 "
           pdb=" CA  TYR A 451 "
           pdb=" CB  TYR A 451 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.64   17.04     0      2.50e+00 1.60e-01 4.65e+01
  dihedral pdb=" N   TYR A 451 "
           pdb=" C   TYR A 451 "
           pdb=" CA  TYR A 451 "
           pdb=" CB  TYR A 451 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.98  -14.18     0      2.50e+00 1.60e-01 3.22e+01
  dihedral pdb=" CA  THR A 196 "
           pdb=" C   THR A 196 "
           pdb=" N   GLN A 197 "
           pdb=" CA  GLN A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.05  -23.95     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 2666 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 705
       0.118 -    0.237: 34
       0.237 -    0.355: 0
       0.355 -    0.473: 0
       0.473 -    0.592: 1
  Chirality restraints: 740
  Sorted by residual:
  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    1.92    0.59 2.00e-01 2.50e+01 8.75e+00
  chirality pdb=" CA  PHE A 221 "
            pdb=" N   PHE A 221 "
            pdb=" C   PHE A 221 "
            pdb=" CB  PHE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  PHE A 695 "
            pdb=" N   PHE A 695 "
            pdb=" C   PHE A 695 "
            pdb=" CB  PHE A 695 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 737 not shown)

  Planarity restraints: 729
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 320 "    0.087 2.00e-02 2.50e+03   4.45e-02 3.95e+01
        pdb=" CG  TYR A 320 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 320 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 320 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 320 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 320 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 320 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 320 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 221 "   -0.038 2.00e-02 2.50e+03   2.78e-02 1.35e+01
        pdb=" CG  PHE A 221 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 221 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 221 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 221 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 221 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 221 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 457 "    0.017 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   THR A 457 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   THR A 457 "    0.023 2.00e-02 2.50e+03
        pdb=" N   TYR A 458 "    0.021 2.00e-02 2.50e+03
  ... (remaining 726 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 1866
        2.92 -     3.42: 4944
        3.42 -     3.91: 7927
        3.91 -     4.41: 9244
        4.41 -     4.90: 14735
  Nonbonded interactions: 38716
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 458 "
            pdb=" OG  SER A 531 "
     model   vdw
     2.429 3.040
  nonbonded pdb=" OH  TYR A 359 "
            pdb=" OD2 ASP A 385 "
     model   vdw
     2.458 3.040
  nonbonded pdb=" O   VAL A 117 "
            pdb=" OG1 THR A 121 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" O   VAL A 340 "
            pdb=" OG1 THR A 344 "
     model   vdw
     2.544 3.040
  nonbonded pdb=" OD1 ASP A  99 "
            pdb=" OG  SER A 101 "
     model   vdw
     2.547 3.040
  ... (remaining 38711 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:             0.140
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.420
  Find NCS groups from input model:        0.020
  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:8.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
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      :  0.008   0.069   4504  Z= 0.392
  Angle     :  1.069  11.747   6125  Z= 0.649
  Chirality :  0.059   0.592    740
  Planarity :  0.008   0.047    729
  Dihedral  : 11.857  73.905   1627
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  2.89 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.23 (0.32), residues: 546
  helix:  0.07 (0.22), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.51 (0.63), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 130 
 TYR   0.087   0.008   TYR A 320 
 PHE   0.061   0.006   PHE A 221 
 TRP   0.042   0.007   TRP A 489 
 HIS   0.005   0.002   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00802 ( 4504)
  covalent geometry    : angle       1.06921 ( 6125)
  hydrogen bonds       : bond        0.17161 (  368)
  hydrogen bonds       : angle       7.03364 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 153
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLN cc_start: 0.7874 (mt0) cc_final: 0.7543 (mt0)
REVERT: A   71 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7208 (pptt)
REVERT: A   76 PHE cc_start: 0.8903 (t80) cc_final: 0.8682 (t80)
REVERT: A  159 GLN cc_start: 0.8590 (tt0) cc_final: 0.8179 (pt0)
REVERT: A  193 TRP cc_start: 0.7977 (t60) cc_final: 0.7738 (t60)
REVERT: A  212 LEU cc_start: 0.8971 (tp) cc_final: 0.8707 (tp)
REVERT: A  234 ASP cc_start: 0.8428 (t0) cc_final: 0.8220 (t0)
REVERT: A  347 MET cc_start: 0.9092 (tmm) cc_final: 0.8809 (tmm)
REVERT: A  434 PHE cc_start: 0.7769 (m-80) cc_final: 0.7487 (m-80)
REVERT: A  469 PHE cc_start: 0.8024 (t80) cc_final: 0.7777 (t80)
  outliers start: 6
  outliers final: 2
  residues processed: 157
  average time/residue: 0.4120
  time to fit residues: 67.4618
Evaluate side-chains
  102 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  511 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 143 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 = 0.3814 r_free = 0.3814 target = 0.129312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100234 restraints weight = 7860.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.42
r_work: 0.3270 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4504  Z= 0.168
  Angle     :  0.693   7.544   6125  Z= 0.352
  Chirality :  0.044   0.165    740
  Planarity :  0.005   0.031    729
  Dihedral  :  7.307 113.428    651
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.05 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.13 (0.35), residues: 546
  helix:  1.71 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop :  0.17 (0.67), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  61 
 TYR   0.028   0.003   TYR A 689 
 PHE   0.031   0.002   PHE A 221 
 TRP   0.015   0.002   TRP A 396 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4504)
  covalent geometry    : angle       0.69335 ( 6125)
  hydrogen bonds       : bond        0.06013 (  368)
  hydrogen bonds       : angle       5.09215 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 PHE cc_start: 0.8823 (t80) cc_final: 0.8599 (t80)
REVERT: A  159 GLN cc_start: 0.8851 (tt0) cc_final: 0.8620 (pt0)
REVERT: A  193 TRP cc_start: 0.8671 (t60) cc_final: 0.8339 (t60)
REVERT: A  212 LEU cc_start: 0.9124 (tp) cc_final: 0.8904 (tp)
REVERT: A  295 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8171 (ttt-90)
REVERT: A  299 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8134 (mp0)
REVERT: A  388 ILE cc_start: 0.9277 (mt) cc_final: 0.9005 (mp)
REVERT: A  394 LEU cc_start: 0.9137 (mt) cc_final: 0.8894 (mt)
REVERT: A  469 PHE cc_start: 0.8822 (t80) cc_final: 0.8495 (t80)
REVERT: A  679 TRP cc_start: 0.7437 (t-100) cc_final: 0.6974 (t-100)
  outliers start: 15
  outliers final: 5
  residues processed: 123
  average time/residue: 0.4231
  time to fit residues: 54.1633
Evaluate side-chains
  103 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  676 CYS
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 48 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.129006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.100120 restraints weight = 7853.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.43
r_work: 0.3261 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4504  Z= 0.166
  Angle     :  0.685  10.743   6125  Z= 0.330
  Chirality :  0.043   0.155    740
  Planarity :  0.004   0.032    729
  Dihedral  :  5.476  55.817    649
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.98 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.52 (0.35), residues: 546
  helix:  1.96 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop :  0.39 (0.72), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  61 
 TYR   0.025   0.002   TYR A 451 
 PHE   0.029   0.002   PHE A 221 
 TRP   0.010   0.001   TRP A 460 
 HIS   0.001   0.000   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4504)
  covalent geometry    : angle       0.68474 ( 6125)
  hydrogen bonds       : bond        0.05524 (  368)
  hydrogen bonds       : angle       4.82661 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7978 (mtm180)
REVERT: A   76 PHE cc_start: 0.8776 (t80) cc_final: 0.8548 (t80)
REVERT: A  159 GLN cc_start: 0.8849 (tt0) cc_final: 0.8599 (pt0)
REVERT: A  164 GLU cc_start: 0.8999 (pm20) cc_final: 0.8731 (pm20)
REVERT: A  193 TRP cc_start: 0.8600 (t60) cc_final: 0.8304 (t60)
REVERT: A  212 LEU cc_start: 0.9092 (tp) cc_final: 0.8877 (tp)
REVERT: A  235 ARG cc_start: 0.8800 (mtm-85) cc_final: 0.8286 (mtm-85)
REVERT: A  299 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8120 (mp0)
REVERT: A  394 LEU cc_start: 0.9114 (mt) cc_final: 0.8879 (mt)
REVERT: A  413 MET cc_start: 0.8066 (tpp) cc_final: 0.7806 (tpp)
REVERT: A  469 PHE cc_start: 0.8875 (t80) cc_final: 0.8502 (t80)
REVERT: A  663 LEU cc_start: 0.9071 (mt) cc_final: 0.8834 (mp)
REVERT: A  679 TRP cc_start: 0.7533 (t-100) cc_final: 0.7198 (t-100)
  outliers start: 12
  outliers final: 6
  residues processed: 114
  average time/residue: 0.4027
  time to fit residues: 47.9663
Evaluate side-chains
  110 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.2980
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 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 = 0.3841 r_free = 0.3841 target = 0.131616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102429 restraints weight = 7877.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.49
r_work: 0.3308 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4504  Z= 0.144
  Angle     :  0.699  12.809   6125  Z= 0.326
  Chirality :  0.043   0.170    740
  Planarity :  0.004   0.032    729
  Dihedral  :  5.305  56.638    649
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.42 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.45 (0.35), residues: 546
  helix:  1.99 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -0.29 (0.69), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  61 
 TYR   0.017   0.001   TYR A 451 
 PHE   0.030   0.002   PHE A 694 
 TRP   0.007   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4504)
  covalent geometry    : angle       0.69929 ( 6125)
  hydrogen bonds       : bond        0.05042 (  368)
  hydrogen bonds       : angle       4.69057 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 PHE cc_start: 0.8743 (t80) cc_final: 0.8521 (t80)
REVERT: A  146 ASP cc_start: 0.8904 (m-30) cc_final: 0.8582 (m-30)
REVERT: A  164 GLU cc_start: 0.8982 (pm20) cc_final: 0.8688 (pm20)
REVERT: A  193 TRP cc_start: 0.8555 (t60) cc_final: 0.8281 (t60)
REVERT: A  195 ASP cc_start: 0.8318 (m-30) cc_final: 0.8048 (m-30)
REVERT: A  235 ARG cc_start: 0.8781 (mtm-85) cc_final: 0.8309 (mtm-85)
REVERT: A  246 ASP cc_start: 0.8152 (m-30) cc_final: 0.7828 (m-30)
REVERT: A  267 LYS cc_start: 0.8955 (mptp) cc_final: 0.8712 (mptm)
REVERT: A  295 ARG cc_start: 0.8612 (ttp80) cc_final: 0.7830 (ttt-90)
REVERT: A  299 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8078 (mp0)
REVERT: A  319 LEU cc_start: 0.9134 (mm) cc_final: 0.8915 (mm)
REVERT: A  396 TRP cc_start: 0.8539 (t-100) cc_final: 0.7254 (t60)
REVERT: A  413 MET cc_start: 0.8046 (tpp) cc_final: 0.7770 (tpp)
REVERT: A  469 PHE cc_start: 0.8884 (t80) cc_final: 0.8502 (t80)
REVERT: A  491 ILE cc_start: 0.8323 (mt) cc_final: 0.8021 (mp)
REVERT: A  663 LEU cc_start: 0.9062 (mt) cc_final: 0.8718 (mp)
REVERT: A  679 TRP cc_start: 0.7626 (t-100) cc_final: 0.7333 (t-100)
  outliers start: 11
  outliers final: 6
  residues processed: 129
  average time/residue: 0.4027
  time to fit residues: 54.3006
Evaluate side-chains
  106 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  272 LYS
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 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 = 0.3787 r_free = 0.3787 target = 0.128366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.099130 restraints weight = 7955.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.42
r_work: 0.3210 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4504  Z= 0.150
  Angle     :  0.706  11.243   6125  Z= 0.334
  Chirality :  0.045   0.370    740
  Planarity :  0.004   0.032    729
  Dihedral  :  4.970  55.215    647
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 21.07 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.42 (0.35), residues: 546
  helix:  1.98 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -0.33 (0.70), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  61 
 TYR   0.018   0.001   TYR A 451 
 PHE   0.028   0.001   PHE A 221 
 TRP   0.006   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4504)
  covalent geometry    : angle       0.70562 ( 6125)
  hydrogen bonds       : bond        0.04983 (  368)
  hydrogen bonds       : angle       4.67595 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 PHE cc_start: 0.8689 (t80) cc_final: 0.8458 (t80)
REVERT: A  146 ASP cc_start: 0.8953 (m-30) cc_final: 0.8730 (m-30)
REVERT: A  164 GLU cc_start: 0.8975 (pm20) cc_final: 0.8698 (pm20)
REVERT: A  193 TRP cc_start: 0.8502 (t60) cc_final: 0.8262 (t60)
REVERT: A  235 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8405 (mtm-85)
REVERT: A  246 ASP cc_start: 0.8305 (m-30) cc_final: 0.7981 (m-30)
REVERT: A  295 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8230 (ttp80)
REVERT: A  299 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8135 (mp0)
REVERT: A  413 MET cc_start: 0.8047 (tpp) cc_final: 0.7770 (tpp)
REVERT: A  469 PHE cc_start: 0.8892 (t80) cc_final: 0.8499 (t80)
REVERT: A  491 ILE cc_start: 0.8219 (mt) cc_final: 0.7906 (mm)
REVERT: A  534 ILE cc_start: 0.8726 (mt) cc_final: 0.8469 (mm)
REVERT: A  663 LEU cc_start: 0.9048 (mt) cc_final: 0.8743 (mp)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.3946
  time to fit residues: 50.2049
Evaluate side-chains
  108 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  272 LYS
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
A 658 HIS
A 672 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.122932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.091969 restraints weight = 8107.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.44
r_work: 0.3090 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   4504  Z= 0.295
  Angle     :  0.771  10.049   6125  Z= 0.374
  Chirality :  0.048   0.361    740
  Planarity :  0.004   0.039    729
  Dihedral  :  5.136  50.588    647
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 21.07 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.20 (0.35), residues: 546
  helix:  1.81 (0.23), residues: 461
  sheet:  None (None), residues: 0
  loop : -0.32 (0.71), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 235 
 TYR   0.023   0.003   TYR A 104 
 PHE   0.031   0.002   PHE A 221 
 TRP   0.004   0.001   TRP A 460 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 ( 4504)
  covalent geometry    : angle       0.77126 ( 6125)
  hydrogen bonds       : bond        0.05617 (  368)
  hydrogen bonds       : angle       4.87760 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ASP cc_start: 0.8912 (m-30) cc_final: 0.8665 (m-30)
REVERT: A  164 GLU cc_start: 0.9019 (pm20) cc_final: 0.8741 (pm20)
REVERT: A  193 TRP cc_start: 0.8566 (t60) cc_final: 0.8303 (t60)
REVERT: A  203 LYS cc_start: 0.8294 (mppt) cc_final: 0.7373 (mmmt)
REVERT: A  235 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8387 (mtm-85)
REVERT: A  246 ASP cc_start: 0.8222 (m-30) cc_final: 0.7902 (m-30)
REVERT: A  319 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8930 (mm)
REVERT: A  413 MET cc_start: 0.8117 (tpp) cc_final: 0.7876 (tpp)
REVERT: A  469 PHE cc_start: 0.8902 (t80) cc_final: 0.8475 (t80)
REVERT: A  663 LEU cc_start: 0.9066 (mt) cc_final: 0.8778 (mp)
  outliers start: 20
  outliers final: 9
  residues processed: 118
  average time/residue: 0.3834
  time to fit residues: 47.2664
Evaluate side-chains
  105 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  272 LYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   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  75 ASN
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 658 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 = 0.3772 r_free = 0.3772 target = 0.127339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.097370 restraints weight = 7944.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.43
r_work: 0.3184 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4504  Z= 0.155
  Angle     :  0.731  14.138   6125  Z= 0.344
  Chirality :  0.045   0.359    740
  Planarity :  0.004   0.040    729
  Dihedral  :  5.113  57.427    647
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.31 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.35 (0.36), residues: 546
  helix:  1.93 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.35 (0.72), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 295 
 TYR   0.019   0.001   TYR A 689 
 PHE   0.026   0.001   PHE A 221 
 TRP   0.006   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4504)
  covalent geometry    : angle       0.73111 ( 6125)
  hydrogen bonds       : bond        0.05032 (  368)
  hydrogen bonds       : angle       4.73733 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 GLU cc_start: 0.9058 (pm20) cc_final: 0.8742 (pm20)
REVERT: A  203 LYS cc_start: 0.8263 (mppt) cc_final: 0.7322 (mmmt)
REVERT: A  235 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8347 (mtm-85)
REVERT: A  299 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7948 (mp0)
REVERT: A  413 MET cc_start: 0.8122 (tpp) cc_final: 0.7787 (tpp)
REVERT: A  451 TYR cc_start: 0.8227 (m-80) cc_final: 0.7990 (m-80)
REVERT: A  469 PHE cc_start: 0.8899 (t80) cc_final: 0.8469 (t80)
REVERT: A  491 ILE cc_start: 0.8180 (mt) cc_final: 0.7830 (mm)
REVERT: A  534 ILE cc_start: 0.8710 (mt) cc_final: 0.8437 (mm)
REVERT: A  663 LEU cc_start: 0.9047 (mt) cc_final: 0.8736 (mp)
  outliers start: 14
  outliers final: 9
  residues processed: 112
  average time/residue: 0.4039
  time to fit residues: 47.1333
Evaluate side-chains
  115 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  272 LYS
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
A 658 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.127217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.096997 restraints weight = 7943.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.44
r_work: 0.3176 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4504  Z= 0.167
  Angle     :  0.735  11.026   6125  Z= 0.349
  Chirality :  0.045   0.330    740
  Planarity :  0.004   0.043    729
  Dihedral  :  5.055  54.366    647
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.73 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.29 (0.36), residues: 546
  helix:  1.88 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -0.30 (0.71), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 295 
 TYR   0.015   0.001   TYR A 451 
 PHE   0.027   0.002   PHE A 221 
 TRP   0.008   0.001   TRP A 432 
 HIS   0.001   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4504)
  covalent geometry    : angle       0.73530 ( 6125)
  hydrogen bonds       : bond        0.05075 (  368)
  hydrogen bonds       : angle       4.73338 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 GLU cc_start: 0.9044 (pm20) cc_final: 0.8729 (pm20)
REVERT: A  203 LYS cc_start: 0.8332 (mppt) cc_final: 0.7355 (mmmt)
REVERT: A  235 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8391 (mtm-85)
REVERT: A  299 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8071 (mp0)
REVERT: A  413 MET cc_start: 0.8137 (tpp) cc_final: 0.7805 (tpp)
REVERT: A  451 TYR cc_start: 0.8238 (m-80) cc_final: 0.8030 (m-80)
REVERT: A  469 PHE cc_start: 0.8888 (t80) cc_final: 0.8433 (t80)
REVERT: A  491 ILE cc_start: 0.8130 (mt) cc_final: 0.7832 (mm)
REVERT: A  534 ILE cc_start: 0.8711 (mt) cc_final: 0.8422 (mm)
REVERT: A  663 LEU cc_start: 0.9036 (mt) cc_final: 0.8746 (mp)
  outliers start: 16
  outliers final: 10
  residues processed: 112
  average time/residue: 0.4307
  time to fit residues: 50.3182
Evaluate side-chains
  115 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  272 LYS
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 7 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    0.1980
   chunk 54 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 658 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 = 0.3800 r_free = 0.3800 target = 0.129431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.100195 restraints weight = 8075.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.45
r_work: 0.3222 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4504  Z= 0.150
  Angle     :  0.764  12.032   6125  Z= 0.357
  Chirality :  0.045   0.373    740
  Planarity :  0.004   0.047    729
  Dihedral  :  5.024  55.628    647
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 24.38 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.30 (0.36), residues: 546
  helix:  1.87 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop : -0.30 (0.73), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 295 
 TYR   0.016   0.002   TYR A 451 
 PHE   0.024   0.001   PHE A 221 
 TRP   0.012   0.001   TRP A 460 
 HIS   0.001   0.000   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4504)
  covalent geometry    : angle       0.76371 ( 6125)
  hydrogen bonds       : bond        0.04918 (  368)
  hydrogen bonds       : angle       4.68607 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 GLU cc_start: 0.9030 (pm20) cc_final: 0.8705 (pm20)
REVERT: A  203 LYS cc_start: 0.8395 (mppt) cc_final: 0.7337 (mmmt)
REVERT: A  235 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8215 (mtm-85)
REVERT: A  299 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8151 (mp0)
REVERT: A  396 TRP cc_start: 0.8359 (t-100) cc_final: 0.7014 (t60)
REVERT: A  413 MET cc_start: 0.8021 (tpp) cc_final: 0.7634 (tpp)
REVERT: A  469 PHE cc_start: 0.8880 (t80) cc_final: 0.8416 (t80)
REVERT: A  534 ILE cc_start: 0.8696 (mt) cc_final: 0.8455 (tp)
REVERT: A  663 LEU cc_start: 0.9038 (mt) cc_final: 0.8740 (mp)
  outliers start: 12
  outliers final: 8
  residues processed: 111
  average time/residue: 0.3729
  time to fit residues: 43.2108
Evaluate side-chains
  113 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  272 LYS
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0370
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 15 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A 703 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.130493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.100681 restraints weight = 7946.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.47
r_work: 0.3235 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4504  Z= 0.153
  Angle     :  0.765  10.751   6125  Z= 0.363
  Chirality :  0.045   0.362    740
  Planarity :  0.004   0.043    729
  Dihedral  :  4.967  55.036    647
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 25.62 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.30 (0.36), residues: 546
  helix:  1.86 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop : -0.24 (0.73), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 270 
 TYR   0.029   0.002   TYR A 451 
 PHE   0.023   0.001   PHE A 221 
 TRP   0.015   0.001   TRP A 460 
 HIS   0.001   0.000   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4504)
  covalent geometry    : angle       0.76505 ( 6125)
  hydrogen bonds       : bond        0.04891 (  368)
  hydrogen bonds       : angle       4.71263 ( 1086)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ASP cc_start: 0.8947 (m-30) cc_final: 0.8686 (m-30)
REVERT: A  164 GLU cc_start: 0.9048 (pm20) cc_final: 0.8701 (pm20)
REVERT: A  203 LYS cc_start: 0.8341 (mppt) cc_final: 0.7286 (mmmt)
REVERT: A  246 ASP cc_start: 0.8295 (m-30) cc_final: 0.7971 (m-30)
REVERT: A  299 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8154 (mp0)
REVERT: A  381 ASN cc_start: 0.7693 (m-40) cc_final: 0.7272 (t0)
REVERT: A  396 TRP cc_start: 0.8335 (t-100) cc_final: 0.6989 (t60)
REVERT: A  413 MET cc_start: 0.7930 (tpp) cc_final: 0.7577 (tpp)
REVERT: A  469 PHE cc_start: 0.8910 (t80) cc_final: 0.8447 (t80)
REVERT: A  534 ILE cc_start: 0.8704 (mt) cc_final: 0.8463 (tp)
REVERT: A  663 LEU cc_start: 0.9024 (mt) cc_final: 0.8730 (mp)
  outliers start: 10
  outliers final: 6
  residues processed: 121
  average time/residue: 0.3680
  time to fit residues: 46.4901
Evaluate side-chains
  111 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  696 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 45 optimal weight:    0.0470
   chunk 19 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 40 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0030
   overall best weight:    0.4688

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

Flipped N/Q/H residues before XYZ refinement:
A 703 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.131820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.102007 restraints weight = 7944.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.49
r_work: 0.3262 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.5095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4504  Z= 0.151
  Angle     :  0.791  11.121   6125  Z= 0.369
  Chirality :  0.045   0.358    740
  Planarity :  0.004   0.042    729
  Dihedral  :  5.161  53.100    647
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 26.86 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.37 (0.36), residues: 546
  helix:  1.92 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.24 (0.73), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 235 
 TYR   0.027   0.002   TYR A 451 
 PHE   0.027   0.001   PHE A 221 
 TRP   0.010   0.001   TRP A 193 
 HIS   0.001   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4504)
  covalent geometry    : angle       0.79144 ( 6125)
  hydrogen bonds       : bond        0.04795 (  368)
  hydrogen bonds       : angle       4.64044 ( 1086)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1453.98 seconds
wall clock time: 25 minutes 32.88 seconds (1532.88 seconds total)