Starting phenix.real_space_refine
on Fri May  9 19:39:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y65_38966/05_2025/8y65_38966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y65_38966/05_2025/8y65_38966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y65_38966/05_2025/8y65_38966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y65_38966/05_2025/8y65_38966.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y65_38966/05_2025/8y65_38966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y65_38966/05_2025/8y65_38966.cif"
  }
  resolution = 3.51
  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=   0.007 sd=   0.171
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      13      5.16       5
     C    2355      2.51       5
     N     574      2.21       5
     O     623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3565
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3553
          Classifications: {'peptide': 467}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 24, 'TRANS': 442}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'URC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.63, per 1000 atoms: 0.74
  Number of scatterers: 3565
  At special positions: 0
  Unit cell: (84.5383, 62.5803, 69.1677, 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      13     16.00
     O     623      8.00
     N     574      7.00
     C    2355      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: 0.85
  Conformation dependent library (CDL) restraints added in 449.6 milliseconds
  

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  848

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      86.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 76
      removed outlier: 4.372A  pdb=" N   PHE A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LEU A  70 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 98
    Processing helix  chain 'A' and resid 102 through 132
      removed outlier: 4.794A  pdb=" N   PHE A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   ALA A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   MET A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 157
    Processing helix  chain 'A' and resid 157 through 162
      removed outlier: 4.116A  pdb=" N   ALA A 161 " --> pdb=" O   CYS A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 193
      removed outlier: 3.742A  pdb=" N   LEU A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      Proline residue:  A 186  - end of helix
      removed outlier: 3.848A  pdb=" N   GLU A 191 " --> pdb=" O   MET A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.625A  pdb=" N   LEU A 201 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 237
      removed outlier: 4.096A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 249
      removed outlier: 3.589A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 252
      No H-bonds generated for 'chain 'A' and resid 250 through 252'
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 3.799A  pdb=" N   LEU A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU A 262 " --> pdb=" O   TYR A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 282 through 299
      removed outlier: 3.501A  pdb=" N   ILE A 299 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 310
    Processing helix  chain 'A' and resid 313 through 331
      removed outlier: 4.333A  pdb=" N   GLY A 331 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 338
    Processing helix  chain 'A' and resid 338 through 345
    Processing helix  chain 'A' and resid 352 through 379
      removed outlier: 4.064A  pdb=" N   LEU A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   GLU A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   HIS A 377 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLY A 379 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 404
    Processing helix  chain 'A' and resid 410 through 412
      No H-bonds generated for 'chain 'A' and resid 410 through 412'
    Processing helix  chain 'A' and resid 413 through 428
      removed outlier: 4.043A  pdb=" N   VAL A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 442
      removed outlier: 4.708A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 476
      Proline residue:  A 470  - end of helix
    Processing helix  chain 'A' and resid 481 through 499
    Processing helix  chain 'A' and resid 506 through 518

    271 hydrogen bonds defined for protein.
    801 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: 0.93

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1101
        1.34 -     1.46: 872
        1.46 -     1.58: 1664
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3655
  Sorted by residual:
  bond pdb=" C4  URC A 601 "
       pdb=" C5  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.358  1.470 -0.112 2.00e-02 2.50e+03 3.15e+01
  bond pdb=" C6  URC A 601 "
       pdb=" N1  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.398  1.317  0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C8  URC A 601 "
       pdb=" N9  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.396  1.316  0.080 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" N   ILE A 335 "
       pdb=" CA  ILE A 335 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.10e+01
  bond pdb=" C2  URC A 601 "
       pdb=" N3  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.376  1.311  0.065 2.00e-02 2.50e+03 1.06e+01
  ... (remaining 3650 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 4930
        2.81 -     5.62: 44
        5.62 -     8.42: 11
        8.42 -    11.23: 3
       11.23 -    14.04: 1
  Bond angle restraints: 4989
  Sorted by residual:
  angle pdb=" N7  URC A 601 "
        pdb=" C8  URC A 601 "
        pdb=" N9  URC A 601 "
      ideal   model   delta    sigma   weight residual
     104.73  118.77  -14.04 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" N   ILE A 436 "
        pdb=" CA  ILE A 436 "
        pdb=" C   ILE A 436 "
      ideal   model   delta    sigma   weight residual
     112.96  108.33    4.63 1.00e+00 1.00e+00 2.15e+01
  angle pdb=" CA  ILE A 335 "
        pdb=" C   ILE A 335 "
        pdb=" N   TRP A 336 "
      ideal   model   delta    sigma   weight residual
     118.13  123.44   -5.31 1.37e+00 5.33e-01 1.50e+01
  angle pdb=" N1  URC A 601 "
        pdb=" C2  URC A 601 "
        pdb=" N3  URC A 601 "
      ideal   model   delta    sigma   weight residual
     114.62  124.69  -10.07 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" N   ILE A 335 "
        pdb=" CA  ILE A 335 "
        pdb=" C   ILE A 335 "
      ideal   model   delta    sigma   weight residual
     113.00  108.67    4.33 1.30e+00 5.92e-01 1.11e+01
  ... (remaining 4984 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 1911
       17.37 -    34.73: 166
       34.73 -    52.10: 26
       52.10 -    69.46: 4
       69.46 -    86.83: 4
  Dihedral angle restraints: 2111
    sinusoidal: 781
      harmonic: 1330
  Sorted by residual:
  dihedral pdb=" CA  GLY A 331 "
           pdb=" C   GLY A 331 "
           pdb=" N   LEU A 332 "
           pdb=" CA  LEU A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.26   16.74     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CB  GLU A 223 "
           pdb=" CG  GLU A 223 "
           pdb=" CD  GLU A 223 "
           pdb=" OE1 GLU A 223 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.83   86.83     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU A 287 "
           pdb=" CG  GLU A 287 "
           pdb=" CD  GLU A 287 "
           pdb=" OE1 GLU A 287 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.24  -86.24     1      3.00e+01 1.11e-03 9.97e+00
  ... (remaining 2108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 425
       0.039 -    0.079: 125
       0.079 -    0.118: 37
       0.118 -    0.158: 3
       0.158 -    0.197: 2
  Chirality restraints: 592
  Sorted by residual:
  chirality pdb=" CB  ILE A 335 "
            pdb=" CA  ILE A 335 "
            pdb=" CG1 ILE A 335 "
            pdb=" CG2 ILE A 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.70e-01
  chirality pdb=" CB  ILE A 197 "
            pdb=" CA  ILE A 197 "
            pdb=" CG1 ILE A 197 "
            pdb=" CG2 ILE A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.33e-01
  chirality pdb=" CA  ILE A 348 "
            pdb=" N   ILE A 348 "
            pdb=" C   ILE A 348 "
            pdb=" CB  ILE A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 589 not shown)

  Planarity restraints: 618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 381 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 382 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 382 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 382 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 255 "    0.038 5.00e-02 4.00e+02   5.83e-02 5.44e+00
        pdb=" N   PRO A 256 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 256 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 256 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 335 "    0.012 2.00e-02 2.50e+03   2.31e-02 5.32e+00
        pdb=" C   ILE A 335 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A 335 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TRP A 336 "    0.014 2.00e-02 2.50e+03
  ... (remaining 615 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 673
        2.76 -     3.30: 3548
        3.30 -     3.83: 6129
        3.83 -     4.37: 6408
        4.37 -     4.90: 11451
  Nonbonded interactions: 28209
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  96 "
            pdb=" O   GLY A 162 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" NE2 GLN A 328 "
            pdb=" OD1 ASN A 458 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OE1 GLN A 328 "
            pdb=" ND2 ASN A 333 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" NZ  LYS A 195 "
            pdb=" OE2 GLU A 288 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   GLY A 136 "
            pdb=" OG1 THR A 140 "
     model   vdw
     2.353 3.040
  ... (remaining 28204 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.980
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5316
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   3655  Z= 0.224
  Angle     :  0.734  14.038   4989  Z= 0.355
  Chirality :  0.041   0.197    592
  Planarity :  0.005   0.063    618
  Dihedral  : 13.646  86.828   1263
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.47 %
  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:  1.81 (0.42), residues: 465
  helix:  1.61 (0.29), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.14 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  93 
 HIS   0.002   0.000   HIS A 377 
 PHE   0.012   0.001   PHE A 208 
 TYR   0.007   0.001   TYR A 327 
 ARG   0.003   0.000   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09191 (  271)
  hydrogen bonds       : angle       4.71183 (  801)
  covalent geometry    : bond        0.00431 ( 3655)
  covalent geometry    : angle       0.73422 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  400 ILE cc_start: 0.7317 (tp) cc_final: 0.6686 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 29
  average time/residue: 0.1486
  time to fit residues: 5.7107
Evaluate side-chains
  23 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 18 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0370
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.276821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.253901 restraints weight = 3972.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.258201 restraints weight = 2379.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.260767 restraints weight = 1609.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.4698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5442
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3655  Z= 0.130
  Angle     :  0.590   7.530   4989  Z= 0.292
  Chirality :  0.041   0.135    592
  Planarity :  0.005   0.045    618
  Dihedral  :  4.139  20.969    500
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.26 %
    Favored  : 95.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.41), residues: 465
  helix:  1.64 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.29 (0.69), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.002   0.000   HIS A 377 
 PHE   0.017   0.001   PHE A 276 
 TYR   0.005   0.001   TYR A 233 
 ARG   0.006   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  271)
  hydrogen bonds       : angle       3.97449 (  801)
  covalent geometry    : bond        0.00287 ( 3655)
  covalent geometry    : angle       0.59024 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.328 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 26
  average time/residue: 0.0966
  time to fit residues: 3.7960
Evaluate side-chains
  24 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 144 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 = 0.4829 r_free = 0.4829 target = 0.276731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.253843 restraints weight = 3978.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.257943 restraints weight = 2379.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.260862 restraints weight = 1624.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.4726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5461
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3655  Z= 0.121
  Angle     :  0.565   6.154   4989  Z= 0.279
  Chirality :  0.041   0.149    592
  Planarity :  0.004   0.035    618
  Dihedral  :  3.978  16.497    498
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.98 %
    Favored  : 91.22 %
  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:  1.85 (0.41), residues: 465
  helix:  1.72 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.42 (0.66), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.013   0.001   PHE A 276 
 TYR   0.006   0.001   TYR A 258 
 ARG   0.004   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  271)
  hydrogen bonds       : angle       3.80788 (  801)
  covalent geometry    : bond        0.00267 ( 3655)
  covalent geometry    : angle       0.56484 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  324 MET cc_start: 0.7218 (mmm) cc_final: 0.6998 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0963
  time to fit residues: 3.8386
Evaluate side-chains
  26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 29 optimal weight:    0.0870
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.273036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.249633 restraints weight = 4036.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.253643 restraints weight = 2441.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.256014 restraints weight = 1678.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.4630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5553
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3655  Z= 0.140
  Angle     :  0.590   5.488   4989  Z= 0.295
  Chirality :  0.042   0.146    592
  Planarity :  0.004   0.031    618
  Dihedral  :  4.061  15.732    498
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.97 %
    Favored  : 86.17 %
  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:  1.59 (0.40), residues: 465
  helix:  1.57 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.84 (0.65), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.003   0.001   HIS A 377 
 PHE   0.008   0.001   PHE A 276 
 TYR   0.007   0.001   TYR A 233 
 ARG   0.003   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  271)
  hydrogen bonds       : angle       3.85548 (  801)
  covalent geometry    : bond        0.00317 ( 3655)
  covalent geometry    : angle       0.59023 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0473 (OUTLIER) cc_final: -0.1254 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1010
  time to fit residues: 4.2512
Evaluate side-chains
  25 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 29 optimal weight:    0.0970
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 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 = 0.4795 r_free = 0.4795 target = 0.272679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.248676 restraints weight = 4030.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.252992 restraints weight = 2442.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.255688 restraints weight = 1682.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.4617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5530
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3655  Z= 0.136
  Angle     :  0.573   5.599   4989  Z= 0.287
  Chirality :  0.042   0.169    592
  Planarity :  0.004   0.031    618
  Dihedral  :  4.093  15.332    498
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.10 %
    Favored  : 84.04 %
  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:  1.48 (0.40), residues: 465
  helix:  1.53 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.00 (0.64), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.009   0.001   PHE A  69 
 TYR   0.006   0.001   TYR A 258 
 ARG   0.002   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  271)
  hydrogen bonds       : angle       3.85624 (  801)
  covalent geometry    : bond        0.00306 ( 3655)
  covalent geometry    : angle       0.57331 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.324 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 28
  average time/residue: 0.1006
  time to fit residues: 4.2384
Evaluate side-chains
  26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0670
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 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 = 0.4798 r_free = 0.4798 target = 0.273004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.248892 restraints weight = 4131.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.252877 restraints weight = 2472.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.256191 restraints weight = 1709.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5546
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3655  Z= 0.122
  Angle     :  0.559   5.952   4989  Z= 0.280
  Chirality :  0.042   0.169    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.049  14.964    498
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.63 %
    Favored  : 83.51 %
  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:  1.59 (0.40), residues: 465
  helix:  1.60 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.97 (0.64), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.010   0.001   PHE A  69 
 TYR   0.006   0.001   TYR A 258 
 ARG   0.002   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  271)
  hydrogen bonds       : angle       3.79354 (  801)
  covalent geometry    : bond        0.00273 ( 3655)
  covalent geometry    : angle       0.55917 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0356 (OUTLIER) cc_final: -0.1170 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 28
  average time/residue: 0.1062
  time to fit residues: 4.4476
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0060
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.4974

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 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 = 0.4797 r_free = 0.4797 target = 0.273657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.250269 restraints weight = 4036.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.254363 restraints weight = 2461.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.256856 restraints weight = 1696.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.4649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5537
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3655  Z= 0.117
  Angle     :  0.551   6.298   4989  Z= 0.274
  Chirality :  0.041   0.173    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.024  14.838    498
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.16 %
    Favored  : 82.98 %
  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:  1.64 (0.40), residues: 465
  helix:  1.62 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.80 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.012   0.001   PHE A 276 
 TYR   0.006   0.001   TYR A 258 
 ARG   0.002   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03421 (  271)
  hydrogen bonds       : angle       3.77142 (  801)
  covalent geometry    : bond        0.00258 ( 3655)
  covalent geometry    : angle       0.55106 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0428 (OUTLIER) cc_final: -0.1243 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 28
  average time/residue: 0.1014
  time to fit residues: 4.2452
Evaluate side-chains
  31 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  480 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0770
   chunk 22 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 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 = 0.4794 r_free = 0.4794 target = 0.273160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.249886 restraints weight = 4027.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.254201 restraints weight = 2447.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.256628 restraints weight = 1681.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.4647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5539
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3655  Z= 0.119
  Angle     :  0.552   6.863   4989  Z= 0.276
  Chirality :  0.041   0.174    592
  Planarity :  0.004   0.032    618
  Dihedral  :  3.994  14.545    498
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.43 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.67 (0.40), residues: 465
  helix:  1.64 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.79 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.000   HIS A 377 
 PHE   0.009   0.001   PHE A  69 
 TYR   0.006   0.001   TYR A 258 
 ARG   0.002   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  271)
  hydrogen bonds       : angle       3.75629 (  801)
  covalent geometry    : bond        0.00266 ( 3655)
  covalent geometry    : angle       0.55174 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0419 (OUTLIER) cc_final: -0.1242 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 30
  average time/residue: 0.1248
  time to fit residues: 5.1758
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  480 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 17 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 16 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 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 = 0.4790 r_free = 0.4790 target = 0.272703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.249611 restraints weight = 3993.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.253688 restraints weight = 2444.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.256689 restraints weight = 1691.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.4612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5516
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3655  Z= 0.121
  Angle     :  0.557   7.461   4989  Z= 0.278
  Chirality :  0.041   0.171    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.017  14.697    498
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.43 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.68 (0.40), residues: 465
  helix:  1.66 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.76 (0.63), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.000   HIS A 377 
 PHE   0.009   0.001   PHE A  69 
 TYR   0.005   0.001   TYR A 312 
 ARG   0.003   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03460 (  271)
  hydrogen bonds       : angle       3.78646 (  801)
  covalent geometry    : bond        0.00271 ( 3655)
  covalent geometry    : angle       0.55694 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0372 (OUTLIER) cc_final: -0.1200 (tp30)
REVERT: A  427 CYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7301 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 27
  average time/residue: 0.0936
  time to fit residues: 3.9156
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  480 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0770
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 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 = 0.4785 r_free = 0.4785 target = 0.272112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.248980 restraints weight = 4019.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.253108 restraints weight = 2441.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.256051 restraints weight = 1691.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.4639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5554
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3655  Z= 0.126
  Angle     :  0.566   7.912   4989  Z= 0.283
  Chirality :  0.041   0.180    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.041  14.788    498
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.69 %
    Favored  : 82.18 %
  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:  1.68 (0.40), residues: 465
  helix:  1.65 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.76 (0.63), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.009   0.001   PHE A  69 
 TYR   0.006   0.001   TYR A 327 
 ARG   0.004   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  271)
  hydrogen bonds       : angle       3.79118 (  801)
  covalent geometry    : bond        0.00285 ( 3655)
  covalent geometry    : angle       0.56598 ( 4989)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0441 (OUTLIER) cc_final: -0.1095 (tp30)
REVERT: A  427 CYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7292 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0977
  time to fit residues: 3.9861
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  480 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0470
   chunk 8 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0000
   chunk 26 optimal weight:    0.0470
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.275027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.251646 restraints weight = 4014.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.255980 restraints weight = 2432.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.258994 restraints weight = 1660.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.4647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5489
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3655  Z= 0.109
  Angle     :  0.540   8.024   4989  Z= 0.269
  Chirality :  0.041   0.207    592
  Planarity :  0.004   0.034    618
  Dihedral  :  3.933  14.275    498
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.69 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.41), residues: 465
  helix:  1.75 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.63 (0.65), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.000   HIS A 377 
 PHE   0.010   0.001   PHE A  69 
 TYR   0.006   0.001   TYR A 327 
 ARG   0.003   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03099 (  271)
  hydrogen bonds       : angle       3.69988 (  801)
  covalent geometry    : bond        0.00235 ( 3655)
  covalent geometry    : angle       0.54015 ( 4989)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1369.50 seconds
wall clock time: 24 minutes 37.77 seconds (1477.77 seconds total)