Starting phenix.real_space_refine
on Wed Mar  5 17:55:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ex8_28654/03_2025/8ex8_28654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ex8_28654/03_2025/8ex8_28654.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ex8_28654/03_2025/8ex8_28654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ex8_28654/03_2025/8ex8_28654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ex8_28654/03_2025/8ex8_28654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ex8_28654/03_2025/8ex8_28654.cif"
  }
  resolution = 4.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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      17      5.16       5
     C    2090      2.51       5
     N     524      2.21       5
     O     546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3177
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3177
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 12, 'TRANS': 401}
          Chain breaks: 2
  Time building chain proxies: 4.57, per 1000 atoms: 1.44
  Number of scatterers: 3177
  At special positions: 0
  Unit cell: (72.688, 62.304, 75.284, 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      17     16.00
     O     546      8.00
     N     524      7.00
     C    2090      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: 0.79
  Conformation dependent library (CDL) restraints added in 356.6 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      91.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 121
      removed outlier: 3.876A  pdb=" N   ALA A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 124
      No H-bonds generated for 'chain 'A' and resid 122 through 124'
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 136 through 160
      removed outlier: 3.909A  pdb=" N   ALA A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   PHE A 147 " --> pdb=" O   LEU A 143 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   ILE A 148 " --> pdb=" O   GLN A 144 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 166 through 186
      removed outlier: 3.900A  pdb=" N   ILE A 170 " --> pdb=" O   ASN A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 221
      removed outlier: 3.930A  pdb=" N   VAL A 203 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   GLY A 204 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ILE A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   SER A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   TYR A 210 " --> pdb=" O   GLY A 206 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A 214 " --> pdb=" O   TYR A 210 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
    Processing helix  chain 'A' and resid 223 through 256
      removed outlier: 4.777A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
      removed outlier: 3.540A  pdb=" N   TYR A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 263
      removed outlier: 3.534A  pdb=" N   TRP A 261 " --> pdb=" O   ASP A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 280
      removed outlier: 4.282A  pdb=" N   VAL A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LEU A 269 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 311
      removed outlier: 3.522A  pdb=" N   ARG A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 347
      Proline residue:  A 337  - end of helix
    Processing helix  chain 'A' and resid 361 through 390
      removed outlier: 4.510A  pdb=" N   LEU A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 422
      removed outlier: 4.557A  pdb=" N   PHE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   VAL A 416 " --> pdb=" O   CYS A 412 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   LYS A 419 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   SER A 420 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ILE A 422 " --> pdb=" O   ALA A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 437
      removed outlier: 3.632A  pdb=" N   VAL A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   THR A 434 " --> pdb=" O   PHE A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 451
    Processing helix  chain 'A' and resid 452 through 454
      No H-bonds generated for 'chain 'A' and resid 452 through 454'
    Processing helix  chain 'A' and resid 455 through 470
    Processing helix  chain 'A' and resid 474 through 490
      removed outlier: 3.755A  pdb=" N   THR A 490 " --> pdb=" O   ILE A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 506
    Processing helix  chain 'A' and resid 506 through 539
      removed outlier: 3.810A  pdb=" N   PHE A 510 " --> pdb=" O   MET A 506 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   VAL A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   SER A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    780 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: 0.85

  Time building geometry restraints manager: 0.95 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: 970
        1.34 -     1.46: 709
        1.46 -     1.58: 1546
        1.58 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 3251
  Sorted by residual:
  bond pdb=" N   VAL A 181 "
       pdb=" CA  VAL A 181 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 1.14e-02 7.69e+03 7.09e+00
  bond pdb=" N   ILE A 175 "
       pdb=" CA  ILE A 175 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.17e-02 7.31e+03 6.60e+00
  bond pdb=" N   PHE A 177 "
       pdb=" CA  PHE A 177 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 5.92e+00
  bond pdb=" N   SER A 179 "
       pdb=" CA  SER A 179 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.33e+00
  bond pdb=" N   TRP A 178 "
       pdb=" CA  TRP A 178 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.26e+00
  ... (remaining 3246 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 4229
        2.12 -     4.23: 154
        4.23 -     6.35: 28
        6.35 -     8.47: 3
        8.47 -    10.58: 2
  Bond angle restraints: 4416
  Sorted by residual:
  angle pdb=" N   PHE A 236 "
        pdb=" CA  PHE A 236 "
        pdb=" C   PHE A 236 "
      ideal   model   delta    sigma   weight residual
     112.38  107.11    5.27 1.22e+00 6.72e-01 1.87e+01
  angle pdb=" CA  VAL A 181 "
        pdb=" C   VAL A 181 "
        pdb=" O   VAL A 181 "
      ideal   model   delta    sigma   weight residual
     121.27  117.28    3.99 1.04e+00 9.25e-01 1.47e+01
  angle pdb=" N   ILE A 175 "
        pdb=" CA  ILE A 175 "
        pdb=" C   ILE A 175 "
      ideal   model   delta    sigma   weight residual
     110.42  107.37    3.05 9.60e-01 1.09e+00 1.01e+01
  angle pdb=" CA  TYR A 116 "
        pdb=" CB  TYR A 116 "
        pdb=" CG  TYR A 116 "
      ideal   model   delta    sigma   weight residual
     113.90  108.27    5.63 1.80e+00 3.09e-01 9.80e+00
  angle pdb=" CA  CYS A 173 "
        pdb=" C   CYS A 173 "
        pdb=" O   CYS A 173 "
      ideal   model   delta    sigma   weight residual
     120.82  117.54    3.28 1.05e+00 9.07e-01 9.76e+00
  ... (remaining 4411 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.20: 1642
       15.20 -    30.41: 166
       30.41 -    45.61: 55
       45.61 -    60.81: 7
       60.81 -    76.01: 2
  Dihedral angle restraints: 1872
    sinusoidal: 692
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CA  MET A 334 "
           pdb=" C   MET A 334 "
           pdb=" N   TRP A 335 "
           pdb=" CA  TRP A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.35  -20.65     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  LEU A 364 "
           pdb=" C   LEU A 364 "
           pdb=" N   ILE A 365 "
           pdb=" CA  ILE A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.43   19.57     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  THR A 223 "
           pdb=" C   THR A 223 "
           pdb=" N   LYS A 224 "
           pdb=" CA  LYS A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.57  -18.43     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 1869 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 360
       0.049 -    0.098: 124
       0.098 -    0.147: 35
       0.147 -    0.197: 0
       0.197 -    0.246: 2
  Chirality restraints: 521
  Sorted by residual:
  chirality pdb=" CA  TRP A 178 "
            pdb=" N   TRP A 178 "
            pdb=" C   TRP A 178 "
            pdb=" CB  TRP A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ILE A 175 "
            pdb=" N   ILE A 175 "
            pdb=" C   ILE A 175 "
            pdb=" CB  ILE A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CB  VAL A 513 "
            pdb=" CA  VAL A 513 "
            pdb=" CG1 VAL A 513 "
            pdb=" CG2 VAL A 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.94e-01
  ... (remaining 518 not shown)

  Planarity restraints: 539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 238 "   -0.036 5.00e-02 4.00e+02   5.47e-02 4.79e+00
        pdb=" N   PRO A 239 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 239 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 239 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 116 "   -0.016 2.00e-02 2.50e+03   1.50e-02 4.50e+00
        pdb=" CG  TYR A 116 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 116 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 116 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 116 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 116 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 116 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 116 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 481 "   -0.014 2.00e-02 2.50e+03   1.34e-02 3.14e+00
        pdb=" CG  PHE A 481 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 481 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 481 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 481 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 481 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 481 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 536 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 92
        2.69 -     3.24: 3787
        3.24 -     3.79: 5401
        3.79 -     4.35: 6672
        4.35 -     4.90: 10236
  Nonbonded interactions: 26188
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 145 "
            pdb=" OH  TYR A 477 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" O   ILE A 486 "
            pdb=" OG  SER A 489 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   LEU A 320 "
            pdb=" OG  SER A 323 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   PRO A 239 "
            pdb=" OG  SER A 242 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   ASP A 118 "
            pdb=" NH2 ARG A 200 "
     model   vdw
     2.231 3.120
  ... (remaining 26183 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:             9.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     14.480
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
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      :  0.007   0.052   3251  Z= 0.459
  Angle     :  0.963  10.583   4416  Z= 0.561
  Chirality :  0.052   0.246    521
  Planarity :  0.006   0.055    539
  Dihedral  : 13.999  76.014   1116
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.41), residues: 408
  helix: -0.32 (0.27), residues: 335
  sheet:  None (None), residues: 0
  loop : -0.39 (0.91), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 440 
 HIS   0.006   0.002   HIS A 341 
 PHE   0.031   0.003   PHE A 481 
 TYR   0.036   0.004   TYR A 116 
 ARG   0.006   0.001   ARG A 530 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  514 LEU cc_start: 0.8583 (mm) cc_final: 0.8376 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1505
  time to fit residues: 10.2081
Evaluate side-chains
  41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    8.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.179367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.144037 restraints weight = 4643.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.146348 restraints weight = 3534.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.148548 restraints weight = 2917.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3251  Z= 0.195
  Angle     :  0.630   6.656   4416  Z= 0.341
  Chirality :  0.043   0.152    521
  Planarity :  0.005   0.041    539
  Dihedral  :  5.079  20.448    444
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.43), residues: 408
  helix:  0.25 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -0.07 (1.11), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 178 
 HIS   0.003   0.002   HIS A 260 
 PHE   0.018   0.002   PHE A 366 
 TYR   0.027   0.002   TYR A 116 
 ARG   0.001   0.000   ARG A 200 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  514 LEU cc_start: 0.8606 (mm) cc_final: 0.8372 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1224
  time to fit residues: 10.2859
Evaluate side-chains
  50 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.174820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.142525 restraints weight = 4800.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.143805 restraints weight = 4355.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.145431 restraints weight = 3560.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3251  Z= 0.281
  Angle     :  0.703   9.082   4416  Z= 0.372
  Chirality :  0.045   0.175    521
  Planarity :  0.005   0.046    539
  Dihedral  :  5.114  20.358    444
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.07 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.43), residues: 408
  helix:  0.29 (0.28), residues: 352
  sheet:  None (None), residues: 0
  loop : -0.15 (1.09), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 178 
 HIS   0.004   0.002   HIS A 468 
 PHE   0.024   0.002   PHE A 366 
 TYR   0.023   0.002   TYR A 235 
 ARG   0.004   0.000   ARG A 342 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  514 LEU cc_start: 0.8681 (mm) cc_final: 0.8433 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 66
  average time/residue: 0.1380
  time to fit residues: 11.3685
Evaluate side-chains
  50 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    0.1980
   chunk 37 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.180903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.150206 restraints weight = 4796.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.149003 restraints weight = 4249.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.150846 restraints weight = 3806.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3251  Z= 0.178
  Angle     :  0.625   6.499   4416  Z= 0.331
  Chirality :  0.044   0.150    521
  Planarity :  0.005   0.037    539
  Dihedral  :  4.861  21.578    444
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.44), residues: 408
  helix:  0.51 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.41 (1.13), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.020   0.001   PHE A 366 
 TYR   0.018   0.001   TYR A 116 
 ARG   0.002   0.000   ARG A 119 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  510 PHE cc_start: 0.7808 (m-10) cc_final: 0.7381 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1286
  time to fit residues: 12.0729
Evaluate side-chains
  54 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 37 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 393 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.179830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148830 restraints weight = 4978.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.147632 restraints weight = 4287.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.150606 restraints weight = 3860.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3251  Z= 0.182
  Angle     :  0.615   6.367   4416  Z= 0.325
  Chirality :  0.043   0.148    521
  Planarity :  0.005   0.037    539
  Dihedral  :  4.771  21.497    444
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.44), residues: 408
  helix:  0.62 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.40 (1.21), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 335 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.019   0.001   PHE A 366 
 TYR   0.012   0.001   TYR A 116 
 ARG   0.002   0.000   ARG A 227 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1194
  time to fit residues: 10.9585
Evaluate side-chains
  59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4192 r_free = 0.4192 target = 0.180170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140664 restraints weight = 5094.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.144370 restraints weight = 3674.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.146742 restraints weight = 2888.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3251  Z= 0.174
  Angle     :  0.621   6.373   4416  Z= 0.325
  Chirality :  0.043   0.147    521
  Planarity :  0.005   0.038    539
  Dihedral  :  4.706  21.866    444
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.44), residues: 408
  helix:  0.66 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.33 (1.16), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.023   0.001   PHE A 498 
 TYR   0.013   0.001   TYR A 116 
 ARG   0.002   0.000   ARG A 227 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.8513 (tt0) cc_final: 0.8285 (tt0)
REVERT: A  221 LEU cc_start: 0.7903 (tp) cc_final: 0.7680 (tp)
REVERT: A  231 LEU cc_start: 0.9004 (tp) cc_final: 0.8784 (tt)
REVERT: A  404 MET cc_start: 0.7496 (mmp) cc_final: 0.7195 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1172
  time to fit residues: 10.8098
Evaluate side-chains
  59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   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 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.179928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.149045 restraints weight = 5101.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.147451 restraints weight = 4720.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.148608 restraints weight = 4154.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3251  Z= 0.189
  Angle     :  0.626   6.350   4416  Z= 0.329
  Chirality :  0.044   0.146    521
  Planarity :  0.005   0.037    539
  Dihedral  :  4.682  21.336    444
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.44), residues: 408
  helix:  0.68 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.22 (1.17), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 440 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.020   0.001   PHE A 498 
 TYR   0.011   0.001   TYR A 116 
 ARG   0.003   0.000   ARG A 227 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.7826 (tp) cc_final: 0.7584 (tp)
REVERT: A  231 LEU cc_start: 0.8984 (tp) cc_final: 0.8768 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1014
  time to fit residues: 8.6549
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.181935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.146343 restraints weight = 4896.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.148953 restraints weight = 3854.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.150642 restraints weight = 3216.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3251  Z= 0.182
  Angle     :  0.620   6.461   4416  Z= 0.324
  Chirality :  0.043   0.146    521
  Planarity :  0.005   0.040    539
  Dihedral  :  4.648  22.590    444
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.44), residues: 408
  helix:  0.76 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.44 (1.17), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 496 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.019   0.001   PHE A 498 
 TYR   0.019   0.002   TYR A 116 
 ARG   0.003   0.000   ARG A 227 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  116 TYR cc_start: 0.8424 (m-80) cc_final: 0.7960 (m-80)
REVERT: A  334 MET cc_start: 0.7994 (ttm) cc_final: 0.7323 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0995
  time to fit residues: 8.9150
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.183464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.151141 restraints weight = 5129.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.151007 restraints weight = 4977.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.152230 restraints weight = 4258.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3251  Z= 0.176
  Angle     :  0.620   6.131   4416  Z= 0.324
  Chirality :  0.044   0.146    521
  Planarity :  0.005   0.036    539
  Dihedral  :  4.676  24.546    444
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.44), residues: 408
  helix:  0.75 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.53 (1.17), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.028   0.001   PHE A 519 
 TYR   0.017   0.001   TYR A 116 
 ARG   0.004   0.000   ARG A 227 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  116 TYR cc_start: 0.8388 (m-80) cc_final: 0.8056 (m-10)
REVERT: A  264 ARG cc_start: 0.6478 (mtm180) cc_final: 0.6243 (mtm180)
REVERT: A  334 MET cc_start: 0.7901 (ttm) cc_final: 0.7336 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1009
  time to fit residues: 8.8551
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.181495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.149099 restraints weight = 4871.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.149043 restraints weight = 4045.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.149126 restraints weight = 3611.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3251  Z= 0.203
  Angle     :  0.632   6.326   4416  Z= 0.333
  Chirality :  0.044   0.145    521
  Planarity :  0.005   0.040    539
  Dihedral  :  4.699  23.049    444
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.44), residues: 408
  helix:  0.72 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop :  0.21 (1.21), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 496 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.031   0.001   PHE A 519 
 TYR   0.021   0.002   TYR A 116 
 ARG   0.004   0.000   ARG A 227 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  116 TYR cc_start: 0.8476 (m-80) cc_final: 0.8000 (m-10)
REVERT: A  334 MET cc_start: 0.7949 (ttm) cc_final: 0.7372 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1072
  time to fit residues: 9.4717
Evaluate side-chains
  58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0020
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.4268 r_free = 0.4268 target = 0.187313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.155384 restraints weight = 4795.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.155106 restraints weight = 4248.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.155968 restraints weight = 3414.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3251  Z= 0.171
  Angle     :  0.617   5.977   4416  Z= 0.321
  Chirality :  0.043   0.149    521
  Planarity :  0.005   0.039    539
  Dihedral  :  4.628  22.334    444
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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:  1.22 (0.44), residues: 408
  helix:  0.97 (0.29), residues: 351
  sheet:  None (None), residues: 0
  loop :  0.35 (1.05), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.022   0.001   PHE A 498 
 TYR   0.015   0.001   TYR A 116 
 ARG   0.003   0.000   ARG A 227 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1314.48 seconds
wall clock time: 23 minutes 55.32 seconds (1435.32 seconds total)