Starting phenix.real_space_refine
on Mon Feb 10 22:50:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ex8_28654/02_2025/8ex8_28654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ex8_28654/02_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_28654/02_2025/8ex8_28654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ex8_28654/02_2025/8ex8_28654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ex8_28654/02_2025/8ex8_28654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ex8_28654/02_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-5592/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: 3.72, per 1000 atoms: 1.17
  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: 0.81
  Conformation dependent library (CDL) restraints added in 418.4 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: 0.35
  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: 0.92

  Time building geometry restraints manager: 0.96 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:             3.380
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.360
-------------------------------------------------------------------------------
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  : 0.330 
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: 0.1422
  time to fit residues: 9.7617
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  : 0.401 
-------------------------------------------------------------------------------
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:    6.9990
   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 = 42)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.144042 restraints weight = 4643.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.146274 restraints weight = 3539.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.148823 restraints weight = 2924.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
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  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  514 LEU cc_start: 0.8602 (mm) cc_final: 0.8368 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1211
  time to fit residues: 10.1474
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  : 0.339 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.176512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.145090 restraints weight = 4757.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.145008 restraints weight = 4362.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145667 restraints weight = 4120.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3251  Z= 0.248
  Angle     :  0.677   9.070   4416  Z= 0.358
  Chirality :  0.045   0.170    521
  Planarity :  0.005   0.049    539
  Dihedral  :  5.037  20.563    444
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  3.88 %
    Favored  : 95.82 %
  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:  0.35 (0.44), residues: 408
  helix:  0.40 (0.28), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.03 (1.12), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 178 
 HIS   0.003   0.002   HIS A 468 
 PHE   0.024   0.002   PHE A 366 
 TYR   0.021   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  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  514 LEU cc_start: 0.8709 (mm) cc_final: 0.8466 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 66
  average time/residue: 0.1397
  time to fit residues: 11.5027
Evaluate side-chains
  51 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4203 r_free = 0.4203 target = 0.181367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.150566 restraints weight = 4762.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.149970 restraints weight = 4126.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.152081 restraints weight = 3929.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2733

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= 0.180
  Angle     :  0.617   6.452   4416  Z= 0.327
  Chirality :  0.043   0.148    521
  Planarity :  0.005   0.036    539
  Dihedral  :  4.809  21.154    444
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  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:  0.71 (0.44), residues: 408
  helix:  0.60 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.46 (1.14), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.019   0.001   PHE A 366 
 TYR   0.017   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  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  510 PHE cc_start: 0.7734 (m-10) cc_final: 0.7311 (m-10)
REVERT: A  514 LEU cc_start: 0.8767 (mm) cc_final: 0.8560 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1319
  time to fit residues: 12.2866
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  : 0.312 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.179921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.141035 restraints weight = 5060.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.144614 restraints weight = 3651.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.147755 restraints weight = 2868.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3061

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= 0.182
  Angle     :  0.614   6.436   4416  Z= 0.325
  Chirality :  0.043   0.148    521
  Planarity :  0.005   0.038    539
  Dihedral  :  4.725  21.416    444
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.57
  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:  0.86 (0.45), residues: 408
  helix:  0.70 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.47 (1.21), 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 260 
 PHE   0.020   0.001   PHE A 366 
 TYR   0.011   0.001   TYR A 116 
 ARG   0.002   0.000   ARG A 342 

*********************** 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  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.8676 (tt0) cc_final: 0.8189 (tt0)
REVERT: A  231 LEU cc_start: 0.9002 (tp) cc_final: 0.8783 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1228
  time to fit residues: 11.1891
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  : 0.337 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4210 r_free = 0.4210 target = 0.182415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.149790 restraints weight = 5116.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.150027 restraints weight = 4471.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.151739 restraints weight = 3750.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.3298

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= 0.175
  Angle     :  0.627   6.460   4416  Z= 0.325
  Chirality :  0.043   0.146    521
  Planarity :  0.005   0.038    539
  Dihedral  :  4.683  22.169    444
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.44), residues: 408
  helix:  0.77 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.26 (1.17), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 496 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.022   0.001   PHE A 498 
 TYR   0.012   0.001   TYR A 116 
 ARG   0.002   0.000   ARG A 264 

*********************** 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
  68 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.7876 (tp) cc_final: 0.7529 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1103
  time to fit residues: 9.7372
Evaluate side-chains
  53 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4205 r_free = 0.4205 target = 0.181413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.150446 restraints weight = 5118.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.148844 restraints weight = 4449.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.149268 restraints weight = 4190.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3508

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= 0.182
  Angle     :  0.613   6.503   4416  Z= 0.322
  Chirality :  0.043   0.147    521
  Planarity :  0.005   0.038    539
  Dihedral  :  4.645  21.136    444
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.42
  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:  1.01 (0.44), residues: 408
  helix:  0.81 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.48 (1.18), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 440 
 HIS   0.002   0.001   HIS A 468 
 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
  61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.7892 (tp) cc_final: 0.7653 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1073
  time to fit residues: 8.8000
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  : 0.354 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 9 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.4202 r_free = 0.4202 target = 0.181214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.145523 restraints weight = 5029.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.147734 restraints weight = 3971.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.150216 restraints weight = 3344.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.3637

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= 0.175
  Angle     :  0.613   6.320   4416  Z= 0.321
  Chirality :  0.042   0.146    521
  Planarity :  0.005   0.041    539
  Dihedral  :  4.636  23.246    444
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 12.26
  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:  1.04 (0.44), residues: 408
  helix:  0.83 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.43 (1.15), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 496 
 HIS   0.001   0.001   HIS A 341 
 PHE   0.019   0.001   PHE A 498 
 TYR   0.013   0.001   TYR A 116 
 ARG   0.004   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
  62 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  334 MET cc_start: 0.7935 (ttm) cc_final: 0.7278 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1050
  time to fit residues: 8.7619
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  : 0.377 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0170
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6018

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.183480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144008 restraints weight = 5165.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.147625 restraints weight = 3839.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.150173 restraints weight = 3073.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.3848

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= 0.170
  Angle     :  0.624   6.360   4416  Z= 0.325
  Chirality :  0.043   0.146    521
  Planarity :  0.005   0.042    539
  Dihedral  :  4.681  23.597    444
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 12.26
  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:  1.03 (0.44), residues: 408
  helix:  0.82 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.48 (1.14), residues: 51

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   0.029   0.001   PHE A 519 
 TYR   0.019   0.002   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
  70 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 ARG cc_start: 0.6484 (mtm180) cc_final: 0.6274 (mtm180)
REVERT: A  365 ILE cc_start: 0.9091 (mt) cc_final: 0.8833 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1081
  time to fit residues: 10.0204
Evaluate side-chains
  57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0870
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.184092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.145248 restraints weight = 5223.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.149060 restraints weight = 3874.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.151854 restraints weight = 3090.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.4000

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= 0.170
  Angle     :  0.623   6.286   4416  Z= 0.325
  Chirality :  0.043   0.146    521
  Planarity :  0.005   0.037    539
  Dihedral  :  4.638  24.169    444
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  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:  1.12 (0.44), residues: 408
  helix:  0.89 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.44 (1.15), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 496 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.033   0.001   PHE A 519 
 TYR   0.015   0.002   TYR A 235 
 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
  65 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  506 MET cc_start: 0.7088 (mmm) cc_final: 0.6885 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1121
  time to fit residues: 9.5967
Evaluate side-chains
  53 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 18 optimal weight:    0.0570
   chunk 19 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0970
   chunk 32 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.2794

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.190745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.159262 restraints weight = 4703.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.158784 restraints weight = 4245.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.159923 restraints weight = 3477.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.4315

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= 0.159
  Angle     :  0.610   6.673   4416  Z= 0.314
  Chirality :  0.042   0.155    521
  Planarity :  0.005   0.034    539
  Dihedral  :  4.558  22.335    444
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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:  1.32 (0.44), residues: 408
  helix:  1.01 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.61 (1.14), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 468 
 PHE   0.012   0.001   PHE A 327 
 TYR   0.018   0.002   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: 1288.97 seconds
wall clock time: 23 minutes 56.01 seconds (1436.01 seconds total)