Starting phenix.real_space_refine
on Fri Aug 22 13:19:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ex8_28654/08_2025/8ex8_28654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ex8_28654/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ex8_28654/08_2025/8ex8_28654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ex8_28654/08_2025/8ex8_28654.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ex8_28654/08_2025/8ex8_28654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ex8_28654/08_2025/8ex8_28654.map"
  }
  resolution = 4.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.08, per 1000 atoms: 0.34
  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: 0.34
  Conformation dependent library (CDL) restraints added in 142.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.11
  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: 0.53

  Time building geometry restraints manager: 0.38 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:             3.760
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.380
  Find NCS groups from input model:        0.010
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.490
-------------------------------------------------------------------------------
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= 0.344
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (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
 ARG   0.006   0.001   ARG A 530 
 TYR   0.036   0.004   TYR A 116 
 PHE   0.031   0.003   PHE A 481 
 TRP   0.014   0.002   TRP A 440 
 HIS   0.006   0.002   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00709 ( 3251)
  covalent geometry    : angle       0.96265 ( 4416)
  hydrogen bonds       : bond        0.12935 (  262)
  hydrogen bonds       : angle       6.01293 (  780)

*********************** 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  : 0.121 
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: 0.0564
  time to fit residues: 4.0070
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0370
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0980
   chunk 37 optimal weight:    9.9990
   overall best weight:    0.5862

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.179599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.148494 restraints weight = 4736.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.147738 restraints weight = 4320.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.149621 restraints weight = 4028.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.150028 restraints weight = 3323.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.150785 restraints weight = 2926.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.1846

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= 0.145
  Angle     :  0.623   6.504   4416  Z= 0.338
  Chirality :  0.042   0.154    521
  Planarity :  0.005   0.039    539
  Dihedral  :  5.022  20.615    444
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.43), residues: 408
  helix:  0.32 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop : -0.06 (1.11), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 394 
 TYR   0.027   0.002   TYR A 116 
 PHE   0.018   0.002   PHE A 366 
 TRP   0.010   0.001   TRP A 335 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3251)
  covalent geometry    : angle       0.62341 ( 4416)
  hydrogen bonds       : bond        0.04736 (  262)
  hydrogen bonds       : angle       4.82674 (  780)

*********************** 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
  68 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  514 LEU cc_start: 0.8629 (mm) cc_final: 0.8417 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0494
  time to fit residues: 4.3698
Evaluate side-chains
  49 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.181144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.150720 restraints weight = 4773.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.149468 restraints weight = 4336.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.150711 restraints weight = 4023.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151479 restraints weight = 3420.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.151893 restraints weight = 2992.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3251  Z= 0.147
  Angle     :  0.612   6.393   4416  Z= 0.330
  Chirality :  0.043   0.152    521
  Planarity :  0.005   0.036    539
  Dihedral  :  4.872  21.344    444
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.43), residues: 408
  helix:  0.62 (0.28), residues: 352
  sheet:  None (None), residues: 0
  loop :  0.41 (1.08), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 342 
 TYR   0.016   0.002   TYR A 235 
 PHE   0.021   0.001   PHE A 366 
 TRP   0.012   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3251)
  covalent geometry    : angle       0.61226 ( 4416)
  hydrogen bonds       : bond        0.04566 (  262)
  hydrogen bonds       : angle       4.61477 (  780)

*********************** 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
  73 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  364 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7393 (tp)
REVERT: A  387 TRP cc_start: 0.6054 (t-100) cc_final: 0.5465 (t60)
REVERT: A  514 LEU cc_start: 0.8728 (mm) cc_final: 0.8506 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0611
  time to fit residues: 5.5675
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.178082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.146153 restraints weight = 4978.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.147159 restraints weight = 4492.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.148781 restraints weight = 3864.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.149362 restraints weight = 3052.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.150303 restraints weight = 2788.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3251  Z= 0.169
  Angle     :  0.646   6.609   4416  Z= 0.346
  Chirality :  0.044   0.153    521
  Planarity :  0.005   0.040    539
  Dihedral  :  4.892  20.687    444
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.43), residues: 408
  helix:  0.58 (0.28), residues: 352
  sheet:  None (None), residues: 0
  loop :  0.27 (1.05), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 227 
 TYR   0.015   0.002   TYR A 116 
 PHE   0.024   0.001   PHE A 366 
 TRP   0.015   0.002   TRP A 178 
 HIS   0.003   0.002   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3251)
  covalent geometry    : angle       0.64643 ( 4416)
  hydrogen bonds       : bond        0.04661 (  262)
  hydrogen bonds       : angle       4.72277 (  780)

*********************** 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
  67 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  510 PHE cc_start: 0.7786 (m-10) cc_final: 0.7359 (m-10)
REVERT: A  514 LEU cc_start: 0.8757 (mm) cc_final: 0.8542 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0517
  time to fit residues: 4.4719
Evaluate side-chains
  51 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 2 optimal weight:    0.2980
   chunk 17 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.181827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.150542 restraints weight = 4851.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.150474 restraints weight = 4226.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.151990 restraints weight = 3731.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.152424 restraints weight = 3219.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.153264 restraints weight = 2856.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3251  Z= 0.136
  Angle     :  0.608   6.551   4416  Z= 0.321
  Chirality :  0.042   0.148    521
  Planarity :  0.005   0.037    539
  Dihedral  :  4.748  21.532    444
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.44), residues: 408
  helix:  0.64 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop :  0.57 (1.22), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 119 
 TYR   0.014   0.001   TYR A 116 
 PHE   0.019   0.001   PHE A 366 
 TRP   0.009   0.001   TRP A 440 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3251)
  covalent geometry    : angle       0.60769 ( 4416)
  hydrogen bonds       : bond        0.04249 (  262)
  hydrogen bonds       : angle       4.57234 (  780)

*********************** 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
  70 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  207 GLU cc_start: 0.8578 (tt0) cc_final: 0.8270 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0480
  time to fit residues: 4.3464
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  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0470
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 2 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.3278

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.183679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.151415 restraints weight = 5002.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.152623 restraints weight = 4670.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.154468 restraints weight = 3831.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.155036 restraints weight = 3123.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.155706 restraints weight = 2802.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3251  Z= 0.127
  Angle     :  0.600   6.244   4416  Z= 0.312
  Chirality :  0.042   0.148    521
  Planarity :  0.005   0.039    539
  Dihedral  :  4.618  21.682    444
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.44), residues: 408
  helix:  0.87 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.47 (1.18), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 119 
 TYR   0.012   0.001   TYR A 116 
 PHE   0.023   0.002   PHE A 498 
 TRP   0.010   0.001   TRP A 335 
 HIS   0.001   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3251)
  covalent geometry    : angle       0.59990 ( 4416)
  hydrogen bonds       : bond        0.04024 (  262)
  hydrogen bonds       : angle       4.41490 (  780)

*********************** 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
  73 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A  334 MET cc_start: 0.7863 (ttm) cc_final: 0.7306 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0450
  time to fit residues: 4.3233
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  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.4149 r_free = 0.4149 target = 0.175725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.136527 restraints weight = 5316.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.139669 restraints weight = 4004.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.141549 restraints weight = 3248.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.143805 restraints weight = 2820.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.144237 restraints weight = 2498.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3251  Z= 0.201
  Angle     :  0.700   6.600   4416  Z= 0.372
  Chirality :  0.046   0.145    521
  Planarity :  0.005   0.043    539
  Dihedral  :  4.868  20.273    444
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.44), residues: 408
  helix:  0.61 (0.28), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.03 (1.12), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.013   0.002   TYR A 120 
 PHE   0.022   0.002   PHE A 366 
 TRP   0.010   0.002   TRP A 496 
 HIS   0.005   0.002   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 3251)
  covalent geometry    : angle       0.69967 ( 4416)
  hydrogen bonds       : bond        0.04783 (  262)
  hydrogen bonds       : angle       4.67011 (  780)

*********************** 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
  63 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.117 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0442
  time to fit residues: 3.6980
Evaluate side-chains
  52 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.177847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.142279 restraints weight = 5027.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144629 restraints weight = 3883.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.147257 restraints weight = 3232.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.148698 restraints weight = 2740.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.149269 restraints weight = 2441.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3251  Z= 0.159
  Angle     :  0.667   9.767   4416  Z= 0.345
  Chirality :  0.044   0.147    521
  Planarity :  0.005   0.043    539
  Dihedral  :  4.794  21.280    444
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.44), residues: 408
  helix:  0.72 (0.28), residues: 352
  sheet:  None (None), residues: 0
  loop :  0.30 (1.09), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 227 
 TYR   0.021   0.002   TYR A 116 
 PHE   0.017   0.001   PHE A 366 
 TRP   0.009   0.001   TRP A 440 
 HIS   0.002   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3251)
  covalent geometry    : angle       0.66730 ( 4416)
  hydrogen bonds       : bond        0.04462 (  262)
  hydrogen bonds       : angle       4.56458 (  780)

*********************** 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
  64 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  404 MET cc_start: 0.7500 (mmp) cc_final: 0.7255 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0373
  time to fit residues: 3.1873
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  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.180262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.148119 restraints weight = 5138.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.147927 restraints weight = 4550.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.148718 restraints weight = 3715.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.149023 restraints weight = 3424.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.149844 restraints weight = 3222.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3251  Z= 0.144
  Angle     :  0.655  11.342   4416  Z= 0.334
  Chirality :  0.043   0.146    521
  Planarity :  0.005   0.048    539
  Dihedral  :  4.694  21.339    444
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.73
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.44), residues: 408
  helix:  0.81 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.47 (1.16), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.029   0.002   TYR A 116 
 PHE   0.015   0.001   PHE A 366 
 TRP   0.008   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3251)
  covalent geometry    : angle       0.65542 ( 4416)
  hydrogen bonds       : bond        0.04223 (  262)
  hydrogen bonds       : angle       4.43615 (  780)

*********************** 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
  65 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  116 TYR cc_start: 0.8376 (m-80) cc_final: 0.7843 (m-10)
REVERT: A  264 ARG cc_start: 0.6487 (mtm180) cc_final: 0.6151 (mtm-85)
REVERT: A  334 MET cc_start: 0.7911 (ttm) cc_final: 0.7219 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0399
  time to fit residues: 3.4261
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  : 0.119 
-------------------------------------------------------------------------------
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 16 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.181112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.146978 restraints weight = 5172.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.148931 restraints weight = 5452.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.149433 restraints weight = 4148.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.150128 restraints weight = 3786.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.151365 restraints weight = 3383.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.3700

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= 0.145
  Angle     :  0.660  11.263   4416  Z= 0.337
  Chirality :  0.044   0.152    521
  Planarity :  0.005   0.046    539
  Dihedral  :  4.715  21.693    444
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.73
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.44), residues: 408
  helix:  0.77 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.30 (1.15), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.023   0.002   TYR A 116 
 PHE   0.016   0.001   PHE A 415 
 TRP   0.010   0.001   TRP A 496 
 HIS   0.002   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3251)
  covalent geometry    : angle       0.65992 ( 4416)
  hydrogen bonds       : bond        0.04252 (  262)
  hydrogen bonds       : angle       4.44322 (  780)

********************** 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
  61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  116 TYR cc_start: 0.8337 (m-80) cc_final: 0.7947 (m-10)
REVERT: A  334 MET cc_start: 0.7894 (ttm) cc_final: 0.7227 (tmm)
REVERT: A  404 MET cc_start: 0.7411 (mmp) cc_final: 0.7163 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0413
  time to fit residues: 3.4131
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  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 40 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.182995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148460 restraints weight = 5555.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.151123 restraints weight = 5375.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.153500 restraints weight = 3827.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.153756 restraints weight = 2975.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.154205 restraints weight = 2743.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.3912

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= 0.138
  Angle     :  0.645  11.266   4416  Z= 0.331
  Chirality :  0.043   0.149    521
  Planarity :  0.005   0.046    539
  Dihedral  :  4.692  21.116    444
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.44), residues: 408
  helix:  0.85 (0.28), residues: 354
  sheet:  None (None), residues: 0
  loop :  0.27 (1.10), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.023   0.002   TYR A 116 
 PHE   0.012   0.001   PHE A 366 
 TRP   0.011   0.001   TRP A 178 
 HIS   0.001   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3251)
  covalent geometry    : angle       0.64535 ( 4416)
  hydrogen bonds       : bond        0.04100 (  262)
  hydrogen bonds       : angle       4.37283 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 660.71 seconds
wall clock time: 12 minutes 2.16 seconds (722.16 seconds total)