Starting phenix.real_space_refine
on Fri May  9 16:25:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jrl_61759/05_2025/9jrl_61759_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jrl_61759/05_2025/9jrl_61759.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jrl_61759/05_2025/9jrl_61759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jrl_61759/05_2025/9jrl_61759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jrl_61759/05_2025/9jrl_61759_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jrl_61759/05_2025/9jrl_61759_neut.cif"
  }
  resolution = 3.25
  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=   0.086
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      10      5.16       5
     C    2103      2.51       5
     N     517      2.21       5
     O     515      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3145
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 3103
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 12, 'TRANS': 373}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'COP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.67, per 1000 atoms: 0.85
  Number of scatterers: 3145
  At special positions: 0
  Unit cell: (68, 65, 74, 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      10     16.00
     O     515      8.00
     N     517      7.00
     C    2103      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: 1.15
  Conformation dependent library (CDL) restraints added in 374.7 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  730

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      90.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 40
      removed outlier: 4.687A  pdb=" N   VAL A  29 " --> pdb=" O   TRP A  25 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN A  40 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 46
      removed outlier: 6.884A  pdb=" N   GLY A  44 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   SER A  46 " --> pdb=" O   PRO A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 60 through 68
      removed outlier: 3.642A  pdb=" N   ILE A  68 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 87
      removed outlier: 4.518A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
    Processing helix  chain 'A' and resid 91 through 112
      removed outlier: 4.164A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 131
      removed outlier: 3.521A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 143
      removed outlier: 3.646A  pdb=" N   TYR A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 147
      No H-bonds generated for 'chain 'A' and resid 145 through 147'
    Processing helix  chain 'A' and resid 148 through 177
      removed outlier: 3.590A  pdb=" N   ARG A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 202
      removed outlier: 3.802A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 263
    Processing helix  chain 'A' and resid 264 through 295
      removed outlier: 3.914A  pdb=" N   ALA A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   GLY A 280 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 327
      removed outlier: 3.621A  pdb=" N   PHE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 390
      removed outlier: 3.578A  pdb=" N   CYS A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
      removed outlier: 3.515A  pdb=" N   SER A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 394
      removed outlier: 7.400A  pdb=" N   GLU A 394 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 391 through 394'
    Processing helix  chain 'A' and resid 395 through 418
    Processing helix  chain 'A' and resid 427 through 456

    246 hydrogen bonds defined for protein.
    735 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: 0.90

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 584
        1.33 -     1.45: 878
        1.45 -     1.57: 1756
        1.57 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3234
  Sorted by residual:
  bond pdb=" C39 COP A 701 "
       pdb=" O41 COP A 701 "
    ideal  model  delta    sigma   weight residual
    1.246  1.332 -0.086 2.00e-02 2.50e+03 1.86e+01
  bond pdb=" N   THR A  49 "
       pdb=" CA  THR A  49 "
    ideal  model  delta    sigma   weight residual
    1.462  1.487 -0.025 7.70e-03 1.69e+04 1.08e+01
  bond pdb=" N   VAL A 418 "
       pdb=" CA  VAL A 418 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.96e+00
  bond pdb=" N   VAL A 144 "
       pdb=" CA  VAL A 144 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.14e-02 7.69e+03 9.19e+00
  bond pdb=" C1  COP A 701 "
       pdb=" C10 COP A 701 "
    ideal  model  delta    sigma   weight residual
    1.443  1.384  0.059 2.00e-02 2.50e+03 8.60e+00
  ... (remaining 3229 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 4215
        1.57 -     3.14: 160
        3.14 -     4.71: 21
        4.71 -     6.27: 5
        6.27 -     7.84: 5
  Bond angle restraints: 4406
  Sorted by residual:
  angle pdb=" CA  HIS A 289 "
        pdb=" CB  HIS A 289 "
        pdb=" CG  HIS A 289 "
      ideal   model   delta    sigma   weight residual
     113.80  107.01    6.79 1.00e+00 1.00e+00 4.61e+01
  angle pdb=" CB  HIS A 289 "
        pdb=" CG  HIS A 289 "
        pdb=" CD2 HIS A 289 "
      ideal   model   delta    sigma   weight residual
     131.20  125.70    5.50 1.30e+00 5.92e-01 1.79e+01
  angle pdb=" CB  HIS A 289 "
        pdb=" CG  HIS A 289 "
        pdb=" ND1 HIS A 289 "
      ideal   model   delta    sigma   weight residual
     122.70  127.38   -4.68 1.50e+00 4.44e-01 9.75e+00
  angle pdb=" CA  VAL A 152 "
        pdb=" C   VAL A 152 "
        pdb=" O   VAL A 152 "
      ideal   model   delta    sigma   weight residual
     120.95  117.98    2.97 1.04e+00 9.25e-01 8.13e+00
  angle pdb=" N   PHE A 103 "
        pdb=" CA  PHE A 103 "
        pdb=" C   PHE A 103 "
      ideal   model   delta    sigma   weight residual
     111.36  108.34    3.02 1.09e+00 8.42e-01 7.68e+00
  ... (remaining 4401 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 1536
       16.74 -    33.48: 226
       33.48 -    50.22: 68
       50.22 -    66.96: 9
       66.96 -    83.70: 4
  Dihedral angle restraints: 1843
    sinusoidal: 707
      harmonic: 1136
  Sorted by residual:
  dihedral pdb=" CA  ARG A  26 "
           pdb=" C   ARG A  26 "
           pdb=" N   HIS A  27 "
           pdb=" CA  HIS A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.04  -16.96     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  LEU A 395 "
           pdb=" C   LEU A 395 "
           pdb=" N   CYS A 396 "
           pdb=" CA  CYS A 396 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.20  -16.80     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  SER A 419 "
           pdb=" C   SER A 419 "
           pdb=" N   ASP A 420 "
           pdb=" CA  ASP A 420 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.80  -16.20     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 1840 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 374
       0.042 -    0.085: 107
       0.085 -    0.127: 24
       0.127 -    0.169: 3
       0.169 -    0.212: 2
  Chirality restraints: 510
  Sorted by residual:
  chirality pdb=" CA  LEU A 337 "
            pdb=" N   LEU A 337 "
            pdb=" C   LEU A 337 "
            pdb=" CB  LEU A 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CB  VAL A 418 "
            pdb=" CA  VAL A 418 "
            pdb=" CG1 VAL A 418 "
            pdb=" CG2 VAL A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.43e-01
  chirality pdb=" CA  VAL A 152 "
            pdb=" N   VAL A 152 "
            pdb=" C   VAL A 152 "
            pdb=" CB  VAL A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 507 not shown)

  Planarity restraints: 526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C29 COP A 701 "   -0.333 2.00e-02 2.50e+03   2.82e-01 9.91e+02
        pdb=" C31 COP A 701 "    0.086 2.00e-02 2.50e+03
        pdb=" C33 COP A 701 "   -0.184 2.00e-02 2.50e+03
        pdb=" N30 COP A 701 "    0.491 2.00e-02 2.50e+03
        pdb=" O32 COP A 701 "   -0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C16 COP A 701 "    0.113 2.00e-02 2.50e+03   1.31e-01 2.13e+02
        pdb=" C19 COP A 701 "   -0.033 2.00e-02 2.50e+03
        pdb=" C21 COP A 701 "    0.156 2.00e-02 2.50e+03
        pdb=" N20 COP A 701 "   -0.216 2.00e-02 2.50e+03
        pdb=" O19 COP A 701 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 168 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.65e+00
        pdb=" C   SER A 168 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   SER A 168 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A 169 "    0.011 2.00e-02 2.50e+03
  ... (remaining 523 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 768
        2.78 -     3.31: 3190
        3.31 -     3.84: 5601
        3.84 -     4.37: 6300
        4.37 -     4.90: 10802
  Nonbonded interactions: 26661
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 276 "
            pdb=" OH  TYR A 438 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OH  TYR A  31 "
            pdb=" O   LEU A 199 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR A 139 "
            pdb=" O   LYS A 204 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OE1 GLU A  45 "
            pdb=" OH  TYR A 126 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" NH2 ARG A 157 "
            pdb=" OE1 GLN A 377 "
     model   vdw
     2.302 3.120
  ... (remaining 26656 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.200
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
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      :  0.005   0.086   3234  Z= 0.274
  Angle     :  0.693   7.843   4406  Z= 0.408
  Chirality :  0.042   0.212    510
  Planarity :  0.015   0.282    526
  Dihedral  : 17.250  83.705   1113
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 23.49 %
    Favored  : 75.00 %
  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:  0.55 (0.42), residues: 380
  helix:  0.86 (0.28), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.92 (0.72), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 270 
 HIS   0.007   0.001   HIS A 289 
 PHE   0.025   0.001   PHE A  84 
 TYR   0.011   0.001   TYR A  31 
 ARG   0.001   0.000   ARG A 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11624 (  246)
  hydrogen bonds       : angle       5.86419 (  735)
  covalent geometry    : bond        0.00468 ( 3234)
  covalent geometry    : angle       0.69293 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.316 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 32
  average time/residue: 0.2320
  time to fit residues: 8.8192
Evaluate side-chains
  27 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3574 r_free = 0.3574 target = 0.142225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.117743 restraints weight = 3568.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.74
r_work: 0.3146 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3234  Z= 0.176
  Angle     :  0.580   6.246   4406  Z= 0.294
  Chirality :  0.039   0.146    510
  Planarity :  0.005   0.050    526
  Dihedral  :  7.565  74.095    449
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.89 %
    Favored  : 73.19 %
  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:  1.92 (0.43), residues: 380
  helix:  1.83 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.85 (0.79), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 358 
 PHE   0.025   0.002   PHE A  84 
 TYR   0.013   0.001   TYR A 438 
 ARG   0.002   0.000   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04415 (  246)
  hydrogen bonds       : angle       4.00402 (  735)
  covalent geometry    : bond        0.00415 ( 3234)
  covalent geometry    : angle       0.57960 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 30
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   32 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7642 (tp)
REVERT: A  155 TYR cc_start: 0.8572 (m-10) cc_final: 0.8239 (m-10)
REVERT: A  289 HIS cc_start: 0.7911 (m-70) cc_final: 0.7651 (m-70)
REVERT: A  424 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6632 (tt)
  outliers start: 13
  outliers final: 7
  residues processed: 40
  average time/residue: 0.1730
  time to fit residues: 8.5287
Evaluate side-chains
  37 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.142216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.116903 restraints weight = 3624.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.83
r_work: 0.3137 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3234  Z= 0.165
  Angle     :  0.552   5.811   4406  Z= 0.280
  Chirality :  0.038   0.128    510
  Planarity :  0.004   0.047    526
  Dihedral  :  7.332  77.008    446
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.69 %
    Favored  : 73.80 %
  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:  2.01 (0.44), residues: 380
  helix:  1.91 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.90 (0.78), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 358 
 PHE   0.024   0.002   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  246)
  hydrogen bonds       : angle       3.92381 (  735)
  covalent geometry    : bond        0.00388 ( 3234)
  covalent geometry    : angle       0.55165 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  155 TYR cc_start: 0.8601 (m-10) cc_final: 0.8211 (m-10)
REVERT: A  424 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6669 (tt)
  outliers start: 15
  outliers final: 8
  residues processed: 43
  average time/residue: 0.1850
  time to fit residues: 9.6707
Evaluate side-chains
  40 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.139837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.114012 restraints weight = 3686.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.91
r_work: 0.3097 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3234  Z= 0.183
  Angle     :  0.561   5.728   4406  Z= 0.286
  Chirality :  0.038   0.127    510
  Planarity :  0.005   0.046    526
  Dihedral  :  7.320  78.155    446
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 21.69 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.43), residues: 380
  helix:  1.80 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -2.02 (0.77), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 358 
 PHE   0.025   0.002   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04305 (  246)
  hydrogen bonds       : angle       3.97470 (  735)
  covalent geometry    : bond        0.00435 ( 3234)
  covalent geometry    : angle       0.56083 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 34
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  155 TYR cc_start: 0.8557 (m-10) cc_final: 0.8139 (m-10)
REVERT: A  424 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6678 (tt)
  outliers start: 20
  outliers final: 14
  residues processed: 49
  average time/residue: 0.1752
  time to fit residues: 10.5181
Evaluate side-chains
  47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.141317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.116067 restraints weight = 3609.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.82
r_work: 0.3127 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3234  Z= 0.152
  Angle     :  0.535   5.911   4406  Z= 0.271
  Chirality :  0.038   0.131    510
  Planarity :  0.004   0.046    526
  Dihedral  :  7.297  79.165    446
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 21.69 %
    Favored  : 71.69 %
  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:  1.89 (0.43), residues: 380
  helix:  1.82 (0.28), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.95 (0.78), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.024   0.002   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  246)
  hydrogen bonds       : angle       3.88740 (  735)
  covalent geometry    : bond        0.00356 ( 3234)
  covalent geometry    : angle       0.53510 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 33
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  119 MET cc_start: 0.8581 (mmt) cc_final: 0.8181 (mmt)
REVERT: A  155 TYR cc_start: 0.8591 (m-10) cc_final: 0.8219 (m-10)
REVERT: A  424 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6733 (tt)
  outliers start: 22
  outliers final: 13
  residues processed: 50
  average time/residue: 0.1833
  time to fit residues: 11.1874
Evaluate side-chains
  46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  424 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0870
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.140550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.115389 restraints weight = 3718.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.83
r_work: 0.3122 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3234  Z= 0.159
  Angle     :  0.533   5.711   4406  Z= 0.271
  Chirality :  0.038   0.123    510
  Planarity :  0.004   0.044    526
  Dihedral  :  7.340  80.341    446
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 22.29 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.43), residues: 380
  helix:  1.79 (0.28), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.98 (0.78), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.024   0.001   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04068 (  246)
  hydrogen bonds       : angle       3.90177 (  735)
  covalent geometry    : bond        0.00374 ( 3234)
  covalent geometry    : angle       0.53261 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 32
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.5013 (ttt180) cc_final: 0.4795 (ttt180)
REVERT: A  155 TYR cc_start: 0.8611 (m-10) cc_final: 0.8238 (m-10)
REVERT: A  424 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6783 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 47
  average time/residue: 0.1967
  time to fit residues: 11.0170
Evaluate side-chains
  45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    0.3980
   chunk 0 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.153582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.131468 restraints weight = 3513.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.61
r_work: 0.3151 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3234  Z= 0.155
  Angle     :  0.543   7.894   4406  Z= 0.272
  Chirality :  0.038   0.118    510
  Planarity :  0.004   0.044    526
  Dihedral  :  7.377  81.335    446
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 23.49 %
    Favored  : 71.69 %
  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:  1.91 (0.43), residues: 380
  helix:  1.83 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.91 (0.79), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.024   0.002   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  246)
  hydrogen bonds       : angle       3.89135 (  735)
  covalent geometry    : bond        0.00362 ( 3234)
  covalent geometry    : angle       0.54302 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 31
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  119 MET cc_start: 0.8593 (mmp) cc_final: 0.8140 (mmt)
REVERT: A  155 TYR cc_start: 0.8597 (m-10) cc_final: 0.8225 (m-10)
REVERT: A  422 ARG cc_start: 0.6527 (mtm180) cc_final: 0.6152 (tmt170)
REVERT: A  424 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6764 (tt)
  outliers start: 16
  outliers final: 15
  residues processed: 42
  average time/residue: 0.1839
  time to fit residues: 9.3078
Evaluate side-chains
  47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 31
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 14 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0980
   overall best weight:    0.3558

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.143768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.119280 restraints weight = 3617.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.79
r_work: 0.3176 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3234  Z= 0.118
  Angle     :  0.501   7.065   4406  Z= 0.250
  Chirality :  0.036   0.118    510
  Planarity :  0.004   0.044    526
  Dihedral  :  7.347  82.391    446
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 24.10 %
    Favored  : 71.69 %
  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:  2.18 (0.44), residues: 380
  helix:  2.03 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.94 (0.79), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.022   0.001   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  246)
  hydrogen bonds       : angle       3.70213 (  735)
  covalent geometry    : bond        0.00266 ( 3234)
  covalent geometry    : angle       0.50111 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.4556 (ttt180) cc_final: 0.4259 (ttt-90)
REVERT: A  119 MET cc_start: 0.8531 (mmp) cc_final: 0.8155 (mmt)
REVERT: A  155 TYR cc_start: 0.8629 (m-10) cc_final: 0.8263 (m-10)
REVERT: A  422 ARG cc_start: 0.6535 (mtm180) cc_final: 0.6161 (tmt170)
  outliers start: 14
  outliers final: 10
  residues processed: 41
  average time/residue: 0.1814
  time to fit residues: 9.0344
Evaluate side-chains
  41 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  452 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 431 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.141782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.117105 restraints weight = 3630.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.81
r_work: 0.3156 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3234  Z= 0.138
  Angle     :  0.504   7.095   4406  Z= 0.257
  Chirality :  0.037   0.120    510
  Planarity :  0.004   0.044    526
  Dihedral  :  7.436  83.186    446
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 24.10 %
    Favored  : 71.69 %
  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:  2.16 (0.43), residues: 380
  helix:  2.01 (0.28), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.94 (0.79), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.023   0.001   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  246)
  hydrogen bonds       : angle       3.73578 (  735)
  covalent geometry    : bond        0.00322 ( 3234)
  covalent geometry    : angle       0.50431 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.4541 (ttt180) cc_final: 0.4215 (ttt-90)
REVERT: A  119 MET cc_start: 0.8559 (mmp) cc_final: 0.8180 (mmt)
REVERT: A  422 ARG cc_start: 0.6511 (mtm180) cc_final: 0.6193 (tmt170)
REVERT: A  424 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6748 (tt)
  outliers start: 14
  outliers final: 12
  residues processed: 40
  average time/residue: 0.1840
  time to fit residues: 8.8817
Evaluate side-chains
  44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 31
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.138541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113846 restraints weight = 3613.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.80
r_work: 0.3113 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3234  Z= 0.178
  Angle     :  0.552   6.911   4406  Z= 0.281
  Chirality :  0.038   0.123    510
  Planarity :  0.004   0.044    526
  Dihedral  :  7.672  83.978    446
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.10 %
    Favored  : 71.99 %
  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:  1.95 (0.43), residues: 380
  helix:  1.83 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.80 (0.79), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A  27 
 PHE   0.025   0.002   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04141 (  246)
  hydrogen bonds       : angle       3.91677 (  735)
  covalent geometry    : bond        0.00421 ( 3234)
  covalent geometry    : angle       0.55250 ( 4406)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 33
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  119 MET cc_start: 0.8579 (mmp) cc_final: 0.8176 (mmt)
REVERT: A  155 TYR cc_start: 0.8579 (m-10) cc_final: 0.8193 (m-10)
REVERT: A  422 ARG cc_start: 0.6551 (mtm180) cc_final: 0.6208 (tmt170)
REVERT: A  424 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6760 (tt)
  outliers start: 13
  outliers final: 11
  residues processed: 41
  average time/residue: 0.1875
  time to fit residues: 9.3245
Evaluate side-chains
  44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 36 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.140609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.115723 restraints weight = 3638.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.83
r_work: 0.3137 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3234  Z= 0.144
  Angle     :  0.527   6.667   4406  Z= 0.266
  Chirality :  0.037   0.116    510
  Planarity :  0.004   0.043    526
  Dihedral  :  7.719  84.685    446
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 24.10 %
    Favored  : 71.39 %
  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:  1.99 (0.43), residues: 380
  helix:  1.86 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.76 (0.79), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.024   0.001   PHE A  84 
 TYR   0.012   0.001   TYR A 438 
 ARG   0.001   0.000   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  246)
  hydrogen bonds       : angle       3.83493 (  735)
  covalent geometry    : bond        0.00334 ( 3234)
  covalent geometry    : angle       0.52663 ( 4406)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1862.62 seconds
wall clock time: 32 minutes 58.96 seconds (1978.96 seconds total)