Starting phenix.real_space_refine
on Fri Aug 22 13:10:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jtv_36653/08_2025/8jtv_36653.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jtv_36653/08_2025/8jtv_36653.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jtv_36653/08_2025/8jtv_36653.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jtv_36653/08_2025/8jtv_36653.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jtv_36653/08_2025/8jtv_36653.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jtv_36653/08_2025/8jtv_36653.map"
  }
  resolution = 3.77
  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=   0.001 sd=   0.107
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      27      5.16       5
     C    2010      2.51       5
     N     505      2.21       5
     O     525      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 3067
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3058
          Classifications: {'peptide': 437}
          Incomplete info: {'truncation_to_alanine': 85}
          Link IDs: {'PTRANS': 21, 'TRANS': 415}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 334
          Unresolved non-hydrogen angles: 426
          Unresolved non-hydrogen dihedrals: 276
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 12, 'TRP:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 2, 'ASP:plan': 7, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 211
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'MF8': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.17, per 1000 atoms: 0.38
  Number of scatterers: 3067
  At special positions: 0
  Unit cell: (70.3625, 88.765, 64.95, 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      27     16.00
     O     525      8.00
     N     505      7.00
     C    2010      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " distance=2.03

  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: 0.31
  Conformation dependent library (CDL) restraints added in 172.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  800

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 1 sheets defined
      78.3% alpha, 0.9% 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 20 through 32
      removed outlier: 3.804A  pdb=" N   ILE A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 35
      No H-bonds generated for 'chain 'A' and resid 33 through 35'
    Processing helix  chain 'A' and resid 36 through 43
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.556A  pdb=" N   GLU A  57 " --> pdb=" O   PRO A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 4.090A  pdb=" N   VAL A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 82
    Processing helix  chain 'A' and resid 104 through 109
      removed outlier: 3.551A  pdb=" N   LEU A 109 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 144 through 173
      removed outlier: 3.703A  pdb=" N   LEU A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 194
    Processing helix  chain 'A' and resid 198 through 228
      removed outlier: 3.752A  pdb=" N   VAL A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 258
    Processing helix  chain 'A' and resid 260 through 273
      Proline residue:  A 271  - end of helix
    Processing helix  chain 'A' and resid 340 through 372
      removed outlier: 3.653A  pdb=" N   ARG A 346 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 385
    Processing helix  chain 'A' and resid 385 through 397
      removed outlier: 3.880A  pdb=" N   GLY A 389 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 423
      removed outlier: 3.658A  pdb=" N   ALA A 407 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 457
      removed outlier: 3.701A  pdb=" N   ALA A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR A 457 " --> pdb=" O   ASN A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 488
      removed outlier: 3.560A  pdb=" N   LEU A 472 " --> pdb=" O   VAL A 468 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
      removed outlier: 4.019A  pdb=" N   ARG A 486 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 510
      removed outlier: 4.456A  pdb=" N   LEU A 496 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50

    243 hydrogen bonds defined for protein.
    717 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: 0.60

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 961
        1.34 -     1.46: 688
        1.46 -     1.58: 1451
        1.58 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 3139
  Sorted by residual:
  bond pdb=" C07 MF8 A 601 "
       pdb=" N08 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.281  1.451 -0.170 2.00e-02 2.50e+03 7.19e+01
  bond pdb=" C07 MF8 A 601 "
       pdb=" N06 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.393  1.252  0.141 2.00e-02 2.50e+03 4.94e+01
  bond pdb=" C04 MF8 A 601 "
       pdb=" N02 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.362  1.444 -0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" C07 MF8 A 601 "
       pdb=" N09 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.358  1.439 -0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" C04 MF8 A 601 "
       pdb=" N06 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.451 -0.064 2.00e-02 2.50e+03 1.03e+01
  ... (remaining 3134 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4201
        1.69 -     3.38: 77
        3.38 -     5.07: 14
        5.07 -     6.77: 7
        6.77 -     8.46: 6
  Bond angle restraints: 4305
  Sorted by residual:
  angle pdb=" N   VAL A 103 "
        pdb=" CA  VAL A 103 "
        pdb=" C   VAL A 103 "
      ideal   model   delta    sigma   weight residual
     111.56  104.18    7.38 8.60e-01 1.35e+00 7.37e+01
  angle pdb=" C   VAL A 103 "
        pdb=" CA  VAL A 103 "
        pdb=" CB  VAL A 103 "
      ideal   model   delta    sigma   weight residual
     111.44  116.67   -5.23 9.50e-01 1.11e+00 3.03e+01
  angle pdb=" N   ASP A 104 "
        pdb=" CA  ASP A 104 "
        pdb=" CB  ASP A 104 "
      ideal   model   delta    sigma   weight residual
     111.09  105.80    5.29 1.24e+00 6.50e-01 1.82e+01
  angle pdb=" N02 MF8 A 601 "
        pdb=" C04 MF8 A 601 "
        pdb=" N05 MF8 A 601 "
      ideal   model   delta    sigma   weight residual
     126.24  117.99    8.25 3.00e+00 1.11e-01 7.57e+00
  angle pdb=" N   ILE A 483 "
        pdb=" CA  ILE A 483 "
        pdb=" C   ILE A 483 "
      ideal   model   delta    sigma   weight residual
     111.81  109.50    2.31 8.60e-01 1.35e+00 7.20e+00
  ... (remaining 4300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.71: 1617
       13.71 -    27.42: 127
       27.42 -    41.13: 54
       41.13 -    54.84: 4
       54.84 -    68.56: 4
  Dihedral angle restraints: 1806
    sinusoidal: 560
      harmonic: 1246
  Sorted by residual:
  dihedral pdb=" CB  CYS A  50 "
           pdb=" SG  CYS A  50 "
           pdb=" SG  CYS A 121 "
           pdb=" CB  CYS A 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   24.44   68.56     1      1.00e+01 1.00e-02 6.09e+01
  dihedral pdb=" CB  CYS A  88 "
           pdb=" SG  CYS A  88 "
           pdb=" SG  CYS A 142 "
           pdb=" CB  CYS A 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.55  -67.55     1      1.00e+01 1.00e-02 5.93e+01
  dihedral pdb=" CA  LEU A 140 "
           pdb=" C   LEU A 140 "
           pdb=" N   VAL A 141 "
           pdb=" CA  VAL A 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.67  -16.33     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 1803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 290
       0.025 -    0.050: 143
       0.050 -    0.076: 56
       0.076 -    0.101: 27
       0.101 -    0.126: 8
  Chirality restraints: 524
  Sorted by residual:
  chirality pdb=" CB  VAL A 385 "
            pdb=" CA  VAL A 385 "
            pdb=" CG1 VAL A 385 "
            pdb=" CG2 VAL A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CA  THR A 480 "
            pdb=" N   THR A 480 "
            pdb=" C   THR A 480 "
            pdb=" CB  THR A 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.41    0.12 2.00e-01 2.50e+01 3.34e-01
  chirality pdb=" CA  LEU A 494 "
            pdb=" N   LEU A 494 "
            pdb=" C   LEU A 494 "
            pdb=" CB  LEU A 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.98e-01
  ... (remaining 521 not shown)

  Planarity restraints: 540
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C01 MF8 A 601 "    0.078 2.00e-02 2.50e+03   6.73e-02 1.02e+02
        pdb=" C03 MF8 A 601 "    0.003 2.00e-02 2.50e+03
        pdb=" C04 MF8 A 601 "   -0.044 2.00e-02 2.50e+03
        pdb=" C07 MF8 A 601 "   -0.017 2.00e-02 2.50e+03
        pdb=" N02 MF8 A 601 "    0.014 2.00e-02 2.50e+03
        pdb=" N05 MF8 A 601 "   -0.008 2.00e-02 2.50e+03
        pdb=" N06 MF8 A 601 "   -0.152 2.00e-02 2.50e+03
        pdb=" N08 MF8 A 601 "    0.037 2.00e-02 2.50e+03
        pdb=" N09 MF8 A 601 "    0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 258 "   -0.038 5.00e-02 4.00e+02   5.82e-02 5.43e+00
        pdb=" N   PRO A 259 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 259 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 259 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  33 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO A  34 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A  34 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  34 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 537 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 868
        2.81 -     3.34: 3172
        3.34 -     3.86: 5115
        3.86 -     4.38: 5226
        4.38 -     4.90: 9313
  Nonbonded interactions: 23694
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  72 "
            pdb=" O   VAL A 103 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG  SER A 409 "
            pdb=" O   GLY A 441 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OD1 ASN A 186 "
            pdb=" NE2 GLN A 209 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" O   CYS A  88 "
            pdb=" NH1 ARG A  89 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" O   ILE A 392 "
            pdb=" OG1 THR A 396 "
     model   vdw
     2.369 3.040
  ... (remaining 23689 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.170
  Find NCS groups from input model:        0.020
  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:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6013
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      :  0.006   0.170   3142  Z= 0.291
  Angle     :  0.664   8.457   4311  Z= 0.366
  Chirality :  0.039   0.126    524
  Planarity :  0.005   0.067    540
  Dihedral  : 12.161  65.075    997
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  1.44 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.62 (0.41), residues: 431
  helix:  1.42 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -2.42 (0.51), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 346 
 TYR   0.013   0.001   TYR A 361 
 PHE   0.014   0.001   PHE A 159 
 TRP   0.009   0.001   TRP A 146 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 3139)
  covalent geometry    : angle       0.66415 ( 4305)
  SS BOND              : bond        0.00087 (    3)
  SS BOND              : angle       0.73877 (    6)
  hydrogen bonds       : bond        0.12014 (  243)
  hydrogen bonds       : angle       5.10393 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   35 ILE cc_start: 0.5840 (mm) cc_final: 0.5552 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 48
  average time/residue: 0.0357
  time to fit residues: 2.3921
Evaluate side-chains
  36 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0970
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 453 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.219163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.196827 restraints weight = 3439.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.199903 restraints weight = 2306.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.202421 restraints weight = 1718.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.203921 restraints weight = 1394.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.204728 restraints weight = 1180.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6041
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3142  Z= 0.127
  Angle     :  0.574   8.487   4311  Z= 0.284
  Chirality :  0.038   0.135    524
  Planarity :  0.004   0.042    540
  Dihedral  :  4.288  39.430    456
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  7.58 %
    Favored  : 89.89 %
  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:  1.14 (0.41), residues: 431
  helix:  1.66 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.91 (0.54), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  89 
 TYR   0.009   0.001   TYR A 361 
 PHE   0.016   0.001   PHE A 348 
 TRP   0.010   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3139)
  covalent geometry    : angle       0.57415 ( 4305)
  SS BOND              : bond        0.00124 (    3)
  SS BOND              : angle       0.71215 (    6)
  hydrogen bonds       : bond        0.04613 (  243)
  hydrogen bonds       : angle       4.15376 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  406 MET cc_start: 0.7063 (tpt) cc_final: 0.6735 (tpt)
REVERT: A  420 MET cc_start: 0.7575 (ttm) cc_final: 0.7329 (tpp)
REVERT: A  435 MET cc_start: 0.6901 (tpp) cc_final: 0.6680 (tpp)
  outliers start: 7
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0383
  time to fit residues: 2.2243
Evaluate side-chains
  37 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0870
   chunk 7 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.236250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.218814 restraints weight = 3293.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.220169 restraints weight = 2492.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.221967 restraints weight = 2104.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.223291 restraints weight = 1752.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.223291 restraints weight = 1565.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6158
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3142  Z= 0.129
  Angle     :  0.567   8.288   4311  Z= 0.278
  Chirality :  0.037   0.128    524
  Planarity :  0.004   0.041    540
  Dihedral  :  4.184  37.266    456
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 11.19 %
    Favored  : 85.92 %
  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:  1.23 (0.42), residues: 431
  helix:  1.68 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.80 (0.56), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 439 
 TYR   0.009   0.001   TYR A 361 
 PHE   0.013   0.001   PHE A 273 
 TRP   0.012   0.001   TRP A 429 
 HIS   0.001   0.000   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3139)
  covalent geometry    : angle       0.56706 ( 4305)
  SS BOND              : bond        0.00113 (    3)
  SS BOND              : angle       0.70304 (    6)
  hydrogen bonds       : bond        0.04547 (  243)
  hydrogen bonds       : angle       4.08893 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  440 MET cc_start: 0.7010 (tmm) cc_final: 0.6565 (ttp)
  outliers start: 8
  outliers final: 5
  residues processed: 44
  average time/residue: 0.0380
  time to fit residues: 2.3911
Evaluate side-chains
  38 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 410 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.207512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.184325 restraints weight = 3412.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.186963 restraints weight = 2449.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.189117 restraints weight = 1895.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.190206 restraints weight = 1574.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.190206 restraints weight = 1392.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6264
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3142  Z= 0.160
  Angle     :  0.628   8.680   4311  Z= 0.309
  Chirality :  0.039   0.141    524
  Planarity :  0.004   0.044    540
  Dihedral  :  3.948  15.757    454
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.16 %
    Favored  : 81.95 %
  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:  1.06 (0.41), residues: 431
  helix:  1.57 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.89 (0.56), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 262 
 TYR   0.007   0.001   TYR A 361 
 PHE   0.010   0.001   PHE A 151 
 TRP   0.016   0.002   TRP A 217 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3139)
  covalent geometry    : angle       0.62800 ( 4305)
  SS BOND              : bond        0.00235 (    3)
  SS BOND              : angle       0.86772 (    6)
  hydrogen bonds       : bond        0.04964 (  243)
  hydrogen bonds       : angle       4.24007 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.099 
Fit side-chains
  outliers start: 8
  outliers final: 8
  residues processed: 43
  average time/residue: 0.0595
  time to fit residues: 3.2367
Evaluate side-chains
  43 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 0 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   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 = 0.4296 r_free = 0.4296 target = 0.209168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.185389 restraints weight = 3402.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.188272 restraints weight = 2404.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.190197 restraints weight = 1863.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.191985 restraints weight = 1549.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.192821 restraints weight = 1339.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3142  Z= 0.147
  Angle     :  0.614   8.625   4311  Z= 0.300
  Chirality :  0.038   0.134    524
  Planarity :  0.004   0.040    540
  Dihedral  :  3.991  15.435    454
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 14.80 %
    Favored  : 81.59 %
  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:  1.09 (0.41), residues: 431
  helix:  1.59 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.91 (0.56), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 462 
 TYR   0.008   0.001   TYR A 361 
 PHE   0.018   0.001   PHE A 273 
 TRP   0.017   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3139)
  covalent geometry    : angle       0.61354 ( 4305)
  SS BOND              : bond        0.00196 (    3)
  SS BOND              : angle       0.72593 (    6)
  hydrogen bonds       : bond        0.04826 (  243)
  hydrogen bonds       : angle       4.18360 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A   35 ILE cc_start: 0.6471 (mm) cc_final: 0.6265 (mm)
REVERT: A  440 MET cc_start: 0.7101 (tmm) cc_final: 0.6543 (ttp)
  outliers start: 10
  outliers final: 9
  residues processed: 42
  average time/residue: 0.0395
  time to fit residues: 2.2947
Evaluate side-chains
  43 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 41 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.207606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.183504 restraints weight = 3448.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.186495 restraints weight = 2448.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.188403 restraints weight = 1891.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.190086 restraints weight = 1571.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.190086 restraints weight = 1382.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3142  Z= 0.148
  Angle     :  0.615   8.657   4311  Z= 0.300
  Chirality :  0.038   0.133    524
  Planarity :  0.004   0.039    540
  Dihedral  :  3.983  14.130    454
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 16.97 %
    Favored  : 79.06 %
  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:  1.07 (0.41), residues: 431
  helix:  1.59 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.95 (0.55), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 439 
 TYR   0.007   0.001   TYR A 361 
 PHE   0.014   0.001   PHE A 273 
 TRP   0.020   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3139)
  covalent geometry    : angle       0.61519 ( 4305)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       0.74788 (    6)
  hydrogen bonds       : bond        0.04837 (  243)
  hydrogen bonds       : angle       4.17901 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.063 
Fit side-chains
REVERT: A   35 ILE cc_start: 0.6683 (mm) cc_final: 0.6463 (mm)
REVERT: A  440 MET cc_start: 0.7131 (tmm) cc_final: 0.6548 (ttp)
  outliers start: 11
  outliers final: 9
  residues processed: 43
  average time/residue: 0.0374
  time to fit residues: 2.2285
Evaluate side-chains
  42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4601 r_free = 0.4601 target = 0.226607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.208527 restraints weight = 3361.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.209972 restraints weight = 2678.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.210313 restraints weight = 2253.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.211881 restraints weight = 2095.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.211926 restraints weight = 1826.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6356
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3142  Z= 0.156
  Angle     :  0.640   9.196   4311  Z= 0.309
  Chirality :  0.038   0.137    524
  Planarity :  0.004   0.039    540
  Dihedral  :  4.028  14.977    454
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.41 %
    Favored  : 78.34 %
  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:  1.00 (0.41), residues: 431
  helix:  1.53 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.95 (0.55), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 439 
 TYR   0.007   0.001   TYR A 361 
 PHE   0.013   0.001   PHE A 273 
 TRP   0.024   0.002   TRP A 429 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3139)
  covalent geometry    : angle       0.63958 ( 4305)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.78011 (    6)
  hydrogen bonds       : bond        0.04943 (  243)
  hydrogen bonds       : angle       4.25948 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 9
  outliers final: 9
  residues processed: 41
  average time/residue: 0.0349
  time to fit residues: 2.0572
Evaluate side-chains
  41 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   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 = 0.4281 r_free = 0.4281 target = 0.206939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.183155 restraints weight = 3520.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.185752 restraints weight = 2495.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.188054 restraints weight = 1942.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.189129 restraints weight = 1625.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.190233 restraints weight = 1442.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3142  Z= 0.146
  Angle     :  0.631   8.712   4311  Z= 0.303
  Chirality :  0.038   0.135    524
  Planarity :  0.004   0.041    540
  Dihedral  :  4.030  14.800    454
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.13 %
    Favored  : 77.26 %
  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 (0.41), residues: 431
  helix:  1.56 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.98 (0.55), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 439 
 TYR   0.008   0.001   TYR A 361 
 PHE   0.012   0.001   PHE A 273 
 TRP   0.028   0.002   TRP A 429 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3139)
  covalent geometry    : angle       0.63119 ( 4305)
  SS BOND              : bond        0.00193 (    3)
  SS BOND              : angle       0.73856 (    6)
  hydrogen bonds       : bond        0.04839 (  243)
  hydrogen bonds       : angle       4.20365 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A  440 MET cc_start: 0.6960 (tmm) cc_final: 0.6379 (ttp)
  outliers start: 10
  outliers final: 9
  residues processed: 41
  average time/residue: 0.0334
  time to fit residues: 1.9791
Evaluate side-chains
  40 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0980
   chunk 28 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   chunk 36 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0170
   overall best weight:    0.3418

-------------------------------------------------------------------------------
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 = 0.4325 r_free = 0.4325 target = 0.212559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.188102 restraints weight = 3556.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.191056 restraints weight = 2505.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.192891 restraints weight = 1940.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.194759 restraints weight = 1624.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.195243 restraints weight = 1436.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6200
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3142  Z= 0.126
  Angle     :  0.598   8.348   4311  Z= 0.286
  Chirality :  0.037   0.127    524
  Planarity :  0.004   0.038    540
  Dihedral  :  3.942  13.522    454
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 20.22 %
    Favored  : 77.26 %
  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:  1.16 (0.41), residues: 431
  helix:  1.66 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -2.01 (0.55), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 462 
 TYR   0.009   0.001   TYR A 361 
 PHE   0.020   0.001   PHE A 273 
 TRP   0.026   0.001   TRP A 429 
 HIS   0.001   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3139)
  covalent geometry    : angle       0.59815 ( 4305)
  SS BOND              : bond        0.00105 (    3)
  SS BOND              : angle       0.65164 (    6)
  hydrogen bonds       : bond        0.04482 (  243)
  hydrogen bonds       : angle       4.02371 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  440 MET cc_start: 0.7113 (tmm) cc_final: 0.6530 (ttp)
  outliers start: 7
  outliers final: 7
  residues processed: 39
  average time/residue: 0.0430
  time to fit residues: 2.3360
Evaluate side-chains
  39 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0970
   chunk 18 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:   10.0000
   chunk 24 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.4313 r_free = 0.4313 target = 0.210783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.187052 restraints weight = 3405.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.189847 restraints weight = 2427.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.191616 restraints weight = 1893.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.193409 restraints weight = 1592.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.194110 restraints weight = 1379.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6207
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3142  Z= 0.132
  Angle     :  0.607   8.439   4311  Z= 0.290
  Chirality :  0.037   0.133    524
  Planarity :  0.004   0.038    540
  Dihedral  :  3.911  13.723    454
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 20.58 %
    Favored  : 76.90 %
  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:  1.12 (0.41), residues: 431
  helix:  1.65 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.08 (0.55), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 462 
 TYR   0.008   0.001   TYR A 361 
 PHE   0.019   0.001   PHE A 273 
 TRP   0.029   0.002   TRP A 217 
 HIS   0.001   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3139)
  covalent geometry    : angle       0.60677 ( 4305)
  SS BOND              : bond        0.00137 (    3)
  SS BOND              : angle       0.66341 (    6)
  hydrogen bonds       : bond        0.04529 (  243)
  hydrogen bonds       : angle       4.01973 (  717)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.064 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 37
  average time/residue: 0.0372
  time to fit residues: 1.9019
Evaluate side-chains
  38 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0970
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4306 r_free = 0.4306 target = 0.209936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.185120 restraints weight = 3464.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.188019 restraints weight = 2462.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.190155 restraints weight = 1918.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.191310 restraints weight = 1614.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.191991 restraints weight = 1431.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6225
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3142  Z= 0.141
  Angle     :  0.626   8.274   4311  Z= 0.299
  Chirality :  0.038   0.133    524
  Planarity :  0.004   0.038    540
  Dihedral  :  3.937  14.422    454
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.94 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.17 (0.41), residues: 431
  helix:  1.64 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.93 (0.55), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 439 
 TYR   0.007   0.001   TYR A 361 
 PHE   0.018   0.001   PHE A 273 
 TRP   0.029   0.002   TRP A 429 
 HIS   0.001   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3139)
  covalent geometry    : angle       0.62587 ( 4305)
  SS BOND              : bond        0.00166 (    3)
  SS BOND              : angle       0.71635 (    6)
  hydrogen bonds       : bond        0.04667 (  243)
  hydrogen bonds       : angle       4.09058 (  717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 655.62 seconds
wall clock time: 11 minutes 54.94 seconds (714.94 seconds total)