Starting phenix.real_space_refine
on Wed Jul 23 10:19:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jtv_36653/07_2025/8jtv_36653.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jtv_36653/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jtv_36653/07_2025/8jtv_36653.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jtv_36653/07_2025/8jtv_36653.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jtv_36653/07_2025/8jtv_36653.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jtv_36653/07_2025/8jtv_36653.cif"
  }
  resolution = 3.77
  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=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 12}
          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: 2.57, per 1000 atoms: 0.84
  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: 0.85
  Conformation dependent library (CDL) restraints added in 405.0 milliseconds
  

  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: 0.34
  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: 0.97

  Time building geometry restraints manager: 0.99 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:             0.550
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.850
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.840
-------------------------------------------------------------------------------
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 (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:  0.62 (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
 TRP   0.009   0.001   TRP A 146 
 HIS   0.003   0.001   HIS A  48 
 PHE   0.014   0.001   PHE A 159 
 TYR   0.013   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 346 

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

*********************** 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  : 0.284 
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: 0.1066
  time to fit residues: 6.9793
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  : 0.267 
-------------------------------------------------------------------------------
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 36 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0170
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.4352 r_free = 0.4352 target = 0.215985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.193950 restraints weight = 3369.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.197009 restraints weight = 2277.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.199323 restraints weight = 1709.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6133
moved from start:          0.1168

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= 0.142
  Angle     :  0.592   8.491   4311  Z= 0.294
  Chirality :  0.038   0.136    524
  Planarity :  0.004   0.043    540
  Dihedral  :  4.312  39.074    456
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  :  8.66 %
    Favored  : 88.45 %
  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:  1.06 (0.41), residues: 431
  helix:  1.57 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.87 (0.55), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.015   0.001   PHE A 348 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.003   0.001   ARG A  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04800 (  243)
  hydrogen bonds       : angle       4.27169 (  717)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.80905 (    6)
  covalent geometry    : bond        0.00308 ( 3139)
  covalent geometry    : angle       0.59195 ( 4305)

*********************** 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
  44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   35 ILE cc_start: 0.6156 (mm) cc_final: 0.5941 (mm)
REVERT: A  420 MET cc_start: 0.7609 (ttm) cc_final: 0.7353 (tpp)
REVERT: A  435 MET cc_start: 0.6947 (tpp) cc_final: 0.6720 (tpp)
  outliers start: 8
  outliers final: 6
  residues processed: 42
  average time/residue: 0.0891
  time to fit residues: 5.2759
Evaluate side-chains
  39 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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  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 11 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5758

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.232432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.214646 restraints weight = 3227.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.216508 restraints weight = 2444.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.217298 restraints weight = 1983.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
moved from start:          0.1522

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= 0.140
  Angle     :  0.590   8.704   4311  Z= 0.290
  Chirality :  0.037   0.134    524
  Planarity :  0.004   0.038    540
  Dihedral  :  4.263  37.611    456
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 10.83 %
    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 (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:  1.15 (0.41), residues: 431
  helix:  1.61 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.76 (0.56), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 429 
 HIS   0.001   0.000   HIS A  49 
 PHE   0.013   0.001   PHE A 273 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.002   0.001   ARG A  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04748 (  243)
  hydrogen bonds       : angle       4.23749 (  717)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       0.77976 (    6)
  covalent geometry    : bond        0.00307 ( 3139)
  covalent geometry    : angle       0.58962 ( 4305)

*********************** 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
  46 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.5990 (t60) cc_final: 0.5787 (t60)
REVERT: A  440 MET cc_start: 0.7045 (tmm) cc_final: 0.6615 (ttp)
  outliers start: 9
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0942
  time to fit residues: 5.6821
Evaluate side-chains
  41 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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  371 THR
Chi-restraints excluded: chain A residue  406 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0970
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.4620 r_free = 0.4620 target = 0.229530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.211725 restraints weight = 3324.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.213100 restraints weight = 2645.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.213453 restraints weight = 2223.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6315
moved from start:          0.1801

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= 0.146
  Angle     :  0.604   8.786   4311  Z= 0.295
  Chirality :  0.038   0.140    524
  Planarity :  0.004   0.042    540
  Dihedral  :  3.930  15.387    454
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.44 %
    Favored  : 82.67 %
  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:  1.13 (0.41), residues: 431
  helix:  1.61 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.86 (0.56), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.011   0.001   PHE A 151 
 TYR   0.008   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04791 (  243)
  hydrogen bonds       : angle       4.19596 (  717)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       0.76030 (    6)
  covalent geometry    : bond        0.00324 ( 3139)
  covalent geometry    : angle       0.60356 ( 4305)

*********************** 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
  42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.5940 (t60) cc_final: 0.5710 (t60)
  outliers start: 8
  outliers final: 7
  residues processed: 40
  average time/residue: 0.1218
  time to fit residues: 6.5061
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  : 0.287 
-------------------------------------------------------------------------------
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  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 4 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0980
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.207340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.183610 restraints weight = 3445.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.186309 restraints weight = 2477.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.187742 restraints weight = 1959.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6282
moved from start:          0.2032

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= 0.155
  Angle     :  0.621   8.824   4311  Z= 0.303
  Chirality :  0.038   0.135    524
  Planarity :  0.004   0.040    540
  Dihedral  :  3.959  14.315    454
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.52 %
    Favored  : 81.23 %
  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:  1.08 (0.41), residues: 431
  helix:  1.56 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.84 (0.57), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.018   0.001   PHE A 273 
 TYR   0.007   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04927 (  243)
  hydrogen bonds       : angle       4.25812 (  717)
  SS BOND              : bond        0.00223 (    3)
  SS BOND              : angle       0.77840 (    6)
  covalent geometry    : bond        0.00348 ( 3139)
  covalent geometry    : angle       0.62108 ( 4305)

*********************** 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
  46 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.6043 (t60) cc_final: 0.5809 (t60)
REVERT: A  440 MET cc_start: 0.7072 (tmm) cc_final: 0.6516 (ttp)
  outliers start: 9
  outliers final: 8
  residues processed: 45
  average time/residue: 0.1436
  time to fit residues: 8.2456
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  : 0.316 
-------------------------------------------------------------------------------
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  464 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   chunk 11 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0870
   chunk 42 optimal weight:    0.5980
   chunk 3 optimal weight:   10.0000
   overall best weight:    0.3958

-------------------------------------------------------------------------------
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 = 0.4321 r_free = 0.4321 target = 0.211839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.187749 restraints weight = 3497.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.190682 restraints weight = 2485.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.192519 restraints weight = 1923.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6209
moved from start:          0.2111

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= 0.128
  Angle     :  0.589   8.517   4311  Z= 0.285
  Chirality :  0.037   0.137    524
  Planarity :  0.004   0.040    540
  Dihedral  :  3.953  13.709    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 :  3.25 %
    Allowed  : 18.05 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.42), residues: 431
  helix:  1.68 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.94 (0.56), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 429 
 HIS   0.001   0.000   HIS A  49 
 PHE   0.014   0.001   PHE A 273 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.003   0.001   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  243)
  hydrogen bonds       : angle       4.05938 (  717)
  SS BOND              : bond        0.00116 (    3)
  SS BOND              : angle       0.62214 (    6)
  covalent geometry    : bond        0.00271 ( 3139)
  covalent geometry    : angle       0.58854 ( 4305)

*********************** 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
  42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.5866 (t60) cc_final: 0.5616 (t60)
REVERT: A  440 MET cc_start: 0.7189 (tmm) cc_final: 0.6553 (ttp)
  outliers start: 9
  outliers final: 7
  residues processed: 41
  average time/residue: 0.1019
  time to fit residues: 5.7779
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  : 0.335 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.205488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.181110 restraints weight = 3502.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.183752 restraints weight = 2499.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.185884 restraints weight = 1958.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3142  Z= 0.165
  Angle     :  0.651   9.189   4311  Z= 0.315
  Chirality :  0.039   0.145    524
  Planarity :  0.004   0.040    540
  Dihedral  :  4.072  15.612    454
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.49 %
    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 (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:  0.99 (0.41), residues: 431
  helix:  1.51 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.91 (0.56), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.012   0.001   PHE A 273 
 TYR   0.007   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05059 (  243)
  hydrogen bonds       : angle       4.30409 (  717)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       0.82823 (    6)
  covalent geometry    : bond        0.00377 ( 3139)
  covalent geometry    : angle       0.65056 ( 4305)

*********************** 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
  41 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.6167 (t60) cc_final: 0.5859 (t60)
  outliers start: 9
  outliers final: 8
  residues processed: 40
  average time/residue: 0.0905
  time to fit residues: 5.0230
Evaluate side-chains
  40 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  464 LEU
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 = 0.4275 r_free = 0.4275 target = 0.206487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.181858 restraints weight = 3483.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.184495 restraints weight = 2508.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.186499 restraints weight = 1972.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6303
moved from start:          0.2479

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= 0.153
  Angle     :  0.635   8.812   4311  Z= 0.306
  Chirality :  0.038   0.136    524
  Planarity :  0.004   0.046    540
  Dihedral  :  4.073  15.977    454
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.49 %
    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 (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:  1.05 (0.41), residues: 431
  helix:  1.58 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.91 (0.54), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.011   0.001   PHE A 273 
 TYR   0.007   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04919 (  243)
  hydrogen bonds       : angle       4.26808 (  717)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.76824 (    6)
  covalent geometry    : bond        0.00343 ( 3139)
  covalent geometry    : angle       0.63519 ( 4305)

*********************** 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
  44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.6144 (t60) cc_final: 0.5841 (t60)
REVERT: A  387 ILE cc_start: 0.6906 (OUTLIER) cc_final: 0.6580 (tp)
REVERT: A  440 MET cc_start: 0.6949 (tmm) cc_final: 0.6501 (ttp)
  outliers start: 10
  outliers final: 7
  residues processed: 42
  average time/residue: 0.1019
  time to fit residues: 5.8924
Evaluate side-chains
  41 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  387 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  464 LEU
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 1 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0470
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.2078

-------------------------------------------------------------------------------
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 = 0.4339 r_free = 0.4339 target = 0.214179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.189925 restraints weight = 3492.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.192268 restraints weight = 2483.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.194821 restraints weight = 1968.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6188
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   0.040   3142  Z= 0.122
  Angle     :  0.589   8.290   4311  Z= 0.282
  Chirality :  0.036   0.128    524
  Planarity :  0.004   0.068    540
  Dihedral  :  3.935  13.622    454
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  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 (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:  1.30 (0.42), residues: 431
  helix:  1.78 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.89 (0.55), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 429 
 HIS   0.001   0.001   HIS A 260 
 PHE   0.010   0.001   PHE A 151 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04421 (  243)
  hydrogen bonds       : angle       3.98763 (  717)
  SS BOND              : bond        0.00067 (    3)
  SS BOND              : angle       0.61327 (    6)
  covalent geometry    : bond        0.00252 ( 3139)
  covalent geometry    : angle       0.58918 ( 4305)

*********************** 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
  42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.6013 (t60) cc_final: 0.5778 (t60)
REVERT: A  387 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6566 (tp)
REVERT: A  440 MET cc_start: 0.7118 (tmm) cc_final: 0.6523 (ttp)
  outliers start: 7
  outliers final: 6
  residues processed: 42
  average time/residue: 0.1034
  time to fit residues: 6.0429
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  : 0.312 
-------------------------------------------------------------------------------
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  387 ILE
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 36 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0770
   chunk 21 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.4359 r_free = 0.4359 target = 0.215651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.190528 restraints weight = 3538.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.193221 restraints weight = 2553.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.195424 restraints weight = 2022.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
moved from start:          0.2448

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= 0.138
  Angle     :  0.621   8.696   4311  Z= 0.293
  Chirality :  0.038   0.131    524
  Planarity :  0.004   0.060    540
  Dihedral  :  3.946  15.189    454
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.86 %
    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 (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:  1.15 (0.41), residues: 431
  helix:  1.69 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.11 (0.54), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.020   0.001   PHE A 273 
 TYR   0.008   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  243)
  hydrogen bonds       : angle       4.03497 (  717)
  SS BOND              : bond        0.00161 (    3)
  SS BOND              : angle       0.68834 (    6)
  covalent geometry    : bond        0.00304 ( 3139)
  covalent geometry    : angle       0.62071 ( 4305)

********************** 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
  44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  217 TRP cc_start: 0.6158 (t60) cc_final: 0.5900 (t60)
REVERT: A  387 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6582 (tp)
  outliers start: 11
  outliers final: 8
  residues processed: 42
  average time/residue: 0.0961
  time to fit residues: 5.5340
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  : 0.299 
-------------------------------------------------------------------------------
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  387 ILE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9980
   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 = 0.4312 r_free = 0.4312 target = 0.211108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.185647 restraints weight = 3530.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.188419 restraints weight = 2501.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.190640 restraints weight = 1948.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6220
moved from start:          0.2489

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= 0.140
  Angle     :  0.638   8.777   4311  Z= 0.300
  Chirality :  0.038   0.129    524
  Planarity :  0.004   0.058    540
  Dihedral  :  3.952  14.884    454
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.58 %
    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 (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:  1.14 (0.41), residues: 431
  helix:  1.67 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -2.07 (0.54), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 429 
 HIS   0.001   0.001   HIS A  48 
 PHE   0.019   0.001   PHE A 273 
 TYR   0.007   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04651 (  243)
  hydrogen bonds       : angle       4.07152 (  717)
  SS BOND              : bond        0.00168 (    3)
  SS BOND              : angle       0.69574 (    6)
  covalent geometry    : bond        0.00312 ( 3139)
  covalent geometry    : angle       0.63759 ( 4305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1290.01 seconds
wall clock time: 22 minutes 51.74 seconds (1371.74 seconds total)