Starting phenix.real_space_refine
on Fri May  9 21:06:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx5_37901/05_2025/8wx5_37901.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx5_37901/05_2025/8wx5_37901.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx5_37901/05_2025/8wx5_37901.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx5_37901/05_2025/8wx5_37901.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx5_37901/05_2025/8wx5_37901.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx5_37901/05_2025/8wx5_37901.cif"
  }
  resolution = 3.91
  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=   0.052
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      22      5.16       5
     C    2552      2.51       5
     N     619      2.21       5
     O     664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3857
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 490, 3741
          Classifications: {'peptide': 490}
          Link IDs: {'PTRANS': 22, 'TRANS': 467}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 116
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Time building chain proxies: 3.13, per 1000 atoms: 0.81
  Number of scatterers: 3857
  At special positions: 0
  Unit cell: (80.51, 77.19, 73.87, 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      22     16.00
     O     664      8.00
     N     619      7.00
     C    2552      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 141 " - pdb=" SG  CYS A 152 " 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: 0.96
  Conformation dependent library (CDL) restraints added in 452.7 milliseconds
  

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  922

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      83.7% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 57
      removed outlier: 3.927A  pdb=" N   ASN A  57 " --> pdb=" O   GLY A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 65
      removed outlier: 3.539A  pdb=" N   ASN A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 97
      Proline residue:  A  90  - end of helix
    Processing helix  chain 'A' and resid 101 through 125
      Proline residue:  A 121  - end of helix
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 146 through 185
      removed outlier: 3.514A  pdb=" N   ALA A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      Proline residue:  A 155  - end of helix
      removed outlier: 4.443A  pdb=" N   THR A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 4.049A  pdb=" N   ASP A 185 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 220
    Processing helix  chain 'A' and resid 221 through 245
      Proline residue:  A 229  - end of helix
      removed outlier: 4.111A  pdb=" N   SER A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 310 through 349
      Proline residue:  A 323  - end of helix
      Proline residue:  A 330  - end of helix
    Processing helix  chain 'A' and resid 354 through 358
      removed outlier: 4.283A  pdb=" N   ILE A 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 394
      Proline residue:  A 382  - end of helix
      Proline residue:  A 390  - end of helix
      removed outlier: 3.897A  pdb=" N   ARG A 394 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 431
    Processing helix  chain 'A' and resid 450 through 452
      No H-bonds generated for 'chain 'A' and resid 450 through 452'
    Processing helix  chain 'A' and resid 453 through 479
      removed outlier: 4.550A  pdb=" N   GLN A 457 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 512
    Processing helix  chain 'A' and resid 526 through 530
    Processing helix  chain 'A' and resid 531 through 556
      removed outlier: 4.067A  pdb=" N   TYR A 535 " --> pdb=" O   TYR A 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 14
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437
      removed outlier: 3.715A  pdb=" N   GLN A 437 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    930 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: 1.06

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 588
        1.31 -     1.43: 1104
        1.43 -     1.56: 2230
        1.56 -     1.69: 0
        1.69 -     1.82: 33
  Bond restraints: 3955
  Sorted by residual:
  bond pdb=" C   SER B   8 "
       pdb=" O   SER B   8 "
    ideal  model  delta    sigma   weight residual
    1.236  1.307 -0.070 1.24e-02 6.50e+03 3.21e+01
  bond pdb=" C   LEU B   7 "
       pdb=" O   LEU B   7 "
    ideal  model  delta    sigma   weight residual
    1.236  1.294 -0.058 1.19e-02 7.06e+03 2.34e+01
  bond pdb=" CA  SER B   8 "
       pdb=" CB  SER B   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.452  0.078 1.69e-02 3.50e+03 2.11e+01
  bond pdb=" C   TYR B   6 "
       pdb=" O   TYR B   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.181  0.054 1.26e-02 6.30e+03 1.84e+01
  bond pdb=" C   GLY B   9 "
       pdb=" O   GLY B   9 "
    ideal  model  delta    sigma   weight residual
    1.235  1.179  0.056 1.35e-02 5.49e+03 1.72e+01
  ... (remaining 3950 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 5238
        2.18 -     4.37: 114
        4.37 -     6.55: 23
        6.55 -     8.73: 5
        8.73 -    10.92: 4
  Bond angle restraints: 5384
  Sorted by residual:
  angle pdb=" N   GLU B   4 "
        pdb=" CA  GLU B   4 "
        pdb=" C   GLU B   4 "
      ideal   model   delta    sigma   weight residual
     112.34  102.39    9.95 1.30e+00 5.92e-01 5.86e+01
  angle pdb=" N   LEU B  10 "
        pdb=" CA  LEU B  10 "
        pdb=" C   LEU B  10 "
      ideal   model   delta    sigma   weight residual
     111.37  100.45   10.92 1.64e+00 3.72e-01 4.43e+01
  angle pdb=" N   TRP B  13 "
        pdb=" CA  TRP B  13 "
        pdb=" C   TRP B  13 "
      ideal   model   delta    sigma   weight residual
     111.37  102.04    9.33 1.65e+00 3.67e-01 3.20e+01
  angle pdb=" N   SER B   8 "
        pdb=" CA  SER B   8 "
        pdb=" C   SER B   8 "
      ideal   model   delta    sigma   weight residual
     111.75  104.52    7.23 1.28e+00 6.10e-01 3.19e+01
  angle pdb=" N   TYR B  12 "
        pdb=" CA  TYR B  12 "
        pdb=" C   TYR B  12 "
      ideal   model   delta    sigma   weight residual
     111.36  117.06   -5.70 1.09e+00 8.42e-01 2.73e+01
  ... (remaining 5379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2037
       17.98 -    35.95: 206
       35.95 -    53.93: 43
       53.93 -    71.91: 3
       71.91 -    89.89: 2
  Dihedral angle restraints: 2291
    sinusoidal: 849
      harmonic: 1442
  Sorted by residual:
  dihedral pdb=" N   SER B   8 "
           pdb=" C   SER B   8 "
           pdb=" CA  SER B   8 "
           pdb=" CB  SER B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.32   10.48     0      2.50e+00 1.60e-01 1.76e+01
  dihedral pdb=" N   LEU B  10 "
           pdb=" C   LEU B  10 "
           pdb=" CA  LEU B  10 "
           pdb=" CB  LEU B  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.37   10.43     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" C   TRP B  13 "
           pdb=" N   TRP B  13 "
           pdb=" CA  TRP B  13 "
           pdb=" CB  TRP B  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.16   -9.44     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 2288 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 564
       0.064 -    0.128: 57
       0.128 -    0.192: 3
       0.192 -    0.256: 1
       0.256 -    0.319: 3
  Chirality restraints: 628
  Sorted by residual:
  chirality pdb=" CA  TRP B  13 "
            pdb=" N   TRP B  13 "
            pdb=" C   TRP B  13 "
            pdb=" CB  TRP B  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  TYR B  12 "
            pdb=" N   TYR B  12 "
            pdb=" C   TYR B  12 "
            pdb=" CB  TYR B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  LEU B  10 "
            pdb=" N   LEU B  10 "
            pdb=" C   LEU B  10 "
            pdb=" CB  LEU B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 625 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B   9 "    0.020 2.00e-02 2.50e+03   4.12e-02 1.70e+01
        pdb=" C   GLY B   9 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   GLY B   9 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LEU B  10 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  10 "    0.013 2.00e-02 2.50e+03   2.64e-02 6.99e+00
        pdb=" C   LEU B  10 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LEU B  10 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU B  11 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 228 "   -0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO A 229 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 229 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 229 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 215
        2.73 -     3.27: 4249
        3.27 -     3.81: 6741
        3.81 -     4.36: 7416
        4.36 -     4.90: 12796
  Nonbonded interactions: 31417
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 349 "
            pdb=" NE2 GLN A 437 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" O   GLN A 337 "
            pdb=" OG1 THR A 341 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER A 355 "
            pdb=" O   THR A 358 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   GLY A 499 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   LEU A 380 "
            pdb=" N   LYS A 384 "
     model   vdw
     2.280 3.120
  ... (remaining 31412 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.590
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
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      :  0.004   0.078   3957  Z= 0.280
  Angle     :  0.867  10.916   5388  Z= 0.555
  Chirality :  0.044   0.319    628
  Planarity :  0.005   0.051    664
  Dihedral  : 14.579  89.886   1363
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.63 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.98 %
    Favored  : 92.52 %
  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: -1.72 (0.34), residues: 498
  helix: -0.26 (0.24), residues: 389
  sheet: -4.91 (0.87), residues: 10
  loop : -4.00 (0.45), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B  13 
 HIS   0.002   0.000   HIS A 362 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.022   0.002   TYR B  12 
 ARG   0.001   0.000   ARG A 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10382 (  315)
  hydrogen bonds       : angle       5.18068 (  930)
  SS BOND              : bond        0.00010 (    2)
  SS BOND              : angle       0.96190 (    4)
  covalent geometry    : bond        0.00411 ( 3955)
  covalent geometry    : angle       0.86662 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 LEU cc_start: 0.9316 (mt) cc_final: 0.9044 (mt)
REVERT: A   63 ASN cc_start: 0.7813 (m110) cc_final: 0.7512 (t0)
REVERT: A  259 ASP cc_start: 0.9094 (m-30) cc_final: 0.8872 (m-30)
REVERT: A  310 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8282 (mm-30)
REVERT: A  409 MET cc_start: 0.9073 (mtt) cc_final: 0.8799 (mtt)
REVERT: A  453 TRP cc_start: 0.7998 (m100) cc_final: 0.7208 (m100)
REVERT: A  465 GLU cc_start: 0.9358 (tp30) cc_final: 0.9097 (tp30)
REVERT: A  470 ILE cc_start: 0.8834 (mm) cc_final: 0.8583 (mm)
REVERT: A  474 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7222 (mt-10)
  outliers start: 2
  outliers final: 1
  residues processed: 158
  average time/residue: 0.1396
  time to fit residues: 27.9528
Evaluate side-chains
  129 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0870
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   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 140 ASN
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
A 356 ASN
A 441 ASN
A 454 GLN
B  14 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.149047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124810 restraints weight = 7523.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.128584 restraints weight = 4279.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131270 restraints weight = 2884.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3957  Z= 0.151
  Angle     :  0.656   7.811   5388  Z= 0.335
  Chirality :  0.041   0.161    628
  Planarity :  0.005   0.052    664
  Dihedral  :  4.704  16.291    538
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 16.46 %
    Favored  : 79.55 %
  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: -0.10 (0.38), residues: 498
  helix:  0.81 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -3.29 (0.50), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A 348 
 PHE   0.018   0.001   PHE A 194 
 TYR   0.034   0.002   TYR B  12 
 ARG   0.008   0.000   ARG A 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04648 (  315)
  hydrogen bonds       : angle       4.67618 (  930)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       0.57755 (    4)
  covalent geometry    : bond        0.00311 ( 3955)
  covalent geometry    : angle       0.65620 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LEU cc_start: 0.9521 (mt) cc_final: 0.9117 (mp)
REVERT: A  120 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8390 (t80)
REVERT: A  240 PHE cc_start: 0.9113 (t80) cc_final: 0.8903 (t80)
REVERT: A  259 ASP cc_start: 0.9109 (m-30) cc_final: 0.8900 (m-30)
REVERT: A  409 MET cc_start: 0.9135 (mtt) cc_final: 0.8736 (mtt)
REVERT: A  423 GLU cc_start: 0.8502 (tp30) cc_final: 0.8148 (tp30)
REVERT: A  426 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8395 (ttp80)
REVERT: A  453 TRP cc_start: 0.8068 (m100) cc_final: 0.7405 (m100)
REVERT: A  465 GLU cc_start: 0.9396 (tp30) cc_final: 0.8975 (tp30)
REVERT: A  470 ILE cc_start: 0.8749 (mm) cc_final: 0.8485 (mm)
REVERT: A  474 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7323 (mt-10)
REVERT: A  501 PHE cc_start: 0.8633 (m-80) cc_final: 0.7566 (t80)
REVERT: A  543 GLN cc_start: 0.9518 (tp40) cc_final: 0.9012 (tp-100)
REVERT: B   13 TRP cc_start: 0.5784 (OUTLIER) cc_final: 0.4629 (t-100)
  outliers start: 16
  outliers final: 8
  residues processed: 147
  average time/residue: 0.1203
  time to fit residues: 23.0161
Evaluate side-chains
  136 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    0.2980
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.147726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124161 restraints weight = 7414.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.127758 restraints weight = 4215.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.130330 restraints weight = 2822.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3957  Z= 0.152
  Angle     :  0.657   8.302   5388  Z= 0.335
  Chirality :  0.042   0.147    628
  Planarity :  0.005   0.059    664
  Dihedral  :  4.653  16.309    537
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.95 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.39 (0.38), residues: 498
  helix:  1.10 (0.27), residues: 390
  sheet:  None (None), residues: 0
  loop : -2.90 (0.54), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  13 
 HIS   0.001   0.001   HIS A 348 
 PHE   0.011   0.001   PHE A 195 
 TYR   0.027   0.002   TYR B  12 
 ARG   0.007   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  315)
  hydrogen bonds       : angle       4.69843 (  930)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       0.49329 (    4)
  covalent geometry    : bond        0.00318 ( 3955)
  covalent geometry    : angle       0.65717 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 TRP cc_start: 0.8961 (m-10) cc_final: 0.8592 (m-10)
REVERT: A  120 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7989 (t80)
REVERT: A  259 ASP cc_start: 0.9134 (m-30) cc_final: 0.8923 (m-30)
REVERT: A  423 GLU cc_start: 0.8485 (tp30) cc_final: 0.8124 (tp30)
REVERT: A  453 TRP cc_start: 0.8049 (m100) cc_final: 0.7368 (m100)
REVERT: A  465 GLU cc_start: 0.9325 (tp30) cc_final: 0.8965 (tp30)
REVERT: A  470 ILE cc_start: 0.8687 (mm) cc_final: 0.8399 (mm)
REVERT: A  474 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7344 (mt-10)
REVERT: A  501 PHE cc_start: 0.8633 (m-80) cc_final: 0.7607 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1176
  time to fit residues: 20.6515
Evaluate side-chains
  132 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.143032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.119422 restraints weight = 7552.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.122905 restraints weight = 4314.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.125138 restraints weight = 2898.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3957  Z= 0.168
  Angle     :  0.650   8.976   5388  Z= 0.335
  Chirality :  0.041   0.134    628
  Planarity :  0.005   0.051    664
  Dihedral  :  4.546  17.390    537
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 25.19 %
    Favored  : 69.83 %
  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:  0.59 (0.39), residues: 498
  helix:  1.15 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.64 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 348 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.029   0.002   TYR A 331 
 ARG   0.003   0.000   ARG A 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04838 (  315)
  hydrogen bonds       : angle       4.79236 (  930)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.34863 (    4)
  covalent geometry    : bond        0.00364 ( 3955)
  covalent geometry    : angle       0.65034 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7310 (m100) cc_final: 0.6981 (m100)
REVERT: A  203 ASN cc_start: 0.8705 (m-40) cc_final: 0.8358 (m-40)
REVERT: A  259 ASP cc_start: 0.9157 (m-30) cc_final: 0.8956 (m-30)
REVERT: A  316 LYS cc_start: 0.8882 (tttt) cc_final: 0.8657 (ttmt)
REVERT: A  426 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8545 (ttp80)
REVERT: A  453 TRP cc_start: 0.8157 (m100) cc_final: 0.7484 (m100)
REVERT: A  465 GLU cc_start: 0.9322 (tp30) cc_final: 0.8995 (tp30)
REVERT: A  470 ILE cc_start: 0.8705 (mm) cc_final: 0.8380 (mm)
REVERT: A  474 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: A  501 PHE cc_start: 0.8685 (m-80) cc_final: 0.7714 (t80)
REVERT: B   13 TRP cc_start: 0.5878 (OUTLIER) cc_final: 0.5193 (m100)
  outliers start: 20
  outliers final: 14
  residues processed: 135
  average time/residue: 0.1108
  time to fit residues: 19.8186
Evaluate side-chains
  139 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  417 PHE
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0970
   chunk 48 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.145233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.120585 restraints weight = 7684.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124164 restraints weight = 4375.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.126783 restraints weight = 2956.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3957  Z= 0.148
  Angle     :  0.650   9.750   5388  Z= 0.328
  Chirality :  0.041   0.153    628
  Planarity :  0.005   0.049    664
  Dihedral  :  4.550  16.757    537
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 28.18 %
    Favored  : 68.08 %
  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:  0.64 (0.39), residues: 498
  helix:  1.16 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.52 (0.62), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  13 
 HIS   0.002   0.000   HIS A 348 
 PHE   0.010   0.001   PHE A 194 
 TYR   0.024   0.002   TYR B  12 
 ARG   0.001   0.000   ARG A 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04679 (  315)
  hydrogen bonds       : angle       4.75108 (  930)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       0.35274 (    4)
  covalent geometry    : bond        0.00312 ( 3955)
  covalent geometry    : angle       0.65046 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7262 (m100) cc_final: 0.7008 (m100)
REVERT: A  203 ASN cc_start: 0.8642 (m-40) cc_final: 0.8298 (m-40)
REVERT: A  259 ASP cc_start: 0.9162 (m-30) cc_final: 0.8960 (m-30)
REVERT: A  310 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8528 (mm-30)
REVERT: A  426 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8554 (ttp80)
REVERT: A  453 TRP cc_start: 0.8119 (m100) cc_final: 0.7457 (m100)
REVERT: A  465 GLU cc_start: 0.9268 (tp30) cc_final: 0.9012 (tp30)
REVERT: A  470 ILE cc_start: 0.8641 (mm) cc_final: 0.8322 (mm)
REVERT: A  474 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7376 (mt-10)
REVERT: A  501 PHE cc_start: 0.8693 (m-80) cc_final: 0.7713 (t80)
REVERT: B   13 TRP cc_start: 0.5689 (OUTLIER) cc_final: 0.5148 (m100)
  outliers start: 15
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1249
  time to fit residues: 21.9402
Evaluate side-chains
  134 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.144862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120442 restraints weight = 7611.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124031 restraints weight = 4315.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126630 restraints weight = 2903.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3957  Z= 0.150
  Angle     :  0.653  10.653   5388  Z= 0.331
  Chirality :  0.041   0.138    628
  Planarity :  0.005   0.044    664
  Dihedral  :  4.499  16.899    537
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 28.43 %
    Favored  : 67.58 %
  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:  0.74 (0.39), residues: 498
  helix:  1.22 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.39 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.010   0.001   PHE A 411 
 TYR   0.022   0.002   TYR B  12 
 ARG   0.001   0.000   ARG A 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04619 (  315)
  hydrogen bonds       : angle       4.75138 (  930)
  SS BOND              : bond        0.00048 (    2)
  SS BOND              : angle       0.32768 (    4)
  covalent geometry    : bond        0.00320 ( 3955)
  covalent geometry    : angle       0.65283 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7301 (m100) cc_final: 0.7091 (m100)
REVERT: A  259 ASP cc_start: 0.9207 (m-30) cc_final: 0.8994 (m-30)
REVERT: A  310 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8659 (mm-30)
REVERT: A  426 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8564 (ttp80)
REVERT: A  453 TRP cc_start: 0.8106 (m100) cc_final: 0.7437 (m100)
REVERT: A  465 GLU cc_start: 0.9247 (tp30) cc_final: 0.8998 (tp30)
REVERT: A  470 ILE cc_start: 0.8614 (mm) cc_final: 0.8359 (mm)
REVERT: A  474 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7406 (mt-10)
REVERT: A  501 PHE cc_start: 0.8695 (m-80) cc_final: 0.7716 (t80)
REVERT: B   13 TRP cc_start: 0.5655 (OUTLIER) cc_final: 0.5215 (m100)
  outliers start: 16
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1309
  time to fit residues: 22.6645
Evaluate side-chains
  132 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0010
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.146782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121779 restraints weight = 7642.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125582 restraints weight = 4352.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.128154 restraints weight = 2939.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3957  Z= 0.149
  Angle     :  0.678  11.364   5388  Z= 0.338
  Chirality :  0.040   0.149    628
  Planarity :  0.005   0.044    664
  Dihedral  :  4.494  16.576    537
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 30.67 %
    Favored  : 65.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.73 (0.39), residues: 498
  helix:  1.20 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.35 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.010   0.001   PHE A 411 
 TYR   0.021   0.002   TYR B  12 
 ARG   0.001   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04592 (  315)
  hydrogen bonds       : angle       4.75230 (  930)
  SS BOND              : bond        0.00041 (    2)
  SS BOND              : angle       0.32012 (    4)
  covalent geometry    : bond        0.00320 ( 3955)
  covalent geometry    : angle       0.67802 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7305 (m100) cc_final: 0.7093 (m100)
REVERT: A  259 ASP cc_start: 0.9220 (m-30) cc_final: 0.9011 (m-30)
REVERT: A  310 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8731 (mm-30)
REVERT: A  426 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8563 (ttp80)
REVERT: A  453 TRP cc_start: 0.8128 (m100) cc_final: 0.7462 (m100)
REVERT: A  474 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: A  501 PHE cc_start: 0.8704 (m-80) cc_final: 0.7749 (t80)
REVERT: B   13 TRP cc_start: 0.5638 (OUTLIER) cc_final: 0.5286 (m100)
  outliers start: 15
  outliers final: 13
  residues processed: 131
  average time/residue: 0.1136
  time to fit residues: 19.6950
Evaluate side-chains
  138 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.146457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.121637 restraints weight = 7562.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125350 restraints weight = 4342.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.128011 restraints weight = 2946.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3957  Z= 0.154
  Angle     :  0.691  11.733   5388  Z= 0.346
  Chirality :  0.041   0.153    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.468  17.220    537
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 31.17 %
    Favored  : 65.09 %
  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:  0.74 (0.39), residues: 498
  helix:  1.21 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.37 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.012   0.001   PHE A 194 
 TYR   0.024   0.002   TYR A 331 
 ARG   0.001   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04653 (  315)
  hydrogen bonds       : angle       4.75641 (  930)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       0.29467 (    4)
  covalent geometry    : bond        0.00336 ( 3955)
  covalent geometry    : angle       0.69145 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8744 (mm-30)
REVERT: A  316 LYS cc_start: 0.8900 (tttt) cc_final: 0.8678 (ttmt)
REVERT: A  426 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8567 (ttp80)
REVERT: A  453 TRP cc_start: 0.8179 (m100) cc_final: 0.7507 (m100)
REVERT: A  474 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7936 (mt-10)
REVERT: A  501 PHE cc_start: 0.8707 (m-80) cc_final: 0.7765 (t80)
REVERT: B   13 TRP cc_start: 0.5690 (OUTLIER) cc_final: 0.5275 (m100)
  outliers start: 15
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1129
  time to fit residues: 19.1989
Evaluate side-chains
  137 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.145331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.120475 restraints weight = 7658.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124241 restraints weight = 4380.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126907 restraints weight = 2959.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3957  Z= 0.163
  Angle     :  0.708  12.315   5388  Z= 0.354
  Chirality :  0.041   0.154    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.483  17.483    537
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 31.92 %
    Favored  : 64.09 %
  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:  0.74 (0.39), residues: 498
  helix:  1.21 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.39 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  13 
 HIS   0.002   0.000   HIS A 348 
 PHE   0.012   0.001   PHE A 411 
 TYR   0.018   0.002   TYR B  12 
 ARG   0.001   0.000   ARG A 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04778 (  315)
  hydrogen bonds       : angle       4.79041 (  930)
  SS BOND              : bond        0.00039 (    2)
  SS BOND              : angle       0.26444 (    4)
  covalent geometry    : bond        0.00358 ( 3955)
  covalent geometry    : angle       0.70861 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8304 (mm-30)
REVERT: A  423 GLU cc_start: 0.8558 (tp30) cc_final: 0.8205 (tp30)
REVERT: A  426 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8551 (ttp80)
REVERT: A  453 TRP cc_start: 0.8228 (m100) cc_final: 0.7376 (m100)
REVERT: A  474 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7372 (mt-10)
REVERT: A  501 PHE cc_start: 0.8712 (m-80) cc_final: 0.7774 (t80)
REVERT: B   13 TRP cc_start: 0.5638 (OUTLIER) cc_final: 0.5180 (m100)
  outliers start: 16
  outliers final: 14
  residues processed: 126
  average time/residue: 0.1181
  time to fit residues: 19.5912
Evaluate side-chains
  139 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0020
   chunk 4 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.3966

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.147270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.123867 restraints weight = 7488.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.127576 restraints weight = 4219.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.130199 restraints weight = 2816.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3957  Z= 0.148
  Angle     :  0.703  12.072   5388  Z= 0.349
  Chirality :  0.041   0.156    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.457  16.957    537
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 32.42 %
    Favored  : 64.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.75 (0.39), residues: 498
  helix:  1.24 (0.26), residues: 398
  sheet:  None (None), residues: 0
  loop : -2.50 (0.63), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  13 
 HIS   0.000   0.000   HIS A 395 
 PHE   0.011   0.001   PHE A 194 
 TYR   0.018   0.001   TYR B  12 
 ARG   0.001   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04590 (  315)
  hydrogen bonds       : angle       4.69542 (  930)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.37904 (    4)
  covalent geometry    : bond        0.00315 ( 3955)
  covalent geometry    : angle       0.70340 ( 5384)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8322 (mm-30)
REVERT: A  316 LYS cc_start: 0.8900 (tttt) cc_final: 0.8678 (ttmt)
REVERT: A  426 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8552 (ttp80)
REVERT: A  453 TRP cc_start: 0.8141 (m100) cc_final: 0.7486 (m100)
REVERT: A  474 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7825 (mt-10)
REVERT: A  501 PHE cc_start: 0.8702 (m-80) cc_final: 0.7758 (t80)
REVERT: B   13 TRP cc_start: 0.5552 (OUTLIER) cc_final: 0.5301 (m100)
  outliers start: 13
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1247
  time to fit residues: 21.3708
Evaluate side-chains
  132 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0970
   chunk 17 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 6 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.146562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123441 restraints weight = 7350.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.127083 restraints weight = 4153.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.129110 restraints weight = 2781.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3957  Z= 0.154
  Angle     :  0.720  12.601   5388  Z= 0.360
  Chirality :  0.041   0.168    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.437  17.113    537
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 32.67 %
    Favored  : 63.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.79 (0.39), residues: 498
  helix:  1.25 (0.26), residues: 398
  sheet:  None (None), residues: 0
  loop : -2.42 (0.64), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.015   0.001   PHE A 411 
 TYR   0.049   0.002   TYR A 535 
 ARG   0.000   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04613 (  315)
  hydrogen bonds       : angle       4.72965 (  930)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       0.29427 (    4)
  covalent geometry    : bond        0.00336 ( 3955)
  covalent geometry    : angle       0.72032 ( 5384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1573.40 seconds
wall clock time: 28 minutes 23.12 seconds (1703.12 seconds total)