Starting phenix.real_space_refine
on Wed Sep 17 04:06:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6n_50235/09_2025/9f6n_50235.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6n_50235/09_2025/9f6n_50235.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6n_50235/09_2025/9f6n_50235.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6n_50235/09_2025/9f6n_50235.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6n_50235/09_2025/9f6n_50235.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6n_50235/09_2025/9f6n_50235.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
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: 5
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     S      21      5.16       5
     C    2416      2.51       5
     N     591      2.21       5
     O     623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3652
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3651
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 16, 'TRANS': 454}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.17, per 1000 atoms: 0.32
  Number of scatterers: 3652
  At special positions: 0
  Unit cell: (83.328, 67.704, 70.308, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      1     24.99
     S      21     16.00
     O     623      8.00
     N     591      7.00
     C    2416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 394 " distance=2.04

  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: 0.38
  Conformation dependent library (CDL) restraints added in 143.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  864

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      87.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 102
      removed outlier: 3.832A  pdb=" N   ALA A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 113
      removed outlier: 4.281A  pdb=" N   LEU A 108 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR A 113 " --> pdb=" O   MET A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 129
      removed outlier: 3.624A  pdb=" N   ALA A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
      removed outlier: 3.836A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 130 through 133'
    Processing helix  chain 'A' and resid 134 through 158
      removed outlier: 3.570A  pdb=" N   LEU A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 170
    Processing helix  chain 'A' and resid 171 through 205
      removed outlier: 3.522A  pdb=" N   ARG A 175 " --> pdb=" O   PRO A 171 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE A 177 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'A' and resid 219 through 232
      removed outlier: 3.809A  pdb=" N   PHE A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 259
    Processing helix  chain 'A' and resid 261 through 271
    Processing helix  chain 'A' and resid 278 through 293
      removed outlier: 4.097A  pdb=" N   ILE A 293 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 3.597A  pdb=" N   LEU A 300 " --> pdb=" O   HIS A 296 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 352
      removed outlier: 3.642A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 367
      removed outlier: 3.560A  pdb=" N   VAL A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 430
      removed outlier: 3.557A  pdb=" N   GLY A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      Proline residue:  A 398  - end of helix
      removed outlier: 3.758A  pdb=" N   LEU A 401 " --> pdb=" O   GLY A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 459
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 460 through 479
    Processing helix  chain 'A' and resid 479 through 490
      Proline residue:  A 485  - end of helix
    Processing helix  chain 'A' and resid 492 through 497
    Processing helix  chain 'A' and resid 502 through 532
      removed outlier: 3.952A  pdb=" N   ASP A 530 " --> pdb=" O   VAL A 526 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LEU A 531 " --> pdb=" O   TYR A 527 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY A 532 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 562

    293 hydrogen bonds defined for protein.
    879 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: 0.58

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1117
        1.35 -     1.47: 936
        1.47 -     1.59: 1651
        1.59 -     1.71: 2
        1.71 -     1.83: 33
  Bond restraints: 3739
  Sorted by residual:
  bond pdb=" CA  PHE A 239 "
       pdb=" C   PHE A 239 "
    ideal  model  delta    sigma   weight residual
    1.524  1.485  0.039 1.27e-02 6.20e+03 9.46e+00
  bond pdb=" CB  ILE A 327 "
       pdb=" CG2 ILE A 327 "
    ideal  model  delta    sigma   weight residual
    1.521  1.604 -0.083 3.30e-02 9.18e+02 6.27e+00
  bond pdb=" CB  ILE A 519 "
       pdb=" CG2 ILE A 519 "
    ideal  model  delta    sigma   weight residual
    1.521  1.597 -0.076 3.30e-02 9.18e+02 5.24e+00
  bond pdb=" N   TYR A 527 "
       pdb=" CA  TYR A 527 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.33e-02 5.65e+03 4.48e+00
  bond pdb=" CB  ILE A 288 "
       pdb=" CG1 ILE A 288 "
    ideal  model  delta    sigma   weight residual
    1.530  1.572 -0.042 2.00e-02 2.50e+03 4.38e+00
  ... (remaining 3734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 4724
        2.06 -     4.11: 280
        4.11 -     6.17: 58
        6.17 -     8.23: 24
        8.23 -    10.28: 3
  Bond angle restraints: 5089
  Sorted by residual:
  angle pdb=" C   LEU A 228 "
        pdb=" N   ASP A 229 "
        pdb=" CA  ASP A 229 "
      ideal   model   delta    sigma   weight residual
     120.44  113.90    6.54 1.30e+00 5.92e-01 2.53e+01
  angle pdb=" N   LEU A 145 "
        pdb=" CA  LEU A 145 "
        pdb=" C   LEU A 145 "
      ideal   model   delta    sigma   weight residual
     111.07  106.69    4.38 1.07e+00 8.73e-01 1.67e+01
  angle pdb=" N   PHE A 239 "
        pdb=" CA  PHE A 239 "
        pdb=" C   PHE A 239 "
      ideal   model   delta    sigma   weight residual
     111.07  106.72    4.35 1.07e+00 8.73e-01 1.65e+01
  angle pdb=" C   ASN A 297 "
        pdb=" N   MET A 298 "
        pdb=" CA  MET A 298 "
      ideal   model   delta    sigma   weight residual
     120.65  115.46    5.19 1.32e+00 5.74e-01 1.55e+01
  angle pdb=" N   ASP A 229 "
        pdb=" CA  ASP A 229 "
        pdb=" C   ASP A 229 "
      ideal   model   delta    sigma   weight residual
     111.07  106.89    4.18 1.07e+00 8.73e-01 1.53e+01
  ... (remaining 5084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 1890
       17.20 -    34.39: 200
       34.39 -    51.58: 56
       51.58 -    68.78: 12
       68.78 -    85.97: 6
  Dihedral angle restraints: 2164
    sinusoidal: 814
      harmonic: 1350
  Sorted by residual:
  dihedral pdb=" CB  CYS A 363 "
           pdb=" SG  CYS A 363 "
           pdb=" SG  CYS A 394 "
           pdb=" CB  CYS A 394 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.95   55.05     1      1.00e+01 1.00e-02 4.10e+01
  dihedral pdb=" CA  ASP A 469 "
           pdb=" CB  ASP A 469 "
           pdb=" CG  ASP A 469 "
           pdb=" OD1 ASP A 469 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.68   59.68     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CA  THR A 490 "
           pdb=" C   THR A 490 "
           pdb=" N   SER A 491 "
           pdb=" CA  SER A 491 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.89   17.11     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 2161 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 406
       0.045 -    0.090: 142
       0.090 -    0.135: 36
       0.135 -    0.179: 12
       0.179 -    0.224: 7
  Chirality restraints: 603
  Sorted by residual:
  chirality pdb=" CG  LEU A 249 "
            pdb=" CB  LEU A 249 "
            pdb=" CD1 LEU A 249 "
            pdb=" CD2 LEU A 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  VAL A 442 "
            pdb=" CA  VAL A 442 "
            pdb=" CG1 VAL A 442 "
            pdb=" CG2 VAL A 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.84    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  ILE A 447 "
            pdb=" CA  ILE A 447 "
            pdb=" CG1 ILE A 447 "
            pdb=" CG2 ILE A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 600 not shown)

  Planarity restraints: 627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 279 "    0.059 5.00e-02 4.00e+02   8.94e-02 1.28e+01
        pdb=" N   PRO A 280 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A 280 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 280 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 297 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.50e+00
        pdb=" C   ASN A 297 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASN A 297 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 298 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 104 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.30e+00
        pdb=" N   PRO A 105 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "    0.032 5.00e-02 4.00e+02
  ... (remaining 624 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.50: 16
        2.50 -     3.10: 2690
        3.10 -     3.70: 5756
        3.70 -     4.30: 7655
        4.30 -     4.90: 12775
  Nonbonded interactions: 28892
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 376 "
            pdb=" OD1 ASP A 377 "
     model   vdw
     1.906 3.040
  nonbonded pdb=" OD2 ASP A 115 "
            pdb="MN    MN A 701 "
     model   vdw
     2.159 2.320
  nonbonded pdb=" O   VAL A 215 "
            pdb=" OG1 THR A 218 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   LEU A 514 "
            pdb=" OG  SER A 518 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER A 491 "
            pdb=" OD1 ASN A 501 "
     model   vdw
     2.306 3.040
  ... (remaining 28887 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:             0.490
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.850
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
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      :  0.008   0.083   3740  Z= 0.346
  Angle     :  1.197  10.281   5091  Z= 0.628
  Chirality :  0.054   0.224    603
  Planarity :  0.008   0.089    627
  Dihedral  : 16.583  85.972   1297
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.41 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.34), residues: 469
  helix: -0.07 (0.23), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.69 (0.64), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 440 
 TYR   0.033   0.002   TYR A 324 
 PHE   0.028   0.002   PHE A 347 
 TRP   0.011   0.001   TRP A 135 
 HIS   0.006   0.002   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00789 ( 3739)
  covalent geometry    : angle       1.19486 ( 5089)
  SS BOND              : bond        0.00959 (    1)
  SS BOND              : angle       3.68490 (    2)
  hydrogen bonds       : bond        0.11422 (  293)
  hydrogen bonds       : angle       5.53104 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7953 (mp0)
REVERT: A  305 VAL cc_start: 0.8895 (t) cc_final: 0.8601 (m)
REVERT: A  471 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8427 (mp)
REVERT: A  476 SER cc_start: 0.8750 (t) cc_final: 0.8168 (p)
REVERT: A  521 MET cc_start: 0.8345 (ttp) cc_final: 0.8027 (mtp)
REVERT: A  537 TYR cc_start: 0.7734 (t80) cc_final: 0.7362 (t80)
REVERT: A  552 PHE cc_start: 0.8790 (m-10) cc_final: 0.8204 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 118
  average time/residue: 0.0444
  time to fit residues: 7.2787
Evaluate side-chains
  108 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  518 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.128368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.106057 restraints weight = 5978.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.109797 restraints weight = 3054.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.112387 restraints weight = 1989.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.114041 restraints weight = 1485.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115040 restraints weight = 1225.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3740  Z= 0.139
  Angle     :  0.588   9.674   5091  Z= 0.301
  Chirality :  0.038   0.141    603
  Planarity :  0.005   0.060    627
  Dihedral  :  6.236  57.948    517
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 22.65 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.37), residues: 469
  helix:  1.47 (0.25), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.51 (0.64), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 440 
 TYR   0.009   0.001   TYR A 547 
 PHE   0.017   0.001   PHE A 438 
 TRP   0.008   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3739)
  covalent geometry    : angle       0.58826 ( 5089)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       0.96675 (    2)
  hydrogen bonds       : bond        0.04316 (  293)
  hydrogen bonds       : angle       4.09114 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.6729 (mp10)
REVERT: A  158 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8701 (p)
REVERT: A  191 MET cc_start: 0.8255 (ttp) cc_final: 0.8012 (ttp)
REVERT: A  305 VAL cc_start: 0.9140 (t) cc_final: 0.8832 (m)
REVERT: A  345 SER cc_start: 0.9163 (t) cc_final: 0.8733 (p)
REVERT: A  476 SER cc_start: 0.8637 (t) cc_final: 0.8152 (p)
REVERT: A  477 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8891 (tp)
REVERT: A  521 MET cc_start: 0.8461 (ttp) cc_final: 0.8174 (mtp)
REVERT: A  552 PHE cc_start: 0.8905 (m-10) cc_final: 0.8446 (m-80)
  outliers start: 22
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0406
  time to fit residues: 6.1502
Evaluate side-chains
  105 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0770
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.127556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.104594 restraints weight = 5881.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.108267 restraints weight = 3130.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.110735 restraints weight = 2087.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112317 restraints weight = 1593.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113398 restraints weight = 1332.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3740  Z= 0.132
  Angle     :  0.581  11.800   5091  Z= 0.289
  Chirality :  0.037   0.114    603
  Planarity :  0.005   0.056    627
  Dihedral  :  5.673  57.807    510
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 23.16 %
    Favored  : 70.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.39), residues: 469
  helix:  2.03 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.44 (0.66), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.014   0.001   TYR A 547 
 PHE   0.019   0.001   PHE A 347 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3739)
  covalent geometry    : angle       0.57952 ( 5089)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       2.00584 (    2)
  hydrogen bonds       : bond        0.04029 (  293)
  hydrogen bonds       : angle       3.89205 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.6813 (mp10)
REVERT: A  158 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8100 (m)
REVERT: A  191 MET cc_start: 0.8183 (ttp) cc_final: 0.7933 (ttp)
REVERT: A  249 LEU cc_start: 0.8713 (mm) cc_final: 0.8494 (mm)
REVERT: A  305 VAL cc_start: 0.9168 (t) cc_final: 0.8902 (m)
REVERT: A  345 SER cc_start: 0.9190 (t) cc_final: 0.8748 (p)
REVERT: A  537 TYR cc_start: 0.7753 (t80) cc_final: 0.7254 (t80)
REVERT: A  552 PHE cc_start: 0.8879 (m-10) cc_final: 0.8402 (m-80)
  outliers start: 23
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0376
  time to fit residues: 5.7996
Evaluate side-chains
  107 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    0.2980
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.123760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.100776 restraints weight = 5981.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.104297 restraints weight = 3166.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.106545 restraints weight = 2113.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.108296 restraints weight = 1631.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.109376 restraints weight = 1358.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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      :  0.004   0.046   3740  Z= 0.176
  Angle     :  0.630  11.832   5091  Z= 0.315
  Chirality :  0.039   0.168    603
  Planarity :  0.005   0.056    627
  Dihedral  :  5.645  59.128    508
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  8.14 %
    Allowed  : 23.41 %
    Favored  : 68.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.39), residues: 469
  helix:  2.01 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.26 (0.67), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 440 
 TYR   0.011   0.001   TYR A 547 
 PHE   0.020   0.001   PHE A 347 
 TRP   0.009   0.001   TRP A 435 
 HIS   0.004   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3739)
  covalent geometry    : angle       0.62417 ( 5089)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       4.39787 (    2)
  hydrogen bonds       : bond        0.04289 (  293)
  hydrogen bonds       : angle       4.06334 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.6677 (mp10)
REVERT: A  158 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8644 (p)
REVERT: A  249 LEU cc_start: 0.8856 (mm) cc_final: 0.8608 (mm)
REVERT: A  305 VAL cc_start: 0.9170 (t) cc_final: 0.8879 (m)
REVERT: A  345 SER cc_start: 0.9186 (t) cc_final: 0.8791 (p)
REVERT: A  476 SER cc_start: 0.8626 (t) cc_final: 0.8165 (p)
REVERT: A  537 TYR cc_start: 0.7772 (t80) cc_final: 0.7280 (t80)
REVERT: A  552 PHE cc_start: 0.8850 (m-10) cc_final: 0.8454 (m-80)
  outliers start: 32
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0388
  time to fit residues: 6.2912
Evaluate side-chains
  106 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  543 VAL
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 1 optimal weight:    0.0070
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.126960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.103918 restraints weight = 5998.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.107582 restraints weight = 3142.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109900 restraints weight = 2077.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.111673 restraints weight = 1593.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112604 restraints weight = 1321.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3740  Z= 0.133
  Angle     :  0.597  12.877   5091  Z= 0.298
  Chirality :  0.038   0.146    603
  Planarity :  0.004   0.055    627
  Dihedral  :  5.466  57.872    508
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 26.97 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.39), residues: 469
  helix:  2.11 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.26 (0.66), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.010   0.001   TYR A 547 
 PHE   0.018   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 435 
 HIS   0.002   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3739)
  covalent geometry    : angle       0.59547 ( 5089)
  SS BOND              : bond        0.00326 (    1)
  SS BOND              : angle       2.27965 (    2)
  hydrogen bonds       : bond        0.04016 (  293)
  hydrogen bonds       : angle       3.91506 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  148 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.6763 (mp10)
REVERT: A  158 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8426 (p)
REVERT: A  192 GLN cc_start: 0.7696 (tt0) cc_final: 0.7488 (tt0)
REVERT: A  249 LEU cc_start: 0.8857 (mm) cc_final: 0.8616 (mm)
REVERT: A  305 VAL cc_start: 0.9170 (t) cc_final: 0.8890 (m)
REVERT: A  345 SER cc_start: 0.9227 (t) cc_final: 0.8825 (p)
REVERT: A  476 SER cc_start: 0.8591 (t) cc_final: 0.8148 (p)
REVERT: A  537 TYR cc_start: 0.7780 (t80) cc_final: 0.7211 (t80)
REVERT: A  552 PHE cc_start: 0.8881 (m-10) cc_final: 0.8454 (m-80)
  outliers start: 24
  outliers final: 18
  residues processed: 106
  average time/residue: 0.0450
  time to fit residues: 6.5274
Evaluate side-chains
  109 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.124575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.102122 restraints weight = 5987.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.105742 restraints weight = 3152.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.108208 restraints weight = 2066.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.109497 restraints weight = 1556.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.110871 restraints weight = 1319.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3740  Z= 0.154
  Angle     :  0.625  11.721   5091  Z= 0.308
  Chirality :  0.039   0.193    603
  Planarity :  0.004   0.056    627
  Dihedral  :  5.436  58.800    508
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 25.95 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.39), residues: 469
  helix:  2.09 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.08 (0.71), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 278 
 TYR   0.009   0.001   TYR A 547 
 PHE   0.019   0.001   PHE A 347 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3739)
  covalent geometry    : angle       0.62447 ( 5089)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       1.75235 (    2)
  hydrogen bonds       : bond        0.04127 (  293)
  hydrogen bonds       : angle       3.95897 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.6527 (mp10)
REVERT: A  158 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8294 (p)
REVERT: A  249 LEU cc_start: 0.8892 (mm) cc_final: 0.8610 (mm)
REVERT: A  305 VAL cc_start: 0.9169 (t) cc_final: 0.8879 (m)
REVERT: A  345 SER cc_start: 0.9243 (t) cc_final: 0.8843 (p)
REVERT: A  537 TYR cc_start: 0.7816 (t80) cc_final: 0.7255 (t80)
REVERT: A  552 PHE cc_start: 0.8902 (m-10) cc_final: 0.8513 (m-80)
  outliers start: 29
  outliers final: 18
  residues processed: 113
  average time/residue: 0.0450
  time to fit residues: 7.0091
Evaluate side-chains
  111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  558 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.125200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.102574 restraints weight = 6105.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.106297 restraints weight = 3189.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.108732 restraints weight = 2093.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110080 restraints weight = 1583.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111483 restraints weight = 1337.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3740  Z= 0.144
  Angle     :  0.635  11.759   5091  Z= 0.306
  Chirality :  0.038   0.139    603
  Planarity :  0.004   0.055    627
  Dihedral  :  5.409  58.883    508
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 26.72 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.39), residues: 469
  helix:  2.15 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.03 (0.71), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 445 
 TYR   0.009   0.001   TYR A 547 
 PHE   0.017   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3739)
  covalent geometry    : angle       0.63467 ( 5089)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       1.46014 (    2)
  hydrogen bonds       : bond        0.04033 (  293)
  hydrogen bonds       : angle       3.92825 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.6483 (mp10)
REVERT: A  158 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8370 (p)
REVERT: A  249 LEU cc_start: 0.8842 (mm) cc_final: 0.8592 (mm)
REVERT: A  305 VAL cc_start: 0.9224 (t) cc_final: 0.8990 (m)
REVERT: A  345 SER cc_start: 0.9228 (t) cc_final: 0.8831 (p)
REVERT: A  363 CYS cc_start: 0.6006 (t) cc_final: 0.5532 (t)
REVERT: A  537 TYR cc_start: 0.7987 (t80) cc_final: 0.7472 (t80)
REVERT: A  552 PHE cc_start: 0.8898 (m-10) cc_final: 0.8505 (m-80)
  outliers start: 28
  outliers final: 19
  residues processed: 110
  average time/residue: 0.0454
  time to fit residues: 6.8314
Evaluate side-chains
  113 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  560 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.125937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.103228 restraints weight = 5999.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.106947 restraints weight = 3153.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.109253 restraints weight = 2080.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111040 restraints weight = 1589.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.111955 restraints weight = 1311.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3740  Z= 0.145
  Angle     :  0.672  15.557   5091  Z= 0.317
  Chirality :  0.039   0.142    603
  Planarity :  0.004   0.056    627
  Dihedral  :  5.395  59.389    508
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 26.46 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.39), residues: 469
  helix:  2.19 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.02 (0.70), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.009   0.001   TYR A 547 
 PHE   0.007   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3739)
  covalent geometry    : angle       0.67140 ( 5089)
  SS BOND              : bond        0.00300 (    1)
  SS BOND              : angle       1.39275 (    2)
  hydrogen bonds       : bond        0.03989 (  293)
  hydrogen bonds       : angle       3.93448 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.6531 (mp10)
REVERT: A  158 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8370 (p)
REVERT: A  249 LEU cc_start: 0.8835 (mm) cc_final: 0.8578 (mm)
REVERT: A  305 VAL cc_start: 0.9227 (t) cc_final: 0.8995 (m)
REVERT: A  345 SER cc_start: 0.9195 (t) cc_final: 0.8779 (p)
REVERT: A  537 TYR cc_start: 0.7962 (t80) cc_final: 0.7444 (t80)
  outliers start: 25
  outliers final: 20
  residues processed: 111
  average time/residue: 0.0403
  time to fit residues: 6.2827
Evaluate side-chains
  112 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0870
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.126033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.102888 restraints weight = 6039.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.106535 restraints weight = 3184.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.109014 restraints weight = 2106.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.110538 restraints weight = 1602.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.111558 restraints weight = 1343.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3740  Z= 0.150
  Angle     :  0.692  13.369   5091  Z= 0.328
  Chirality :  0.040   0.245    603
  Planarity :  0.004   0.054    627
  Dihedral  :  5.404  59.521    508
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  8.40 %
    Allowed  : 26.72 %
    Favored  : 64.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.39), residues: 469
  helix:  2.16 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.03 (0.70), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 278 
 TYR   0.009   0.001   TYR A 547 
 PHE   0.016   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 135 
 HIS   0.003   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3739)
  covalent geometry    : angle       0.69109 ( 5089)
  SS BOND              : bond        0.00446 (    1)
  SS BOND              : angle       1.62056 (    2)
  hydrogen bonds       : bond        0.04088 (  293)
  hydrogen bonds       : angle       3.98628 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8963 (m-80) cc_final: 0.8454 (m-80)
REVERT: A  148 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.6624 (mp10)
REVERT: A  158 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8332 (p)
REVERT: A  249 LEU cc_start: 0.8805 (mm) cc_final: 0.8535 (mm)
REVERT: A  305 VAL cc_start: 0.9227 (t) cc_final: 0.8993 (m)
REVERT: A  345 SER cc_start: 0.9180 (t) cc_final: 0.8751 (p)
REVERT: A  347 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7483 (t80)
REVERT: A  537 TYR cc_start: 0.7991 (t80) cc_final: 0.7463 (t80)
REVERT: A  552 PHE cc_start: 0.8734 (m-10) cc_final: 0.8384 (m-80)
  outliers start: 33
  outliers final: 23
  residues processed: 107
  average time/residue: 0.0426
  time to fit residues: 6.2350
Evaluate side-chains
  114 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  363 CYS
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0970
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 413 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.126805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.104174 restraints weight = 6007.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.107865 restraints weight = 3133.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.110339 restraints weight = 2054.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.112032 restraints weight = 1550.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.112645 restraints weight = 1281.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3740  Z= 0.138
  Angle     :  0.719  14.982   5091  Z= 0.332
  Chirality :  0.039   0.150    603
  Planarity :  0.004   0.057    627
  Dihedral  :  5.352  58.123    508
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 27.74 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.40), residues: 469
  helix:  2.16 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -1.07 (0.70), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 278 
 TYR   0.009   0.001   TYR A 547 
 PHE   0.010   0.001   PHE A 523 
 TRP   0.006   0.001   TRP A 556 
 HIS   0.003   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3739)
  covalent geometry    : angle       0.71872 ( 5089)
  SS BOND              : bond        0.00365 (    1)
  SS BOND              : angle       1.43234 (    2)
  hydrogen bonds       : bond        0.03948 (  293)
  hydrogen bonds       : angle       3.95376 (  879)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8936 (m-80) cc_final: 0.8474 (m-80)
REVERT: A  148 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.6405 (mp10)
REVERT: A  158 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8351 (p)
REVERT: A  249 LEU cc_start: 0.8724 (mm) cc_final: 0.8458 (mm)
REVERT: A  305 VAL cc_start: 0.9232 (t) cc_final: 0.9008 (m)
REVERT: A  347 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7393 (t80)
REVERT: A  537 TYR cc_start: 0.7988 (t80) cc_final: 0.7477 (t80)
REVERT: A  552 PHE cc_start: 0.8723 (m-10) cc_final: 0.8327 (m-80)
  outliers start: 28
  outliers final: 22
  residues processed: 107
  average time/residue: 0.0380
  time to fit residues: 5.5782
Evaluate side-chains
  115 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  363 CYS
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.124509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.101769 restraints weight = 5964.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.105347 restraints weight = 3131.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.107664 restraints weight = 2066.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.109251 restraints weight = 1580.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.110442 restraints weight = 1324.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3740  Z= 0.167
  Angle     :  0.725  13.319   5091  Z= 0.342
  Chirality :  0.040   0.161    603
  Planarity :  0.005   0.053    627
  Dihedral  :  5.361  57.707    508
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 27.74 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.40), residues: 469
  helix:  2.10 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -1.04 (0.71), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 440 
 TYR   0.009   0.001   TYR A 547 
 PHE   0.008   0.001   PHE A 523 
 TRP   0.005   0.001   TRP A 404 
 HIS   0.004   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3739)
  covalent geometry    : angle       0.72455 ( 5089)
  SS BOND              : bond        0.00395 (    1)
  SS BOND              : angle       1.49812 (    2)
  hydrogen bonds       : bond        0.04177 (  293)
  hydrogen bonds       : angle       4.06328 (  879)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 772.56 seconds
wall clock time: 13 minutes 58.31 seconds (838.31 seconds total)